From sotirisnik at gmail.com Tue Mar 3 08:00:34 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Mar 2020 15:00:34 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi, I am getting this error when i am running make composer install --no-dev > mkdir -p project/libraries Loading composer repositories with package information Installing dependencies from lock file Package operations: 0 installs, 0 updates, 4 removals - Removing facebook/webdriver (dev-master) [RuntimeException] Source directory /var/www/loris/vendor/facebook/webdriver has unpushed chan ges on the current branch: M lib/WebDriverTargetLocator.php install [--prefer-source] [--prefer-dist] Thanks ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma ??????: > Hi Sotirios, > > You will need to customize the dicom_archive modules which resides under > /modules/dicom_archive, we recommend against modifying directly > the module, instead you copy that module into project/modules to do any > customization there, then run "composer install" to let the Loris know that > you want to use your customized version. Then you need to run "make" under > the to compile jsx to js. > > The table and the filter are written in ReactJS, as long as you have some > knowledge of ReactJS and PHP, you could go ahead to do it. > > Best regards, > Ling Ma > > On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> We would like to customize the Selection Filter given in >> https://demo.loris.ca/dicom_archive/ page. Also we would like to add a >> new column on the existing table shown ( that batch column will be >> contained in the files table ). Could you give some info on how to proceed? >> >> The desired result is as shown in that image >> >> [image: image.png] >> >> Thank you >> >> Sotirios >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: From lingyun.ma at mcin.ca Tue Mar 3 10:10:51 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Tue, 3 Mar 2020 10:10:51 -0500 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi Sotirios, You must have run with "composer install" early, so why do you run "composer install --no-dev" now? You can delete the vendor/facebook, then re-run the "composer install --no-dev". The cause could be something to do with facebook package, which is out of the consideration of Loris. Hope this helps. Thanks. Best regards, Ling Ma On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > I am getting this error when i am running make > > composer install --no-dev > > mkdir -p project/libraries > Loading composer repositories with package information > Installing dependencies from lock file > Package operations: 0 installs, 0 updates, 4 removals > - Removing facebook/webdriver (dev-master) > > > > [RuntimeException] > > Source directory /var/www/loris/vendor/facebook/webdriver has unpushed > chan > ges on the current branch: > > M lib/WebDriverTargetLocator.php > > > > > install [--prefer-source] [--prefer-dist] > > Thanks > > ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma > ??????: > >> Hi Sotirios, >> >> You will need to customize the dicom_archive modules which resides under >> /modules/dicom_archive, we recommend against modifying directly >> the module, instead you copy that module into project/modules to do any >> customization there, then run "composer install" to let the Loris know that >> you want to use your customized version. Then you need to run "make" under >> the to compile jsx to js. >> >> The table and the filter are written in ReactJS, as long as you have some >> knowledge of ReactJS and PHP, you could go ahead to do it. >> >> Best regards, >> Ling Ma >> >> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> We would like to customize the Selection Filter given in >>> https://demo.loris.ca/dicom_archive/ page. Also we would like to add a >>> new column on the existing table shown ( that batch column will be >>> contained in the files table ). Could you give some info on how to proceed? >>> >>> The desired result is as shown in that image >>> >>> [image: image.png] >>> >>> Thank you >>> >>> Sotirios >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Mar 3 11:30:39 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Mar 2020 18:30:39 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi, I just runned make and it auto runned composer install --no-dev on its own. To make it run i needed to delete the vendor directory. Also when placing the dicom_archive under project/ directory i see it has no effect at the web interface but it worked when i replaced the original module. At the moment I will work at the path of the original module, no harm since we using docker to replace the original path at the building process. To display the values of my new column, which files should I edit? I believe it's the FilterableDataTable.js but how does it get its data for the table? ( I am new to React ) Thanks Thanks ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma ??????: > Hi Sotirios, > > You must have run with "composer install" early, so why do you run > "composer install --no-dev" now? You can delete the vendor/facebook, then > re-run the "composer install --no-dev". The cause could be something to do > with facebook package, which is out of the consideration of Loris. > > Hope this helps. Thanks. > > Best regards, > Ling Ma > > On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> I am getting this error when i am running make >> >> composer install --no-dev >> > mkdir -p project/libraries >> Loading composer repositories with package information >> Installing dependencies from lock file >> Package operations: 0 installs, 0 updates, 4 removals >> - Removing facebook/webdriver (dev-master) >> >> >> >> [RuntimeException] >> >> Source directory /var/www/loris/vendor/facebook/webdriver has unpushed >> chan >> ges on the current branch: >> >> M lib/WebDriverTargetLocator.php >> >> >> >> >> install [--prefer-source] [--prefer-dist] >> >> Thanks >> >> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma >> ??????: >> >>> Hi Sotirios, >>> >>> You will need to customize the dicom_archive modules which resides under >>> /modules/dicom_archive, we recommend against modifying directly >>> the module, instead you copy that module into project/modules to do any >>> customization there, then run "composer install" to let the Loris know that >>> you want to use your customized version. Then you need to run "make" under >>> the to compile jsx to js. >>> >>> The table and the filter are written in ReactJS, as long as you have >>> some knowledge of ReactJS and PHP, you could go ahead to do it. >>> >>> Best regards, >>> Ling Ma >>> >>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> We would like to customize the Selection Filter given in >>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to add a >>>> new column on the existing table shown ( that batch column will be >>>> contained in the files table ). Could you give some info on how to proceed? >>>> >>>> The desired result is as shown in that image >>>> >>>> [image: image.png] >>>> >>>> Thank you >>>> >>>> Sotirios >>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: From lingyun.ma at mcin.ca Tue Mar 3 11:40:03 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Tue, 3 Mar 2020 11:40:03 -0500 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi Sotirios, To make the new module work, I suggest you put it in project/modules, but it is up to you to choose where to put. Last time I asked "You will need to customize the dicom_archive modules which resides under /modules/dicom_archive", I don't believe FilterableDataTable.js is the right place to do. You will need to read the dicom_archive module files, I believe it is straightforward to see what to modify there. The data is passed via JSON function of php/dicom_archive.class.inc or others. Best regards, Ling Ma On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > I just runned make and it auto runned composer install --no-dev on its > own. To make it run i needed to delete the vendor directory. Also when > placing the dicom_archive under project/ directory i see it has no effect > at the web interface but it worked when i replaced the original module. At > the moment I will work at the path of the original module, no harm since we > using docker to replace the original path at the building process. > > To display the values of my new column, which files should I edit? I > believe it's the FilterableDataTable.js but how does it get its data for > the table? ( I am new to React ) > > Thanks > > Thanks > > ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma > ??????: > >> Hi Sotirios, >> >> You must have run with "composer install" early, so why do you run >> "composer install --no-dev" now? You can delete the vendor/facebook, then >> re-run the "composer install --no-dev". The cause could be something to do >> with facebook package, which is out of the consideration of Loris. >> >> Hope this helps. Thanks. >> >> Best regards, >> Ling Ma >> >> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> I am getting this error when i am running make >>> >>> composer install --no-dev >>> > mkdir -p project/libraries >>> Loading composer repositories with package information >>> Installing dependencies from lock file >>> Package operations: 0 installs, 0 updates, 4 removals >>> - Removing facebook/webdriver (dev-master) >>> >>> >>> >>> [RuntimeException] >>> >>> Source directory /var/www/loris/vendor/facebook/webdriver has unpushed >>> chan >>> ges on the current branch: >>> >>> M lib/WebDriverTargetLocator.php >>> >>> >>> >>> >>> install [--prefer-source] [--prefer-dist] >>> >>> Thanks >>> >>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma >>> ??????: >>> >>>> Hi Sotirios, >>>> >>>> You will need to customize the dicom_archive modules which resides >>>> under /modules/dicom_archive, we recommend against modifying >>>> directly the module, instead you copy that module into project/modules to >>>> do any customization there, then run "composer install" to let the Loris >>>> know that you want to use your customized version. Then you need to run >>>> "make" under the to compile jsx to js. >>>> >>>> The table and the filter are written in ReactJS, as long as you have >>>> some knowledge of ReactJS and PHP, you could go ahead to do it. >>>> >>>> Best regards, >>>> Ling Ma >>>> >>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> We would like to customize the Selection Filter given in >>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to add >>>>> a new column on the existing table shown ( that batch column will be >>>>> contained in the files table ). Could you give some info on how to proceed? >>>>> >>>>> The desired result is as shown in that image >>>>> >>>>> [image: image.png] >>>>> >>>>> Thank you >>>>> >>>>> Sotirios >>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: From lingyun.ma at mcin.ca Tue Mar 3 14:55:33 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Tue, 3 Mar 2020 14:55:33 -0500 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi Sotirios, As a further precision, "dicom_archive/jsx/dicom_archive.js" could be js file you need to modify, "fields" of the line 120 could be the filter definition ... The implemented behavior will depend on what you need to do On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: > Hi Sotirios, > > To make the new module work, I suggest you put it in project/modules, but > it is up to you to choose where to put. > > Last time I asked "You will need to customize the dicom_archive modules > which resides under /modules/dicom_archive", I don't believe > FilterableDataTable.js is the right place to do. You will need to read the > dicom_archive module files, I believe it is straightforward to see what to > modify there. The data is passed via JSON function of > php/dicom_archive.class.inc or others. > > Best regards, > Ling Ma > > > > On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> I just runned make and it auto runned composer install --no-dev on its >> own. To make it run i needed to delete the vendor directory. Also when >> placing the dicom_archive under project/ directory i see it has no effect >> at the web interface but it worked when i replaced the original module. At >> the moment I will work at the path of the original module, no harm since we >> using docker to replace the original path at the building process. >> >> To display the values of my new column, which files should I edit? I >> believe it's the FilterableDataTable.js but how does it get its data for >> the table? ( I am new to React ) >> >> Thanks >> >> Thanks >> >> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >> ??????: >> >>> Hi Sotirios, >>> >>> You must have run with "composer install" early, so why do you run >>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>> re-run the "composer install --no-dev". The cause could be something to do >>> with facebook package, which is out of the consideration of Loris. >>> >>> Hope this helps. Thanks. >>> >>> Best regards, >>> Ling Ma >>> >>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I am getting this error when i am running make >>>> >>>> composer install --no-dev >>>> > mkdir -p project/libraries >>>> Loading composer repositories with package information >>>> Installing dependencies from lock file >>>> Package operations: 0 installs, 0 updates, 4 removals >>>> - Removing facebook/webdriver (dev-master) >>>> >>>> >>>> >>>> [RuntimeException] >>>> >>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>> unpushed chan >>>> ges on the current branch: >>>> >>>> M lib/WebDriverTargetLocator.php >>>> >>>> >>>> >>>> >>>> install [--prefer-source] [--prefer-dist] >>>> >>>> Thanks >>>> >>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma >>>> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> You will need to customize the dicom_archive modules which resides >>>>> under /modules/dicom_archive, we recommend against modifying >>>>> directly the module, instead you copy that module into project/modules to >>>>> do any customization there, then run "composer install" to let the Loris >>>>> know that you want to use your customized version. Then you need to run >>>>> "make" under the to compile jsx to js. >>>>> >>>>> The table and the filter are written in ReactJS, as long as you have >>>>> some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>> >>>>> Best regards, >>>>> Ling Ma >>>>> >>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> We would like to customize the Selection Filter given in >>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to add >>>>>> a new column on the existing table shown ( that batch column will be >>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>> >>>>>> The desired result is as shown in that image >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> Thank you >>>>>> >>>>>> Sotirios >>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: From sotirisnik at gmail.com Wed Mar 4 07:26:07 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Mar 2020 14:26:07 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi Ling, I found the sql query https://github.com/aueb-wim/LORIS-for-MIP/blob/master/dicom_archive/php/dicomarchiverowprovisioner.class.inc#L40 and modified to get our Batch column and the dropdown box works too ( I made it based on Site ). [image: image.png] Now I would like to place the Button Is this how I should proceed for it? [image: image.png] Thanks Sotirios ???? ???, 3 ??? 2020 ???? 9:55 ?.?., ?/? Ling Ma ??????: > Hi Sotirios, > > As a further precision, "dicom_archive/jsx/dicom_archive.js" could be js > file you need to modify, "fields" of the line 120 could be the filter > definition ... > > The implemented behavior will depend on what you need to do > > > On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: > >> Hi Sotirios, >> >> To make the new module work, I suggest you put it in project/modules, >> but it is up to you to choose where to put. >> >> Last time I asked "You will need to customize the dicom_archive modules >> which resides under /modules/dicom_archive", I don't believe >> FilterableDataTable.js is the right place to do. You will need to read the >> dicom_archive module files, I believe it is straightforward to see what to >> modify there. The data is passed via JSON function of >> php/dicom_archive.class.inc or others. >> >> Best regards, >> Ling Ma >> >> >> >> On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> I just runned make and it auto runned composer install --no-dev on its >>> own. To make it run i needed to delete the vendor directory. Also when >>> placing the dicom_archive under project/ directory i see it has no effect >>> at the web interface but it worked when i replaced the original module. At >>> the moment I will work at the path of the original module, no harm since we >>> using docker to replace the original path at the building process. >>> >>> To display the values of my new column, which files should I edit? I >>> believe it's the FilterableDataTable.js but how does it get its data for >>> the table? ( I am new to React ) >>> >>> Thanks >>> >>> Thanks >>> >>> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >>> ??????: >>> >>>> Hi Sotirios, >>>> >>>> You must have run with "composer install" early, so why do you run >>>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>>> re-run the "composer install --no-dev". The cause could be something to do >>>> with facebook package, which is out of the consideration of Loris. >>>> >>>> Hope this helps. Thanks. >>>> >>>> Best regards, >>>> Ling Ma >>>> >>>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> I am getting this error when i am running make >>>>> >>>>> composer install --no-dev >>>>> > mkdir -p project/libraries >>>>> Loading composer repositories with package information >>>>> Installing dependencies from lock file >>>>> Package operations: 0 installs, 0 updates, 4 removals >>>>> - Removing facebook/webdriver (dev-master) >>>>> >>>>> >>>>> >>>>> [RuntimeException] >>>>> >>>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>>> unpushed chan >>>>> ges on the current branch: >>>>> >>>>> M lib/WebDriverTargetLocator.php >>>>> >>>>> >>>>> >>>>> >>>>> install [--prefer-source] [--prefer-dist] >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma >>>>> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> You will need to customize the dicom_archive modules which resides >>>>>> under /modules/dicom_archive, we recommend against modifying >>>>>> directly the module, instead you copy that module into project/modules to >>>>>> do any customization there, then run "composer install" to let the Loris >>>>>> know that you want to use your customized version. Then you need to run >>>>>> "make" under the to compile jsx to js. >>>>>> >>>>>> The table and the filter are written in ReactJS, as long as you have >>>>>> some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>>> >>>>>> Best regards, >>>>>> Ling Ma >>>>>> >>>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> We would like to customize the Selection Filter given in >>>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to >>>>>>> add a new column on the existing table shown ( that batch column will be >>>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>>> >>>>>>> The desired result is as shown in that image >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> Thank you >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 770441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42968 bytes Desc: not available URL: From sotirisnik at gmail.com Wed Mar 4 09:28:56 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Mar 2020 16:28:56 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi, I found out how to make the button and its functionality. Thanks, Sotirios ???? ???, 4 ??? 2020 ???? 2:26 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi Ling, > > I found the sql query > https://github.com/aueb-wim/LORIS-for-MIP/blob/master/dicom_archive/php/dicomarchiverowprovisioner.class.inc#L40 > and modified to get our Batch column and the dropdown box works too ( I > made it based on Site ). > > [image: image.png] > > Now I would like to place the Button > > Is this how I should proceed for it? > > [image: image.png] > > Thanks > > Sotirios > > > ???? ???, 3 ??? 2020 ???? 9:55 ?.?., ?