[Loris-dev] Upgrading to Loris 21 - new make file

[Sotirios Nikoloutsopoulos]

No, it didn't work, i also tried space/tabs because most of the errors
where about indentation, also there are some errors about React.

Thanks

lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init
? How would you like to configure ESLint? Answer questions about your style
? Which version of ECMAScript do you use? ES2015
? Are you using ES6 modules? Yes
? Where will your code run? Browser
? Do you use CommonJS? Yes
? Do you use JSX? Yes
? Do you use React? Yes
? What style of indentation do you use? Spaces
? What quotes do you use for strings? Single
? What line endings do you use? Unix
? Do you require semicolons? Yes
? What format do you want your config file to be in? JSON
The config that you've selected requires the following dependencies:

eslint-plugin-react at latest
Successfully created .eslintrc.json file in /var/www/loris

lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output
npm WARN The package prop-types is included as both a dev and production
dependency.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4
(node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for
fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current:
{"os":"linux","arch":"x64"})

npm ERR! code ELIFECYCLE
npm ERR! errno 2
npm ERR! loris at 1.0.0 compile: `webpack`
npm ERR! Exit status 2
npm ERR!
npm ERR! Failed at the loris at 1.0.0 compile script.
npm ERR! This is probably not a problem with npm. There is likely
additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log

Στις Τετ, 14 Αυγ 2019 στις 2:29 π.μ., ο/η Shen Wang <wangshen.mcin at gmail.com>
έγραψε:

> Hi Sotirios,
> When you do make command, please make sure with sudo at the beginning.
> [sudo make]
> If it still doesn't work for you.
> Then try the solutions below.
> solution 1:
> [image: 屏幕快照 2019-08-13 19.21.15.png]
> Regards
> Shen
>
>
>
>
> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> I think that the files exists although i redownloaded the eslintrc.json i
>> checked others files that had similar errors.
>>
>> lorisadmin at hbp:/var/www/loris$ ls -l
>> ./node_modules/eslint-loader/index.js
>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 Οκτ  26  1985
>> ./node_modules/eslint-loader/index.js
>>
>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json
>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 Αύγ  14 00:04 .eslintrc.json
>>
>> Maybe this can help
>>
>> Module build failed (from ./node_modules/eslint-loader/index.js):
>>     SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json
>>     Error: Unexpected token < in JSON at position 6
>>         at JSON.parse (<anonymous>)
>>         at loadJSONConfigFile
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>         at loadConfigFile
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>         at loadFromDisk
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>         at Object.load
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>         at Config.getLocalConfigHierarchy
>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>         at Config.getConfigHierarchy
>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>         at Config.getConfigVector
>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>         at Config.getConfig
>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>         at processText
>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>         at CLIEngine.executeOnText
>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>         at lint
>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>         at Object.module.exports
>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>
>>     ERROR in ./modules/imaging_uploader/jsx/index.js
>>     Module build failed (from ./node_modules/eslint-loader/index.js):
>>     SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json
>>     Error: Unexpected token < in JSON at position 6
>>         at JSON.parse (<anonymous>)
>>         at loadJSONConfigFile
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>         at loadConfigFile
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>         at loadFromDisk
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>         at Object.load
>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>         at Config.getLocalConfigHierarchy
>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>         at Config.getConfigHierarchy
>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>         at Config.getConfigVector
>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>         at Config.getConfig
>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>         at processText
>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>         at CLIEngine.executeOnText
>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>         at lint
>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>         at Object.module.exports
>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>
>>
>>
>> Στις Τρί, 13 Αυγ 2019 στις 11:52 μ.μ., ο/η John Saigle <
>> john.saigle at mcin.ca> έγραψε:
>>
>>> HI Sotirios,
>>>
>>> The make_output.txt file shows webpack failing because it can't find the
>>> ESLint config file.
>>>
>>> Can you confirm whether the file `.eslintrc.json` exists within your
>>> loris root directory (usually `/var/www/loris/`)? When I delete my file I
>>> get the same errors as you.
>>>
>>> If you find that it's missing, you can make a local copy with the
>>> contents found here:
>>>
>>>
>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json
>>>
>>> Once you know it exists, try running `make` again.
>>>
>>> Let us know if that moves you forward.
>>>
>>> Best,
>>> John
>>>
>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi,
>>>> I executed  the commands for the node and now i am get the followings:
>>>>
>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output
>>>> npm WARN The package prop-types is included as both a dev and
>>>> production dependency.
>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4
>>>> (node_modules/fsevents):
>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for
>>>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current:
>>>> {"os":"linux","arch":"x64"})
>>>>
>>>> npm ERR! code ELIFECYCLE
>>>> npm ERR! errno 2
>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>> npm ERR! Exit status 2
>>>> npm ERR!
>>>> npm ERR! Failed at the loris at 1.0.0 compile script.
>>>> npm ERR! This is probably not a problem with npm. There is likely
>>>> additional logging output above.
>>>>
>>>> npm ERR! A complete log of this run can be found in:
>>>> npm ERR!
>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log
>>>> make: *** [javascript] Error 2
>>>>
>>>> Thanks,
>>>> Sotirios
>>>>
>>>>
>>>> Στις Δευ, 12 Αυγ 2019 στις 10:19 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose
>>>>> version of node doesn't work well with webpack, due to updated packages
>>>>> they're missing.
>>>>> If so, update your node :
>>>>>
>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>> sudo apt-get install -y nodejs
>>>>>
>>>>> Let us know how that goes -- please send us output from the same log
>>>>> if any issues.
>>>>> Best,
>>>>> Christine
>>>>>
>>>>>
>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> It's not a disk space issue, as you can see below i have still 74GB
>>>>>> available.
>>>>>>
>>>>>> lorisadmin at hbp:/var/www/loris$ df -h
>>>>>> Filesystem        Size  Used Avail Use% Mounted on
>>>>>> udev              2,9G     0  2,9G   0% /dev
>>>>>> tmpfs             597M  8,6M  588M   2% /run
>>>>>> /dev/sda1          98G   19G   74G  21% /
>>>>>>
>>>>>> Maybe we have to pass a flag to get into strict mode? as stated
>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not
>>>>>> yet supported outside strict mode"
>>>>>>
>>>>>> Thanks,
>>>>>> Sotirios
>>>>>>
>>>>>> Στις Πέμ, 8 Αυγ 2019 στις 4:32 μ.μ., ο/η Dave MacFarlane <
>>>>>> dave.macfarlane at mcin.ca> έγραψε:
>>>>>>
>>>>>>> It looks like the javascript snippet shown in the error message when
>>>>>>> trying to compile the js is truncated. Have you run out of disk space?
>>>>>>>
>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I runned make and also included the file it reports at the end.
>>>>>>>>
>>>>>>>> lorisadmin at hbp:/var/www/loris$ make