/? Ling Ma > ??????: > >> Hi Sotirios, >> >> As a further precision, "dicom_archive/jsx/dicom_archive.js" could be js >> file you need to modify, "fields" of the line 120 could be the filter >> definition ... >> >> The implemented behavior will depend on what you need to do >> >> >> On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: >> >>> Hi Sotirios, >>> >>> To make the new module work, I suggest you put it in project/modules, >>> but it is up to you to choose where to put. >>> >>> Last time I asked "You will need to customize the dicom_archive modules >>> which resides under /modules/dicom_archive", I don't believe >>> FilterableDataTable.js is the right place to do. You will need to read the >>> dicom_archive module files, I believe it is straightforward to see what to >>> modify there. The data is passed via JSON function of >>> php/dicom_archive.class.inc or others. >>> >>> Best regards, >>> Ling Ma >>> >>> >>> >>> On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I just runned make and it auto runned composer install --no-dev on its >>>> own. To make it run i needed to delete the vendor directory. Also when >>>> placing the dicom_archive under project/ directory i see it has no effect >>>> at the web interface but it worked when i replaced the original module. At >>>> the moment I will work at the path of the original module, no harm since we >>>> using docker to replace the original path at the building process. >>>> >>>> To display the values of my new column, which files should I edit? I >>>> believe it's the FilterableDataTable.js but how does it get its data for >>>> the table? ( I am new to React ) >>>> >>>> Thanks >>>> >>>> Thanks >>>> >>>> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >>>> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> You must have run with "composer install" early, so why do you run >>>>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>>>> re-run the "composer install --no-dev". The cause could be something to do >>>>> with facebook package, which is out of the consideration of Loris. >>>>> >>>>> Hope this helps. Thanks. >>>>> >>>>> Best regards, >>>>> Ling Ma >>>>> >>>>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am getting this error when i am running make >>>>>> >>>>>> composer install --no-dev >>>>>> > mkdir -p project/libraries >>>>>> Loading composer repositories with package information >>>>>> Installing dependencies from lock file >>>>>> Package operations: 0 installs, 0 updates, 4 removals >>>>>> - Removing facebook/webdriver (dev-master) >>>>>> >>>>>> >>>>>> >>>>>> [RuntimeException] >>>>>> >>>>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>>>> unpushed chan >>>>>> ges on the current branch: >>>>>> >>>>>> M lib/WebDriverTargetLocator.php >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> install [--prefer-source] [--prefer-dist] >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma >>>>>> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> You will need to customize the dicom_archive modules which resides >>>>>>> under /modules/dicom_archive, we recommend against modifying >>>>>>> directly the module, instead you copy that module into project/modules to >>>>>>> do any customization there, then run "composer install" to let the Loris >>>>>>> know that you want to use your customized version. Then you need to run >>>>>>> "make" under the to compile jsx to js. >>>>>>> >>>>>>> The table and the filter are written in ReactJS, as long as you have >>>>>>> some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>>>> >>>>>>> Best regards, >>>>>>> Ling Ma >>>>>>> >>>>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> We would like to customize the Selection Filter given in >>>>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to >>>>>>>> add a new column on the existing table shown ( that batch column will be >>>>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>>>> >>>>>>>> The desired result is as shown in that image >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> Thank you >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 770441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42968 bytes Desc: not available URL: From ioannis at berkeley.edu Wed Mar 4 20:03:21 2020 From: ioannis at berkeley.edu (Ioannis Pappas) Date: Wed, 4 Mar 2020 17:03:21 -0800 Subject: [Loris-dev] question regarding MRI uploader Message-ID: Hi loris dev team I have a question about uploading some of the data. For now I am experimenting with the GUI and I uploaded a .zip folder containing some BOLD for one participant. However, I am getting an error message saying that it cannot read the PatientName field in one of the dicoms. However that dicom header field exists (itself is a struct containing a field named FamilyName with the name of the patient). Now the bar is stuck and it says "in progress". What is your advice on this? 2. I am still confused as to how each uploaded dicom zip will be assigned to each mri type via the mri_protocol table. For example if I upload the pscid_candid_V1_BOLD_resting_MtzVA_8.zip file that corresponds to my BOLD data, is the regex expression in the mri_protocol the one that I will need to modify in order to assign my mri_scan_type of bold to that particular upload? 3. What is the easiest way to remove patients and their associated data? For example now my data is stuck "in progress" and I would like to get rid of it. Thank you very much in advance. Best wishes, Ioannis -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Wed Mar 4 22:56:39 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Wed, 4 Mar 2020 22:56:39 -0500 Subject: [Loris-dev] question regarding MRI uploader In-Reply-To: References: Message-ID: Hi Ioannis, I try to answer your question without checking in detail. My memory might not be accurate. 1). GUI imaging uploader is just a tool that helps you to upload a zip file without actually processing it. So when it is stuck with "in progress", then this uploading task could be considered dead, you can just open the page to start over again. Of course you could remove the record. Since this is only a tool helping you upload images, this tool won't read the DICOM information, it just read the file name to process. 2). As I remember, the MRI type in the file name won't be taken into consideration, instead I suppose the DICOM information should be used, I could check later for details. 3). if you just upload an image, it failed without having been processed, you can just remove the record from "mri_upload" table or just start over again, you can remove the corresponding file if you wish to free up the used space. Of course you should be careful in doing so. I feel that you are not using image processing tool up to right now, the imaging uploader is not all, the uploading doesn't do all the work as you assume, The purpose of the "Imaging Uploader" is "The imaging uploader is intended to allow users to upload, browse, and track pipeline insertion progress." (source: https://github.com/aces/Loris/tree/master/modules/imaging_uploader/README.md ) Instead the real work is done by imaging processing package Loris-MRI ( https://github.com/aces/Loris-MRI). If the files have been processed but without being successful, under the image uploading processing tool package Loris-MRI, ( https://github.com/aces/Loris-MRI), there is a folder called "tools", there is a delete_imaging_upload.pl, which could be used to easily remove any unsuccessful imaging loading. Hope this could help you out. Best regards, Ling Ma On Wed, Mar 4, 2020 at 8:03 PM Ioannis Pappas wrote: > Hi loris dev team > I have a question about uploading some of the data. > > For now I am experimenting with the GUI and I uploaded a .zip folder > containing some BOLD for one participant. However, I am getting an error > message saying that it cannot read the PatientName field in one of the > dicoms. However that dicom header field exists (itself is a struct > containing a field named FamilyName with the name of the patient). Now the > bar is stuck and it says "in progress". What is your advice on this? > > 2. I am still confused as to how each uploaded dicom zip will be assigned > to each mri type via the mri_protocol table. For example if I upload the > pscid_candid_V1_BOLD_resting_MtzVA_8.zip file that corresponds to my BOLD > data, is the regex expression in the mri_protocol the one that I will need > to modify in order to assign my mri_scan_type of bold to that particular > upload? > > 3. What is the easiest way to remove patients and their associated data? > For example now my data is stuck "in progress" and I would like to get rid > of it. > > Thank you very much in advance. > Best wishes, > Ioannis > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Thu Mar 5 09:14:27 2020 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Thu, 5 Mar 2020 09:14:27 -0500 Subject: [Loris-dev] question regarding MRI uploader In-Reply-To: References: Message-ID: Hi Ioannis, I would also recommend reading the documentation in the LORIS-MRI repo here to get a better understanding on how the insertion pipelines work. Re-2) the protocol identification is performed based on the scan's TR, TE, TI, slice thickness parameters read from the image (see section 2.2.1 of this page with explanation of the mri_scan_type, mri_protocol and mri_protocol_checks tables). Hope this helps, C?cile On Wed, Mar 4, 2020 at 10:57 PM Ling Ma wrote: > Hi Ioannis, > > I try to answer your question without checking in detail. My memory might > not be accurate. > > 1). GUI imaging uploader is just a tool that helps you to upload a zip > file without actually processing it. So when it is stuck with "in > progress", then this uploading task could be considered dead, you can just > open the page to start over again. Of course you could remove the record. > Since this is only a tool helping you upload images, this tool won't read > the DICOM information, it just read the file name to process. > 2). As I remember, the MRI type in the file name won't be taken into > consideration, instead I suppose the DICOM information should be used, I > could check later for details. > 3). if you just upload an image, it failed without having been processed, > you can just remove the record from "mri_upload" table or just start over > again, you can remove the corresponding file if you wish to free up the > used space. Of course you should be careful in doing so. > > I feel that you are not using image processing tool up to right now, the > imaging uploader is not all, the uploading doesn't do all the work as you > assume, The purpose of the "Imaging Uploader" is "The imaging uploader is > intended to allow users to upload, browse, and track pipeline insertion > progress." (source: > https://github.com/aces/Loris/tree/master/modules/imaging_uploader/README.md > ) > > Instead the real work is done by imaging processing package Loris-MRI ( > https://github.com/aces/Loris-MRI). > > If the files have been processed but without being successful, under the > image uploading processing tool package Loris-MRI, ( > https://github.com/aces/Loris-MRI), there is a folder called "tools", > there is a delete_imaging_upload.pl, which could be used to easily remove > any unsuccessful imaging loading. > > Hope this could help you out. > > Best regards, > Ling Ma > > On Wed, Mar 4, 2020 at 8:03 PM Ioannis Pappas > wrote: > >> Hi loris dev team >> I have a question about uploading some of the data. >> >> For now I am experimenting with the GUI and I uploaded a .zip folder >> containing some BOLD for one participant. However, I am getting an error >> message saying that it cannot read the PatientName field in one of the >> dicoms. However that dicom header field exists (itself is a struct >> containing a field named FamilyName with the name of the patient). Now the >> bar is stuck and it says "in progress". What is your advice on this? >> >> 2. I am still confused as to how each uploaded dicom zip will be assigned >> to each mri type via the mri_protocol table. For example if I upload