>>>>>>>> npm install
>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>> /chokidar/fsevents:
>>>>>>>> npm WARN notsup Not compatible with your operating system or
>>>>>>>> architecture: fsevents at 1.2.9
>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>> /watchpack/chokidar/fsevents:
>>>>>>>> npm WARN notsup Not compatible with your operating system or
>>>>>>>> architecture: fsevents at 1.2.9
>>>>>>>> npm run compile
>>>>>>>>
>>>>>>>> > loris at 1.0.0 compile /var/www/loris
>>>>>>>> > webpack
>>>>>>>>
>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86
>>>>>>>> let notify =
>>>>>>>> ^^^
>>>>>>>>
>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function,
>>>>>>>> class) not yet supported outside strict mode
>>>>>>>>     at exports.runInThisContext (vm.js:53:16)
>>>>>>>>     at Module._compile (module.js:374:25)
>>>>>>>>     at Object.Module._extensions..js (module.js:417:10)
>>>>>>>>     at Module.load (module.js:344:32)
>>>>>>>>     at Function.Module._load (module.js:301:12)
>>>>>>>>     at Function.Module.runMain (module.js:442:10)
>>>>>>>>     at startup (node.js:136:18)
>>>>>>>>     at node.js:966:3
>>>>>>>>
>>>>>>>> npm ERR! Linux 4.15.0-55-generic
>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile"
>>>>>>>> npm ERR! node v4.2.6
>>>>>>>> npm ERR! npm  v3.5.2
>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>> npm ERR! Exit status 1
>>>>>>>> npm ERR!
>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'.
>>>>>>>> npm ERR! Make sure you have the latest version of node.js and npm
>>>>>>>> installed.
>>>>>>>> npm ERR! If you do, this is most likely a problem with the loris
>>>>>>>> package,
>>>>>>>> npm ERR! not with npm itself.
>>>>>>>> npm ERR! Tell the author that this fails on your system:
>>>>>>>> npm ERR!     webpack
>>>>>>>> npm ERR! You can get information on how to open an issue for this
>>>>>>>> project with:
>>>>>>>> npm ERR!     npm bugs loris
>>>>>>>> npm ERR! Or if that isn't available, you can get their info via:
>>>>>>>> npm ERR!     npm owner ls loris
>>>>>>>> npm ERR! There is likely additional logging output above.
>>>>>>>>
>>>>>>>> npm ERR! Please include the following file with any support request:
>>>>>>>> npm ERR!     /var/www/loris/npm-debug.log
>>>>>>>> Makefile:14: recipe for target 'javascript' failed
>>>>>>>> make: *** [javascript] Error 1
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>> Στις Τετ, 7 Αυγ 2019 στις 5:41 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Thanks, have you tried all of these steps?
>>>>>>>>> - clear your browser cache (and refresh a few times)
>>>>>>>>> - delete any files in your smarty/templates_c directory (this will
>>>>>>>>> clear the template cache - do Not touch smarty/templates/)
>>>>>>>>> - run `make` (per the 21 release notes, this replaces the composer
>>>>>>>>> commands used in previous releases to update your dependencies)
>>>>>>>>> - restart apache (doesn't hurt)
>>>>>>>>>
>>>>>>>>> Let us know how it goes -- let us know what difference you see
>>>>>>>>> after, with your logs.  A
>>>>>>>>> lso please send us your Config path settings (see these
>>>>>>>>> Troubleshooting Queries
>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>)
>>>>>>>>> if you're still seeing front-end issues.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Christine
>>>>>>>>>
>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat
>>>>>>>>>> /var/log/apache2/error.log
>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267]
>>>>>>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming
>>>>>>>>>> normal operations
>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267]
>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2'
>>>>>>>>>>
>>>>>>>>>> And as for the access.log the content are empty
>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>> -rw-r----- 1 root adm 0 Ιούν 28 14:09 /var/log/apache2/access.log
>>>>>>>>>>
>>>>>>>>>> Also i noticed a loris_access.log.
>>>>>>>>>>
>>>>>>>>>> The only non-blank pages are:
>>>>>>>>>> mri_violations, dataquery does not exist at all, statistics,
>>>>>>>>>> data_team_helper, genomic_browser, configuration and
>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for
>>>>>>>>>> Server Processes Manager are missing. Cannot continue."
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 6 Αυγ 2019 στις 10:13 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios and LORIS community --
>>>>>>>>>>>
>>>>>>>>>>> When upgrading to brand-new release 21 --  just a reminder to
>>>>>>>>>>> follow the release notes and run the new *make* file to update
>>>>>>>>>>> your dependencies (instead of using *composer* commands).
>>>>>>>>>>> We've also updated the Wiki page
>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Updating-your-LORIS> to
>>>>>>>>>>> clarify that the release notes for each version will tell you what to run.
>>>>>>>>>>>
>>>>>>>>>>> If your current version is not the last release (20.3), it's
>>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2,
>>>>>>>>>>> 20.3) before making the leap to 21.0.
>>>>>>>>>>>
>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your
>>>>>>>>>>> cache.
>>>>>>>>>>>
>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please
>>>>>>>>>>> don't hesitate to let us know.
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Christine
>>>>>>>>>>> The LORIS team
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>> Could you also let us know -- on which pages is content
>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you?
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Christine
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. <
>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks Sotirios,
>>>>>>>>>>>>> That's good to know.  It sounds like you've checked that your
>>>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Please send us the last few errors you're seeing in your
>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's
>>>>>>>>>>>>> happening with your front end --
>>>>>>>>>>>>> Run these Troubleshooting Queries
>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying
>>>>>>>>>>>>> fully.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The Loris-MRI repo
>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21
>>>>>>>>>>>>> install/upgrade would then be your next steps.
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am using a VM. What i did was:
>>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and
>>>>>>>>>>>>>> replace them to my existing /vaw/www/loris folder.
>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer
>>>>>>>>>>>>>> dump-autoload  as mentioned here
>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS.
>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because
>>>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the
>>>>>>>>>>>>>> install.sh successfully
>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed
>>>>>>>>>>>>>> the installdb.php
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotorios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root
>>>>>>>>>>>>>>> path / VM or might some of your old system setting still apply?
>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you
>>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339
>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/pull/339>) split into
>>>>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which
>>>>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of
>>>>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to
>>>>>>>>>>>>>>> ensure they match.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is
>>>>>>>>>>>>>>>> not visible at all at most pages.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following
>>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query
>>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range
>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1
>>>>>>>>>>>>>>>>>  path is /data/incoming/
>>>>>>>>>>>>>>>>>  type is .tar.gz
>>>>>>>>>>>>>>>>>  fullpath is /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range'
>>>>>>>>>>>>>>>>> in 'where clause' at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without
>>>>>>>>>>>>>>>>> execute() at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986.
>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric
>>>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm
>>>>>>>>>>>>>>>>> line 1995.
>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range'
>>>>>>>>>>>>>>>>> in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>>>>>>>>>>>>>>>> 562.
>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>  No Mincs inserted
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η Christine Rogers,
>>>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> First, just a note:  we've released LORIS 21 this week
>>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in
>>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the
>>>>>>>>>>>>>>>>>> LORIS
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/releases/tag/v21.0.0> and
>>>>>>>>>>>>>>>>>> Loris-MRI
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0>
>>>>>>>>>>>>>>>>>> repos.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol
>>>>>>>>>>>>>>>>>> table should be at the root of these issues :
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a
>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't
>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1,
>>>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release
>>>>>>>>>>>>>>>>>> branch are here
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>
>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden
>>>>>>>>>>>>>>>>>> their parameters to match all your scan types.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans
>>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing
>>>>>>>>>>>>>>>>>> "all types" of scans from a given session :
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>    - "defaced" means that a defacing script
>>>>>>>>>>>>>>>>>>    <https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md>
>>>>>>>>>>>>>>>>>>    has masked the subject's face in the volume (for patient privacy)
>>>>>>>>>>>>>>>>>>    - "native" means that no pre-processing has been
>>>>>>>>>>>>>>>>>>    performed on the scan (it's raw data),
>>>>>>>>>>>>>>>>>>    -  "selected" will show only volumes that have been
>>>>>>>>>>>>>>>>>>    QC'd and "selected" as the best of their type -- used to display only the
>>>>>>>>>>>>>>>>>>    best quality T1 image instead of all T1s acquired in a session, e.g.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> re QC Comments --
>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the
>>>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View
>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each
>>>>>>>>>>>>>>>>>> visit.
>>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to
>>>>>>>>>>>>>>>>>> each scan.  (Table name: feedback_mri_comments)
>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.)
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging
>>>>>>>>>>>>>>>>>> Setup guide
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md>
>>>>>>>>>>>>>>>>>> -
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video
>>>>>>>>>>>>>>>>>> <https://www.youtube.com/watch?v=HDWC6RUbI6A> can also
>>>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00
>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since
>>>>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your
>>>>>>>>>>>>>>>>>> mri_protocol table -
>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me
>>>>>>>>>>>>>>>>>>> to imaging_browser
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results (
>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ).
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the
>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted?
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced,
>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc
>>>>>>>>>>>>>>>>>>> comments stored?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit
>>>>>>>>>>>>>>>>>>>> labels.  To follow up on your last few emails:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert
>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>
>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label
>>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is
>>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/
>>>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user
>>>>>>>>>>>>>>>>>>>> password, including Admin.  (See info on setting up / resetting User
>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>
>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to
>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown.
>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol)
>>>>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol
>>>>>>>>>>>>>>>>>>>> database table.
>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide,
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this
>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted").
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here)
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/tree/minor/modules/mri_violations>will show
>>>>>>>>>>>>>>>>>>>> you the details of this mismatch --
>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your
>>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next