the >> pscid_candid_V1_BOLD_resting_MtzVA_8.zip file that corresponds to my BOLD >> data, is the regex expression in the mri_protocol the one that I will need >> to modify in order to assign my mri_scan_type of bold to that particular >> upload? >> >> 3. What is the easiest way to remove patients and their associated data? >> For example now my data is stuck "in progress" and I would like to get rid >> of it. >> >> Thank you very much in advance. >> Best wishes, >> Ioannis >> _______________________________________________ >> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Mar 9 09:12:48 2020 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 9 Mar 2020 13:12:48 +0000 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> Message-ID: <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> Dear Loris DevTeam, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo > wrote: Hi C?cile, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo > wrote: Hi C?cile, Thank you for your answer. I will use it once some uploading processes are finished so that I can upgrade LORIS to the its last version where the script is available. I will tell you how it goes. Best, Alfredo. On Feb 4, 2020, at 9:46 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Indeed, the delete_imaging_upload.pl script was designed to properly remove imaging dataset without touching the other tables in the database. By defaults, the script will create a backup of the removed dataset (files + MySQL entries) which is always nice to have in case the delete script was run on a wrong dataset. Run "delete_imaging_upload.pl -h " to see the list of options that can be used. Let me know if you have any questions. C?cile On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, In IPMSA we need to re-upload a whole study in terms of MRI images. Given that I already created all the centers, users in centers, candidates, and visits (clinical and mri), would it be possible to only remove the MRI images previously uploaded? Looking at the script delete_imaging_upload.pl it seems to be possible (I can get all the Tarchive IDs assoicated) but I want to confirm before I move forward. Please let me know if this is possible. Thank you for all your help. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Mar 9 11:17:51 2020 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 9 Mar 2020 11:17:51 -0400 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> Message-ID: Hi Alfredo, Have you tested your MRI code since you did the upgrade on the LORIS? There might be some SQL changes impacting the LORIS-MRI side as well (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN and MAX columns for example). If all works well, you can try downloading and testing the delete_imaging_upload.pl and it may work as is. Let me know how this goes! C?cile On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear Loris DevTeam, > > I finally upgraded LORIS to v21.0.0 so that we can delete images using the > scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, > I am currently running v18.0.0. > > Given that I have made modification to the core of the library (MRI.pm) > and created scripts for uploading masks and transformation that are working > properly and might be impacted if I upgrade the code, would it be possible > to ?import? and use the script delete_imaging_upload.pl without upgrading > LORIS-MRI? > > Let me know if this is possible. I would prefer to keep the library as it > is cause it?s working perfect for us right now. > > Regards, > Alfredo. > > On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > Hi C?cile, > > I finally upgraded LORIS to v21.0.0 so that we can delete images using the > scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I > am currently running v18.0.0. > > Given that I have made modification to the core of the library (MRI.pm) > and created scripts for uploading masks and transformation that are working > properly and might be impacted if I upgrade the code, would it be > possible to ?import? and use the script delete_imaging_upload.pl without > upgrading LORIS-MRI? > > Let me know if this is possible. I would prefer to keep the library as it > is cause it?s working perfect for us right now. > > Regards, > Alfredo. > > On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > Hi C?cile, > > Thank you for your answer. I will use it once some uploading processes are > finished so that I can upgrade LORIS to the its last version where the > script is available. I will tell you how it goes. > > Best, > Alfredo. > > On Feb 4, 2020, at 9:46 AM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > Indeed, the delete_imaging_upload.pl script was designed to properly > remove imaging dataset without touching the other tables in the database. > By defaults, the script will create a backup of the removed dataset > (files + MySQL entries) which is always nice to have in case the delete > script was run on a wrong dataset. > > Run "delete_imaging_upload.pl -h " to see the list of options that can be > used. > > Let me know if you have any questions. > > C?cile > > On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Cecile, >> >> In IPMSA we need to re-upload a whole study in terms of MRI images. Given >> that I already created all the centers, users in centers, candidates, and >> visits (clinical and mri), would it be possible to only remove the MRI >> images previously uploaded? Looking at the script >> delete_imaging_upload.pl >> it >> seems to be possible (I can get all the Tarchive IDs assoicated) but I want >> to confirm before I move forward. Please let me know if this is possible. >> >> Thank you for all your help. >> >> Regards, >> Alfredo. >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From aashim1garg at gmail.com Wed Mar 11 17:00:08 2020 From: aashim1garg at gmail.com (Aashim Garg) Date: Thu, 12 Mar 2020 02:30:08 +0530 Subject: [Loris-dev] Regarding GSoC 2020 Message-ID: Hi everyone. I want to contribute to LORIS Candidate module as a part of my GSoC project. Just read the project description thoroughly. I am interested in working on this project . I have worked with JS, React, HTML 5,CSS, PHP in my past projects. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Thu Mar 12 10:03:42 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Thu, 12 Mar 2020 10:03:42 -0400 Subject: [Loris-dev] Regarding GSoC 2020 In-Reply-To: References: Message-ID: Hi Aashim, Thanks for your interest in LORIS, I try to answer your request in a general way. you can always contribute to the project by different mays, your contributions are always welcome, Unfortunately I don't know what your contribution will be as a GSoC, neither what Candidate module needs to do nor whether it is necessary. Personally I don't feel your request will be easy to go through. Wish you success in your study. Best regards, Ling Ma Dev Consultant On Wed, Mar 11, 2020 at 5:00 PM Aashim Garg wrote: > Hi everyone. I want to contribute to LORIS Candidate module as a part of > my GSoC project. Just read the project description thoroughly. I am > interested in working on this project . I have worked with JS, React, HTML > 5,CSS, PHP in my past projects. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From melanie.legault2 at mcgill.ca Thu Mar 12 10:08:55 2020 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Thu, 12 Mar 2020 14:08:55 +0000 Subject: [Loris-dev] Regarding GSoC 2020 In-Reply-To: References: , Message-ID: Hello Aashim, We do accept candidate for GCoC. All request have to be done through https://www.incf.org/training/gsoc. Your request will be evaluated there and if approved we will welcome you in our project. If not, you may still contribute on a voluntary basis. M?lanie GSoC Co-mentor for LORIS ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ling Ma Sent: March 12, 2020 10:03 To: Aashim Garg Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Regarding GSoC 2020 Hi Aashim, Thanks for your interest in LORIS, I try to answer your request in a general way. you can always contribute to the project by different mays, your contributions are always welcome, Unfortunately I don't know what your contribution will be as a GSoC, neither what Candidate module needs to do nor whether it is necessary. Personally I don't feel your request will be easy to go through. Wish you success in your study. Best regards, Ling Ma Dev Consultant On Wed, Mar 11, 2020 at 5:00 PM Aashim Garg > wrote: Hi everyone. I want to contribute to LORIS Candidate module as a part of my GSoC project. Just read the project description thoroughly. I am interested in working on this project . I have worked with JS, React, HTML 5,CSS, PHP in my past projects. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Thu Mar 12 10:46:49 2020 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Thu, 12 Mar 2020 14:46:49 +0000 Subject: [Loris-dev] Regarding GSoC 2020 In-Reply-To: References: Message-ID: Hi Aashim, Please me directly to discuss GSOC. As you will have seen in our project description on Neurostars, my address is the lead contact for our GSOC program this year. Happy to discuss either on Neurostars or directly by email, the Loris-dev community will be involved only later in the year. Best, Christine Sent from my iPhone On Mar 12, 2020, at 10:09 AM, Melanie Legault, Mrs wrote: ? Hello Aashim, We do accept candidate for GCoC. All request have to be done through https://www.incf.org/training/gsoc. Your request will be evaluated there and if approved we will welcome you in our project. If not, you may still contribute on a voluntary basis. M?lanie GSoC Co-mentor for LORIS ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ling Ma Sent: March 12, 2020 10:03 To: Aashim Garg Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Regarding GSoC 2020 Hi Aashim, Thanks for your interest in LORIS, I try to answer your request in a general way. you can always contribute to the project by different mays, your contributions are always welcome, Unfortunately I don't know what your contribution will be as a GSoC, neither what Candidate module needs to do nor whether it is necessary. Personally I don't feel your request will be easy to go through. Wish you success in your study. Best regards, Ling Ma Dev Consultant On Wed, Mar 11, 2020 at 5:00 PM Aashim Garg > wrote: Hi everyone. I want to contribute to LORIS Candidate module as a part of my GSoC project. Just read the project description thoroughly. I am interested in working on this project . I have worked with JS, React, HTML 5,CSS, PHP in my past projects. _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Mon Mar 16 10:28:04 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 16 Mar 2020 16:28:04 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi, I would like to get some columns from the files tables at the imaging_browser module. According to this sql query https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L157 I see that it uses the files table on inner join and is named as f but i can't refer to the table for some reason here https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L226 Thanks Sotirios ???? ???, 4 ??? 2020 ???? 4:28 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > I found out how to make the button and its functionality. > > Thanks, > > Sotirios > > ???? ???, 4 ??? 2020 ???? 2:26 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi Ling, >> >> I found the sql query >> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/dicom_archive/php/dicomarchiverowprovisioner.class.inc#L40 >> and modified to get our Batch column and the dropdown box works too ( I >> made it based on Site ). >> >> [image: image.png] >> >> Now I would like to place the Button >> >> Is this how I should proceed for it? >> >> [image: image.png] >> >> Thanks >> >> Sotirios >> >> >> ???? ???, 3 ??? 2020 ???? 9:55 ?.?., ?/? Ling Ma >> ??????: >> >>> Hi Sotirios, >>> >>> As a further precision, "dicom_archive/jsx/dicom_archive.js" could be js >>> file you need to modify, "fields" of the line 120 could be the filter >>> definition ... >>> >>> The implemented behavior will depend on what you need to do >>> >>> >>> On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: >>> >>>> Hi Sotirios, >>>> >>>> To make the new module work, I suggest you put it in project/modules, >>>> but it is up to you to choose where to put. >>>> >>>> Last time I asked "You will need to customize the dicom_archive modules >>>> which resides under /modules/dicom_archive", I don't believe >>>> FilterableDataTable.js is the right place to do. You will need to read the >>>> dicom_archive module files, I believe it is straightforward to see what to >>>> modify there. The data is passed via JSON function of >>>> php/dicom_archive.class.inc or others. >>>> >>>> Best regards, >>>> Ling Ma >>>> >>>> >>>> >>>> On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> I just runned make and it auto runned composer install --no-dev on its >>>>> own. To make it run i needed to delete the vendor directory. Also when >>>>> placing the dicom_archive under project/ directory i see it has no effect >>>>> at the web interface but it worked when i replaced the original module. At >>>>> the moment I will work at the path of the original module, no harm since we >>>>> using docker to replace the original path at the building process. >>>>> >>>>> To display the values of my new column, which files should I edit? I >>>>> believe it's the FilterableDataTable.js but how does it get its data for >>>>> the table? ( I am new to React ) >>>>> >>>>> Thanks >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >>>>> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> You must have run with "composer install" early, so why do you run >>>>>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>>>>> re-run the "composer install --no-dev". The cause could be something to do >>>>>> with facebook package, which is out of the consideration of Loris. >>>>>> >>>>>> Hope this helps. Thanks. >>>>>> >>>>>> Best regards, >>>>>> Ling Ma >>>>>> >>>>>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am getting this error when i am running make >>>>>>> >>>>>>> composer install --no-dev >>>>>>> > mkdir -p project/libraries >>>>>>> Loading composer repositories with package information >>>>>>> Installing dependencies from lock file >>>>>>> Package operations: 0 installs, 0 updates, 4 removals >>>>>>> - Removing facebook/webdriver (dev-master) >>>>>>> >>>>>>> >>>>>>> >>>>>>> [RuntimeException] >>>>>>> >>>>>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>>>>> unpushed chan >>>>>>> ges on the current branch: >>>>>>> >>>>>>> M lib/WebDriverTargetLocator.php >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> install [--prefer-source] [--prefer-dist] >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma < >>>>>>> lingyun.ma at mcin.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> You will need to customize the dicom_archive modules which resides >>>>>>>> under /modules/dicom_archive, we recommend against modifying >>>>>>>> directly the module, instead you copy that module into project/modules to >>>>>>>> do any customization there, then run "composer install" to let the Loris >>>>>>>> know that you want to use your customized version. Then you need to run >>>>>>>> "make" under the to compile jsx to js. >>>>>>>> >>>>>>>> The table and the filter are written in ReactJS, as long as you >>>>>>>> have some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Ling Ma >>>>>>>> >>>>>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> We would like to customize the Selection Filter given in >>>>>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to >>>>>>>>> add a new column on the existing table shown ( that batch column will be >>>>>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>>>>> >>>>>>>>> The desired result is as shown in that image >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> Thank you >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 770441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42968 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Mar 16 10:42:12 2020 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 16 Mar 2020 16:42:12 +0200 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Accordng to the error, since it's not an aggregated column i can't have access to it. ???? ???, 16 ??? 2020 ???? 4:28 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > I would like to get some columns from the files tables at the > imaging_browser module. According to this sql query > > > https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L157 > > I see that it uses the files table on inner join and is named as f but i > can't refer to the table for some reason here > > https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L226 > > Thanks > > Sotirios > > ???? ???, 4 ??? 2020 ???? 4:28 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> I found out how to make the button and its functionality. >> >> Thanks, >> >> Sotirios >> >> ???? ???, 4 ??? 2020 ???? 2:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi Ling, >>> >>> I found the sql query >>> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/dicom_archive/php/dicomarchiverowprovisioner.class.inc#L40 >>> and modified to get our Batch column and the dropdown box works too ( I >>> made it based on Site ). >>> >>> [image: image.png] >>> >>> Now I would like to place the Button >>> >>> Is this how I should proceed for it? >>> >>> [image: image.png] >>> >>> Thanks >>> >>> Sotirios >>> >>> >>> ???? ???, 3 ??? 2020 ???? 9:55 ?.?., ?/? Ling Ma >>> ??????: >>> >>>> Hi Sotirios, >>>> >>>> As a further precision, "dicom_archive/jsx/dicom_archive.js" could be >>>> js file you need to modify, "fields" of the line 120 could be the filter >>>> definition ... >>>> >>>> The implemented behavior will depend on what you need to do >>>> >>>> >>>> On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: >>>> >>>>> Hi Sotirios, >>>>> >>>>> To make the new module work, I suggest you put it in project/modules, >>>>> but it is up to you to choose where to put. >>>>> >>>>> Last time I asked "You will need to customize the dicom_archive >>>>> modules which resides under /modules/dicom_archive", I don't >>>>> believe FilterableDataTable.js is the right place to do. You will need to >>>>> read the dicom_archive module files, I believe it is straightforward to see >>>>> what to modify there. The data is passed via JSON function of >>>>> php/dicom_archive.class.inc or others. >>>>> >>>>> Best regards, >>>>> Ling Ma >>>>> >>>>> >>>>> >>>>> On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I just runned make and it auto runned composer install --no-dev on >>>>>> its own. To make it run i needed to delete the vendor directory. Also when >>>>>> placing the dicom_archive under project/ directory i see it has no effect >>>>>> at the web interface but it worked when i replaced the original module. At >>>>>> the moment I will work at the path of the original module, no harm since we >>>>>> using docker to replace the original path at the building process. >>>>>> >>>>>> To display the values of my new column, which files should I edit? I >>>>>> believe it's the FilterableDataTable.js but how does it get its data for >>>>>> the table? ( I am new to React ) >>>>>> >>>>>> Thanks >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >>>>>> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> You must have run with "composer install" early, so why do you run >>>>>>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>>>>>> re-run the "composer install --no-dev". The cause could be something to do >>>>>>> with facebook package, which is out of the consideration of Loris. >>>>>>> >>>>>>> Hope this helps. Thanks. >>>>>>> >>>>>>> Best regards, >>>>>>> Ling Ma >>>>>>> >>>>>>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am getting this error when i am running make >>>>>>>> >>>>>>>> composer install --no-dev >>>>>>>> > mkdir -p project/libraries >>>>>>>> Loading composer repositories with package information >>>>>>>> Installing dependencies from lock file >>>>>>>> Package operations: 0 installs, 0 updates, 4 removals >>>>>>>> - Removing facebook/webdriver (dev-master) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> [RuntimeException] >>>>>>>> >>>>>>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>>>>>> unpushed chan >>>>>>>> ges on the current branch: >>>>>>>> >>>>>>>> M lib/WebDriverTargetLocator.php >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> install [--prefer-source] [--prefer-dist] >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma < >>>>>>>> lingyun.ma at mcin.