>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the
>>>>>>>>>>>>>>>>>>>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values
>>>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk
>>>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on
>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit
>>>>>>>>>>>>>>>>>>>>> label disappeared.
>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>   --> The minc file cannot be registered since the
>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash
>>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows
>>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of
>>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and
>>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to
>>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password  hash in the
>>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still
>>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the
>>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ).
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the
>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the
>>>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to
>>>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a
>>>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit
>>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...).
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not
>>>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed  $subjectID{'createVisitLabel'} to 1 as you had
>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for
>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not
>>>>>>>>>>>>>>>>>>>>>>>>> exist
>>>>>>>>>>>>>>>>>>>>>>>>>  -> WARNING: This candidate was invalid. Logging to
>>>>>>>>>>>>>>>>>>>>>>>>>               MRICandidateErrors table with reason
>>>>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>> of mincs fails. Please see the output.txt file i attached. Also is there
>>>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress!
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact
>>>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this:
>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC"
>>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center";
>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure
>>>>>>>>>>>>>>>>>>>>>>>>>>> to change the Aliases between sites, they should all be unique).
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes!
>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now
>>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix
>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i
>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that )
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think  the mistake was that in the wiki it suggested to use $PROJECT  for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 5:05 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 3:38 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ./batch_uploads_imageuploader -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις 5:00 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a blank studyUID, maybe someone accidentally removed it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my patients and uploads?: because i want to try to reupload all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; #
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to your questions will be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019 στις 12:02
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> π.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank on the header?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789)  but V02 was not yet created for MTL0123; the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started".
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC  file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>>> 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
>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>> 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
>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> 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
>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>> Loris-dev mailing list
>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> 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
>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>
>>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
>
> --
> Shen Wang
> Loris <https://github.com/aces/Loris>  Developer
> Montreal Neurological Institute
> McGill University
>
>
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0 info it worked if it ends with ok
1 verbose cli [ '/usr/bin/node', '/usr/bin/npm', 'run', 'compile' ]
2 info using npm at 6.4.1
3 info using node at v8.16.0
4 verbose run-script [ 'precompile', 'compile', 'postcompile' ]
5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0
6 info lifecycle loris at 1.0.0~compile: loris at 1.0.0
7 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true
8 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/var/www/loris/node_modules/.bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
9 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris
10 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ]
11 silly lifecycle loris at 1.0.0~compile: Returned: code: 2  signal: null
12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script
13 verbose stack Error: loris at 1.0.0 compile: `webpack`
13 verbose stack Exit status 2
13 verbose stack     at EventEmitter.<anonymous> (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16)
13 verbose stack     at emitTwo (events.js:126:13)
13 verbose stack     at EventEmitter.emit (events.js:214:7)
13 verbose stack     at ChildProcess.<anonymous> (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14)
13 verbose stack     at emitTwo (events.js:126:13)
13 verbose stack     at ChildProcess.emit (events.js:214:7)
13 verbose stack     at maybeClose (internal/child_process.js:915:16)
13 verbose stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5)
14 verbose pkgid loris at 1.0.0
15 verbose cwd /var/www/loris
16 verbose Linux 4.15.0-55-generic
17 verbose argv "/usr/bin/node" "/usr/bin/npm" "run" "compile"
18 verbose node v8.16.0
19 verbose npm  v6.4.1
20 error code ELIFECYCLE
21 error errno 2
22 error loris at 1.0.0 compile: `webpack`
22 error Exit status 2
23 error Failed at the loris at 1.0.0 compile script.
23 error This is probably not a problem with npm. There is likely additional logging output above.
24 verbose exit [ 2, true ]
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