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> You will need to customize the dicom_archive modules which resides >>>>>>>>> under /modules/dicom_archive, we recommend against modifying >>>>>>>>> directly the module, instead you copy that module into project/modules to >>>>>>>>> do any customization there, then run "composer install" to let the Loris >>>>>>>>> know that you want to use your customized version. Then you need to run >>>>>>>>> "make" under the to compile jsx to js. >>>>>>>>> >>>>>>>>> The table and the filter are written in ReactJS, as long as you >>>>>>>>> have some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> Ling Ma >>>>>>>>> >>>>>>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> We would like to customize the Selection Filter given in >>>>>>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like to >>>>>>>>>> add a new column on the existing table shown ( that batch column will be >>>>>>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>>>>>> >>>>>>>>>> The desired result is as shown in that image >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> Thank you >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 770441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42968 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris_error Type: application/octet-stream Size: 7632 bytes Desc: not available URL: From lingyun.ma at mcin.ca Mon Mar 16 11:11:42 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Mon, 16 Mar 2020 11:11:42 -0400 Subject: [Loris-dev] Customize page In-Reply-To: References: Message-ID: Hi Sotirios, This kind of issue has nothing to do with Loris because you are trying to modify something in Loris. You can use the following suggestion or use other method according to case requirements. Explanation: https://dev.mysql.com/doc/refman/5.7/en/group-by-handling.html Solution: "It?s likely because you have the ONLY_FULL_GROUP_BY function enabled. To fix this, you have to disable it. Run this command: mysql > SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROUP_BY','')); Another way to turn it off is that to find and modify the config file my.cnf. Usually it?s in /etc/my.cnf or /etc/mysql/my.cnf. First, check the sql_mode by running this query: SELECT @@sql_mode; The result should be something similar to this: ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION Copy the sql_mode values, remove ONLY_FULL_GROUP_BY, edit my.cnf and put the rest together in a line under [mysqld] section: sql_mode=STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION Then restart the mysql server." Source: https://tableplus.com/blog/2018/08/mysql-how-to-turn-off-only-full-group-by.html Hope this helps. Ling Ma On Mon, Mar 16, 2020 at 10:42 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Accordng to the error, since it's not an aggregated column i can't have > access to it. > > ???? ???, 16 ??? 2020 ???? 4:28 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> I would like to get some columns from the files tables at the >> imaging_browser module. According to this sql query >> >> >> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L157 >> >> I see that it uses the files table on inner join and is named as f but i >> can't refer to the table for some reason here >> >> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/loris/modules/imaging_browser/php/imaging_browser.class.inc#L226 >> >> Thanks >> >> Sotirios >> >> ???? ???, 4 ??? 2020 ???? 4:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi, >>> >>> I found out how to make the button and its functionality. >>> >>> Thanks, >>> >>> Sotirios >>> >>> ???? ???, 4 ??? 2020 ???? 2:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi Ling, >>>> >>>> I found the sql query >>>> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/dicom_archive/php/dicomarchiverowprovisioner.class.inc#L40 >>>> and modified to get our Batch column and the dropdown box works too ( I >>>> made it based on Site ). >>>> >>>> [image: image.png] >>>> >>>> Now I would like to place the Button >>>> >>>> Is this how I should proceed for it? >>>> >>>> [image: image.png] >>>> >>>> Thanks >>>> >>>> Sotirios >>>> >>>> >>>> ???? ???, 3 ??? 2020 ???? 9:55 ?.?., ?/? Ling Ma >>>> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> As a further precision, "dicom_archive/jsx/dicom_archive.js" could be >>>>> js file you need to modify, "fields" of the line 120 could be the filter >>>>> definition ... >>>>> >>>>> The implemented behavior will depend on what you need to do >>>>> >>>>> >>>>> On Tue, Mar 3, 2020 at 11:40 AM Ling Ma wrote: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> To make the new module work, I suggest you put it in >>>>>> project/modules, but it is up to you to choose where to put. >>>>>> >>>>>> Last time I asked "You will need to customize the dicom_archive >>>>>> modules which resides under /modules/dicom_archive", I don't >>>>>> believe FilterableDataTable.js is the right place to do. You will need to >>>>>> read the dicom_archive module files, I believe it is straightforward to see >>>>>> what to modify there. The data is passed via JSON function of >>>>>> php/dicom_archive.class.inc or others. >>>>>> >>>>>> Best regards, >>>>>> Ling Ma >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Mar 3, 2020 at 11:30 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I just runned make and it auto runned composer install --no-dev on >>>>>>> its own. To make it run i needed to delete the vendor directory. Also when >>>>>>> placing the dicom_archive under project/ directory i see it has no effect >>>>>>> at the web interface but it worked when i replaced the original module. At >>>>>>> the moment I will work at the path of the original module, no harm since we >>>>>>> using docker to replace the original path at the building process. >>>>>>> >>>>>>> To display the values of my new column, which files should I edit? I >>>>>>> believe it's the FilterableDataTable.js but how does it get its data for >>>>>>> the table? ( I am new to React ) >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 3 ??? 2020 ???? 5:11 ?.?., ?/? Ling Ma >>>>>>> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> You must have run with "composer install" early, so why do you run >>>>>>>> "composer install --no-dev" now? You can delete the vendor/facebook, then >>>>>>>> re-run the "composer install --no-dev". The cause could be something to do >>>>>>>> with facebook package, which is out of the consideration of Loris. >>>>>>>> >>>>>>>> Hope this helps. Thanks. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Ling Ma >>>>>>>> >>>>>>>> On Tue, Mar 3, 2020 at 8:00 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I am getting this error when i am running make >>>>>>>>> >>>>>>>>> composer install --no-dev >>>>>>>>> > mkdir -p project/libraries >>>>>>>>> Loading composer repositories with package information >>>>>>>>> Installing dependencies from lock file >>>>>>>>> Package operations: 0 installs, 0 updates, 4 removals >>>>>>>>> - Removing facebook/webdriver (dev-master) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> [RuntimeException] >>>>>>>>> >>>>>>>>> Source directory /var/www/loris/vendor/facebook/webdriver has >>>>>>>>> unpushed chan >>>>>>>>> ges on the current branch: >>>>>>>>> >>>>>>>>> M lib/WebDriverTargetLocator.php >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> install [--prefer-source] [--prefer-dist] >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 27 ??? 2020 ???? 6:27 ?.?., ?/? Ling Ma < >>>>>>>>> lingyun.ma at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> You will need to customize the dicom_archive modules which >>>>>>>>>> resides under /modules/dicom_archive, we recommend against >>>>>>>>>> modifying directly the module, instead you copy that module into >>>>>>>>>> project/modules to do any customization there, then run "composer install" >>>>>>>>>> to let the Loris know that you want to use your customized version. Then >>>>>>>>>> you need to run "make" under the to compile jsx to js. >>>>>>>>>> >>>>>>>>>> The table and the filter are written in ReactJS, as long as you >>>>>>>>>> have some knowledge of ReactJS and PHP, you could go ahead to do it. >>>>>>>>>> >>>>>>>>>> Best regards, >>>>>>>>>> Ling Ma >>>>>>>>>> >>>>>>>>>> On Thu, Feb 27, 2020 at 11:09 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> We would like to customize the Selection Filter given in >>>>>>>>>>> https://demo.loris.ca/dicom_archive/ page. Also we would like >>>>>>>>>>> to add a new column on the existing table shown ( that batch column will be >>>>>>>>>>> contained in the files table ). Could you give some info on how to proceed? >>>>>>>>>>> >>>>>>>>>>> The desired result is as shown in that image >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Thank you >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 221775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 770441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42968 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Mon Mar 30 20:08:04 2020 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 31 Mar 2020 00:08:04 +0000 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> Message-ID: <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> Hi C?cile and LorisDev team, Indeed, there are some breaking changes so I decided to upgrade to LORIS-MRI v21.0.0. After upgrading I am running the suggested script ? cleanup_paths_of_violation_tables.pl? before running the deletion script but I get the following error: === bin/mri/tools$ perl cleanup_paths_of_violation_tables.pl Can't locate DICOM/DICOM.pm in @INC (you may need to install the DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. BEGIN failed--compilation aborted at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. Compilation failed in require at cleanup_paths_of_violation_tables.pl line 9. BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl line 9. === Any idea how to solve it? I couldn?t find it in the troubleshooting guideline (https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md) Regards, Alfredo. On Mar 9, 2020, at 11:17 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Have you tested your MRI code since you did the upgrade on the LORIS? There might be some SQL changes impacting the LORIS-MRI side as well (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN and MAX columns for example). If all works well, you can try downloading and testing the delete_imaging_upload.pl and it may work as is. Let me know how this goes! C?cile On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo > wrote: Dear Loris DevTeam, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo > wrote: Hi C?cile, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo > wrote: Hi C?cile, Thank you for your answer. I will use it once some uploading processes are finished so that I can upgrade LORIS to the its last version where the script is available. I will tell you how it goes. Best, Alfredo. On Feb 4, 2020, at 9:46 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Indeed, the delete_imaging_upload.pl script was designed to properly remove imaging dataset without touching the other tables in the database. By defaults, the script will create a backup of the removed dataset (files + MySQL entries) which is always nice to have in case the delete script was run on a wrong dataset. Run "delete_imaging_upload.pl -h " to see the list of options that can be used. Let me know if you have any questions. C?cile On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, In IPMSA we need to re-upload a whole study in terms of MRI images. Given that I already created all the centers, users in centers, candidates, and visits (clinical and mri), would it be possible to only remove the MRI images previously uploaded? Looking at the script delete_imaging_upload.pl it seems to be possible (I can get all the Tarchive IDs assoicated) but I want to confirm before I move forward. Please let me know if this is possible. Thank you for all your help. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Mon Mar 30 21:49:31 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Mon, 30 Mar 2020 21:49:31 -0400 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> Message-ID: Hi Alfredo, I believe you need to read the https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment, which says: "Ensure that /home/lorisadmin/.bashrc includes the statement: source /data/$projectname/bin/mri/environment Then source the .bashrc file." Regards, Ling Ma On Mon, Mar 30, 2020 at 8:08 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi C?cile and LorisDev team, > > Indeed, there are some breaking changes so I decided to upgrade to > LORIS-MRI v21.0.0. After upgrading I am running the suggested script ? > cleanup_paths_of_violation_tables.pl? before running the deletion script > but I get the following error: > > === > *bin/mri/tools*$ perl cleanup_paths_of_violation_tables.pl > Can't locate DICOM/DICOM.pm in @INC (you may need to install the > DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl > /opt/minc/1.9.16/pipeline > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl > /opt/minc/1.9.16/pipeline > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl > /opt/minc/1.9.16/pipeline > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 > /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 > /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 > /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. > BEGIN failed--compilation aborted at > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. > Compilation failed in require at cleanup_paths_of_violation_tables.pl > line 9. > BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl > line 9. > === > > Any idea how to solve it? I couldn?t find it in the troubleshooting > guideline ( > https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md > ) > > Regards, > Alfredo. > > On Mar 9, 2020, at 11:17 AM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > Have you tested your MRI code since you did the upgrade on the LORIS? > There might be some SQL changes impacting the LORIS-MRI side as well > (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN > and MAX columns for example). > > If all works well, you can try downloading and testing the > delete_imaging_upload.pl and it may work as is. > > Let me know how this goes! > > C?cile > > On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear Loris DevTeam, >> >> I finally upgraded LORIS to v21.0.0 so that we can delete images using >> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to >> v21.0.0, I am currently running v18.0.0. >> >> Given that I have made modification to the core of the library (MRI.pm) >> and created scripts for uploading masks and transformation that are working >> properly and might be impacted if I upgrade the code, would it be possible >> to ?import? and use the script delete_imaging_upload.pl without >> upgrading LORIS-MRI? >> >> Let me know if this is possible. I would prefer to keep the library as it >> is cause it?s working perfect for us right now. >> >> Regards, >> Alfredo. >> >> On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo < >> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >> >> Hi C?cile, >> >> I finally upgraded LORIS to v21.0.0 so that we can delete images using >> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to >> v21.0.0, I am currently running v18.0.0. >> >> Given that I have made modification to the core of the library (MRI.pm) >> and created scripts for uploading masks and transformation that are working >> properly and might be impacted if I upgrade the code, would it be >> possible to ?import? and use the script delete_imaging_upload.pl without >> upgrading LORIS-MRI? >> >> Let me know if this is possible. I would prefer to keep the library as it >> is cause it?s working perfect for us right now. >> >> Regards, >> Alfredo. >> >> On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo < >> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >> >> Hi C?cile, >> >> Thank you for your answer. I will use it once some uploading processes >> are finished so that I can upgrade LORIS to the its last version where the >> script is available. I will tell you how it goes. >> >> Best, >> Alfredo. >> >> On Feb 4, 2020, at 9:46 AM, Cecile Madjar wrote: >> >> External Email - Use Caution >> >> Hi Alfredo, >> >> Indeed, the delete_imaging_upload.pl script was designed to properly >> remove imaging dataset without touching the other tables in the database. >> By defaults, the script will create a backup of the removed dataset >> (files + MySQL entries) which is always nice to have in case the delete >> script was run on a wrong dataset. >> >> Run "delete_imaging_upload.pl -h " to see the list of options that can >> be used. >> >> Let me know if you have any questions. >> >> C?cile >> >> On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Cecile, >>> >>> In IPMSA we need to re-upload a whole study in terms of MRI images. >>> Given that I already created all the centers, users in centers, candidates, >>> and visits (clinical and mri), would it be possible to only remove the MRI >>> images previously uploaded? Looking at the script >>> delete_imaging_upload.pl >>> it >>> seems to be possible (I can get all the Tarchive IDs assoicated) but I want >>> to confirm before I move forward. Please let me know if this is possible. >>> >>> Thank you for all your help. >>> >>> Regards, >>> Alfredo. >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Mar 30 22:18:00 2020 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 31 Mar 2020 02:18:00 +0000 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> Message-ID: <47901747-89AB-42F0-A530-B6A290E8D07F@bwh.harvard.edu> Hi Ling Ma, Thank you for the prompt response. I already had the statement because I am upgrading from v18.0.0. However I double checked and the .bashrc file has the statement. Any other ideas of where to look for? Regards, Alfredo. On Mar 30, 2020, at 9:49 PM, Ling Ma > wrote: External Email - Use Caution Hi Alfredo, I believe you need to read the https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment, which says: "Ensure that /home/lorisadmin/.bashrc includes the statement: source /data/$projectname/bin/mri/environment Then source the .bashrc file." Regards, Ling Ma On Mon, Mar 30, 2020 at 8:08 PM Morales Pinzon, Alfredo > wrote: Hi C?cile and LorisDev team, Indeed, there are some breaking changes so I decided to upgrade to LORIS-MRI v21.0.0. After upgrading I am running the suggested script ? cleanup_paths_of_violation_tables.pl? before running the deletion script but I get the following error: === bin/mri/tools$ perl cleanup_paths_of_violation_tables.pl Can't locate DICOM/DICOM.pm in @INC (you may need to install the DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. BEGIN failed--compilation aborted at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. Compilation failed in require at cleanup_paths_of_violation_tables.pl line 9. BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl line 9. === Any idea how to solve it? I couldn?t find it in the troubleshooting guideline (https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md) Regards, Alfredo. On Mar 9, 2020, at 11:17 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Have you tested your MRI code since you did the upgrade on the LORIS? There might be some SQL changes impacting the LORIS-MRI side as well (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN and MAX columns for example). If all works well, you can try downloading and testing the delete_imaging_upload.pl and it may work as is. Let me know how this goes! C?cile On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo > wrote: Dear Loris DevTeam, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo > wrote: Hi C?cile, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo > wrote: Hi C?cile, Thank you for your answer. I will use it once some uploading processes are finished so that I can upgrade LORIS to the its last version where the script is available. I will tell you how it goes. Best, Alfredo. On Feb 4, 2020, at 9:46 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Indeed, the delete_imaging_upload.pl script was designed to properly remove imaging dataset without touching the other tables in the database. By defaults, the script will create a backup of the removed dataset (files + MySQL entries) which is always nice to have in case the delete script was run on a wrong dataset. Run "delete_imaging_upload.pl -h " to see the list of options that can be used. Let me know if you have any questions. C?cile On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, In IPMSA we need to re-upload a whole study in terms of MRI images. Given that I already created all the centers, users in centers, candidates, and visits (clinical and mri), would it be possible to only remove the MRI images previously uploaded? Looking at the script delete_imaging_upload.pl it seems to be possible (I can get all the Tarchive IDs assoicated) but I want to confirm before I move forward. Please let me know if this is possible. Thank you for all your help. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Mon Mar 30 22:28:49 2020 From: lingyun.ma at mcin.ca (Ling Ma) Date: Mon, 30 Mar 2020 22:28:49 -0400 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: <47901747-89AB-42F0-A530-B6A290E8D07F@bwh.harvard.edu> References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> <47901747-89AB-42F0-A530-B6A290E8D07F@bwh.harvard.edu> Message-ID: Hi Alfredo, Have you source that environment file? Or you can logout then login to try to activate that file. What you need is: PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB. So I suppose that my suggested method should work for you, if not, try to check PERL5LIB with "echo $PERL5LIB" Good luck. Ling Ma On Mon, Mar 30, 2020 at 10:18 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Ling Ma, > > Thank you for the prompt response. > > I already had the statement because I am upgrading from v18.0.0. However I > double checked and the .bashrc file has the statement. > > Any other ideas of where to look for? > > Regards, > Alfredo. > > On Mar 30, 2020, at 9:49 PM, Ling Ma wrote: > > External Email - Use Caution > > Hi Alfredo, > > I believe you need to read the > https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment, > which says: > > "Ensure that /home/lorisadmin/.bashrc includes the statement: > > source /data/$projectname/bin/mri/environment > > Then source the .bashrc file." > > Regards, > > Ling Ma > > On Mon, Mar 30, 2020 at 8:08 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi C?cile and LorisDev team, >> >> Indeed, there are some breaking changes so I decided to upgrade to >> LORIS-MRI v21.0.0. After upgrading I am running the suggested script ? >> cleanup_paths_of_violation_tables.pl? before running the deletion script >> but I get the following error: >> >> === >> *bin/mri/tools*$ perl cleanup_paths_of_violation_tables.pl >> Can't locate DICOM/DICOM.pm in @INC (you may need to install the >> DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl >> /opt/minc/1.9.16/pipeline >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl >> /opt/minc/1.9.16/pipeline >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl >> /opt/minc/1.9.16/pipeline >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl >> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 >> /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 >> /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 >> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. >> BEGIN failed--compilation aborted at >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. >> Compilation failed in require at cleanup_paths_of_violation_tables.pl >> line 9. >> BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl >> line 9. >> === >> >> Any idea how to solve it? I couldn?t find it in the troubleshooting >> guideline ( >> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md >> ) >> >> Regards, >> Alfredo. >> >> On Mar 9, 2020, at 11:17 AM, Cecile Madjar wrote: >> >> External Email - Use Caution >> >> Hi Alfredo, >> >> Have you tested your MRI code since you did the upgrade on the LORIS? >> There might be some SQL changes impacting the LORIS-MRI side as well >> (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN >> and MAX columns for example). >> >> If all works well, you can try downloading and testing the >> delete_imaging_upload.pl and it may work as is. >> >> Let me know how this goes! >> >> C?cile >> >> On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Dear Loris DevTeam, >>> >>> I finally upgraded LORIS to v21.0.0 so that we can delete images using >>> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to >>> v21.0.0, I am currently running v18.0.0. >>> >>> Given that I have made modification to the core of the library (MRI.pm) >>> and created scripts for uploading masks and transformation that are working >>> properly and might be impacted if I upgrade the code, would it be possible >>> to ?import? and use the script delete_imaging_upload.pl without >>> upgrading LORIS-MRI? >>> >>> Let me know if this is possible. I would prefer to keep the library as >>> it is cause it?s working perfect for us right now. >>> >>> Regards, >>> Alfredo. >>> >>> On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo < >>> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >>> >>> Hi C?cile, >>> >>> I finally upgraded LORIS to v21.0.0 so that we can delete images using >>> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to >>> v21.0.0, I am currently running v18.0.0. >>> >>> Given that I have made modification to the core of the library (MRI.pm) >>> and created scripts for uploading masks and transformation that are working >>> properly and might be impacted if I upgrade the code, would it be >>> possible to ?import? and use the script delete_imaging_upload.pl without >>> upgrading LORIS-MRI? >>> >>> Let me know if this is possible. I would prefer to keep the library as >>> it is cause it?s working perfect for us right now. >>> >>> Regards, >>> Alfredo. >>> >>> On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo < >>> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >>> >>> Hi C?cile, >>> >>> Thank you for your answer. I will use it once some uploading processes >>> are finished so that I can upgrade LORIS to the its last version where the >>> script is available. I will tell you how it goes. >>> >>> Best, >>> Alfredo. >>> >>> On Feb 4, 2020, at 9:46 AM, Cecile Madjar wrote: >>> >>> External Email - Use Caution >>> >>> Hi Alfredo, >>> >>> Indeed, the delete_imaging_upload.pl script was designed to properly >>> remove imaging dataset without touching the other tables in the database. >>> By defaults, the script will create a backup of the removed dataset >>> (files + MySQL entries) which is always nice to have in case the delete >>> script was run on a wrong dataset. >>> >>> Run "delete_imaging_upload.pl -h " to see the list of options that can >>> be used. >>> >>> Let me know if you have any questions. >>> >>> C?cile >>> >>> On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Hi Cecile, >>>> >>>> In IPMSA we need to re-upload a whole study in terms of MRI images. >>>> Given that I already created all the centers, users in centers, candidates, >>>> and visits (clinical and mri), would it be possible to only remove the MRI >>>> images previously uploaded? Looking at the script >>>> delete_imaging_upload.pl >>>> it >>>> seems to be possible (I can get all the Tarchive IDs assoicated) but I want >>>> to confirm before I move forward. Please let me know if this is possible. >>>> >>>> Thank you for all your help. >>>> >>>> Regards, >>>> Alfredo. >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Mar 30 22:34:17 2020 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 31 Mar 2020 02:34:17 +0000 Subject: [Loris-dev] [IPMSA] Remove MRI files from a project In-Reply-To: References: <24C64308-4219-40CE-804B-F7B9B01AC190@bwh.harvard.edu> <3A572594-945A-485D-B019-FC18C67FF494@bwh.harvard.edu> <9699DFC7-7A67-45D7-842C-1FF5BE8AFE81@bwh.harvard.edu> <5809C6CF-B2BE-4F20-AC4F-3860863B46E8@bwh.harvard.edu> <47901747-89AB-42F0-A530-B6A290E8D07F@bwh.harvard.edu> Message-ID: <8E01BA13-6B27-45FF-A8C7-81AF5B1525EA@bwh.harvard.edu> Hi Ling Ma, You are right, I missed this part in the environment file: /data/%PROJECT%/bin/mri/dicom-archive I have another error now but I guess I need to install Moose module. Thank you. Regards, Alfredo. On Mar 30, 2020, at 10:28 PM, Ling Ma > wrote: External Email - Use Caution Hi Alfredo, Have you source that environment file? Or you can logout then login to try to activate that file. What you need is: PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB. So I suppose that my suggested method should work for you, if not, try to check PERL5LIB with "echo $PERL5LIB" Good luck. Ling Ma On Mon, Mar 30, 2020 at 10:18 PM Morales Pinzon, Alfredo > wrote: Hi Ling Ma, Thank you for the prompt response. I already had the statement because I am upgrading from v18.0.0. However I double checked and the .bashrc file has the statement. Any other ideas of where to look for? Regards, Alfredo. On Mar 30, 2020, at 9:49 PM, Ling Ma > wrote: External Email - Use Caution Hi Alfredo, I believe you need to read the https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment, which says: "Ensure that /home/lorisadmin/.bashrc includes the statement: source /data/$projectname/bin/mri/environment Then source the .bashrc file." Regards, Ling Ma On Mon, Mar 30, 2020 at 8:08 PM Morales Pinzon, Alfredo > wrote: Hi C?cile and LorisDev team, Indeed, there are some breaking changes so I decided to upgrade to LORIS-MRI v21.0.0. After upgrading I am running the suggested script ? cleanup_paths_of_violation_tables.pl? before running the deletion script but I get the following error: === bin/mri/tools$ perl cleanup_paths_of_violation_tables.pl Can't locate DICOM/DICOM.pm in @INC (you may need to install the DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl /opt/minc/1.9.16/pipeline /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. BEGIN failed--compilation aborted at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47. Compilation failed in require at cleanup_paths_of_violation_tables.pl line 9. BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl line 9. === Any idea how to solve it? I couldn?t find it in the troubleshooting guideline (https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md) Regards, Alfredo. On Mar 9, 2020, at 11:17 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Have you tested your MRI code since you did the upgrade on the LORIS? There might be some SQL changes impacting the LORIS-MRI side as well (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN and MAX columns for example). If all works well, you can try downloading and testing the delete_imaging_upload.pl and it may work as is. Let me know how this goes! C?cile On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo > wrote: Dear Loris DevTeam, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo > wrote: Hi C?cile, I finally upgraded LORIS to v21.0.0 so that we can delete images using the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to v21.0.0, I am currently running v18.0.0. Given that I have made modification to the core of the library (MRI.pm) and created scripts for uploading masks and transformation that are working properly and might be impacted if I upgrade the code, would it be possible to ?import? and use the script delete_imaging_upload.pl without upgrading LORIS-MRI? Let me know if this is possible. I would prefer to keep the library as it is cause it?s working perfect for us right now. Regards, Alfredo. On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo > wrote: Hi C?cile, Thank you for your answer. I will use it once some uploading processes are finished so that I can upgrade LORIS to the its last version where the script is available. I will tell you how it goes. Best, Alfredo. On Feb 4, 2020, at 9:46 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Indeed, the delete_imaging_upload.pl script was designed to properly remove imaging dataset without touching the other tables in the database. By defaults, the script will create a backup of the removed dataset (files + MySQL entries) which is always nice to have in case the delete script was run on a wrong dataset. Run "delete_imaging_upload.pl -h " to see the list of options that can be used. Let me know if you have any questions. C?cile On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, In IPMSA we need to re-upload a whole study in terms of MRI images. Given that I already created all the centers, users in centers, candidates, and visits (clinical and mri), would it be possible to only remove the MRI images previously uploaded? Looking at the script delete_imaging_upload.pl it seems to be possible (I can get all the Tarchive IDs assoicated) but I want to confirm before I move forward. Please let me know if this is possible. Thank you for all your help. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. 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