From cecile.madjar at gmail.com Fri Apr 6 11:39:50 2018 From: cecile.madjar at gmail.com (Cecile Madjar) Date: Fri, 6 Apr 2018 11:39:50 -0400 Subject: [Loris-dev] LORIS-MRI - filterParameters() function of the profile file Message-ID: Dear LORIS-MRI users, We are planning on moving the filterParameters() function out of the profile file (often called 'prod') present in the dicom-archive/.loris-mri folder. However, before doing this change, we would like to make sure that no project has customized this function in their profile file. Here is the code for the function. # ----------- OPTIONAL SUBROUTINE # Takes a NeuroDB::File object, and manipulates its parameters # in this case, removes all parameters of length > 1000 sub filterParameters { my $fileRef = shift; my $file = $$fileRef; my $parametersRef = $file->getParameters(); foreach my $key (keys %{$parametersRef}) { if(($key ne 'header') && (length($parametersRef->{$key}) > 1000)) { #print "\n\tFilter active on: $key with length ".length($parametersRef->{$key})."\n"; $file->removeParameter($key); } } } Could you please let me know whether you have customized this function for your project? If by the end of next week, I have not heard of any project that has customized this function, I will go ahead and move it out of the profile file to include it in the LORIS-MRI scripts instead. Let me know. Best wishes, C?cile -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at gmail.com Fri Apr 13 14:27:50 2018 From: cecile.madjar at gmail.com (Cecile Madjar) Date: Fri, 13 Apr 2018 14:27:50 -0400 Subject: [Loris-dev] LORIS-MRI - filterParameters() function of the profile file In-Reply-To: References: Message-ID: Hi all, Since I have not heard of any project that customized the function* filterParameters() *present in their profile file, *note that this function will be removed from the profileTemplate in LORIS-MRI and moved to the LORIS-MRI scripts instead*. Thank you! C?cile On Fri, Apr 6, 2018 at 11:39 AM, Cecile Madjar wrote: > Dear LORIS-MRI users, > > We are planning on moving the filterParameters() function out of the > profile file (often called 'prod') present in the dicom-archive/.loris-mri > folder. > > However, before doing this change, we would like to make sure that no > project has customized this function in their profile file. Here is the > code for the function. > > # ----------- OPTIONAL SUBROUTINE > # Takes a NeuroDB::File object, and manipulates its parameters > # in this case, removes all parameters of length > 1000 > sub filterParameters { > my $fileRef = shift; > my $file = $$fileRef; > my $parametersRef = $file->getParameters(); > > foreach my $key (keys %{$parametersRef}) { > if(($key ne 'header') && (length($parametersRef->{$key}) > 1000)) { > #print "\n\tFilter active on: $key with length ".length($parametersRef->{$key})."\n"; > $file->removeParameter($key); > } > } > } > > Could you please let me know whether you have customized this function for > your project? > > If by the end of next week, I have not heard of any project that has > customized this function, I will go ahead and move it out of the profile > file to include it in the LORIS-MRI scripts instead. > > Let me know. > Best wishes, > > C?cile > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ousmane.diallo3 at mcgill.ca Wed Apr 25 09:43:54 2018 From: ousmane.diallo3 at mcgill.ca (Ousmane Diallo) Date: Wed, 25 Apr 2018 09:43:54 -0400 Subject: [Loris-dev] LORIS first steps Message-ID: <1524663834.21043.87.camel@Linux29549> Hi, I have installed LORIS and want to see how it can help in manasing our samples. My aim is to analyse SNP, CNV from GWAS data. First, to understand the LORIS web interface I tried to use the Demo, but I don't understand much about it. I don't know which files are used and which data are compareted to what? I tried to upload a csv file but the system gives an file format error. I wan't to know what kind of file format are used to upload in LORIS? Is there a readme which help to understand the Demo. Is there a specific team that I can contact for support? -- Ousmane Diallo Bioinformatics specialist Guy Rouleau laboratory MNI - McGill University 514-398-6761 ousmane.diallo3 at mcgill.ca From xavier.lecoursboucher at mcgill.ca Wed Apr 25 11:02:56 2018 From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr) Date: Wed, 25 Apr 2018 15:02:56 +0000 Subject: [Loris-dev] LORIS first steps In-Reply-To: <1524663834.21043.87.camel@Linux29549> References: <1524663834.21043.87.camel@Linux29549> Message-ID: Hi, Thank you for your interest in using LORIS. First of all, our genomic-browser module is in a beta version and still have room for improvements. I will try to answer you questions assuming you downloaded and install version 19.0 or 19.1 "Is there a specific team that I can contact for support?" That would be me. "I wan't to know what kind of file format are used to upload in LORIS?" Under the file tab in the genomic browser you can upload a specific format for Methylation beta-values, or any Other. Selecting the first one will trigger the importation of the file content after some validation. For the Other category it will simply store the file on the file system. Both will move the file under /data/loris/data/genomics/ (this path can be changed in the configuraion module). "Is there a readme ..." Yes: https://github.com/aces/Loris/tree/v19.0.1/modules/genomic_browser "which help to understand the Demo?" Not yet. There is an help section in the top right corner of the screen but it is really limited. Here a brief overview The genomic browser is divided into 6 tabs: * Profile: This tab show a list of PSCID (subject ID) and the available omic data for each of them under the Files,SNPs, CNVs and CPGs columns. * GWAS: This tab is intended to present GWAS results (a list of snps + annotations and the associated p-value) (this is empty on the demo site) * SNP: A table where each row is the genotype of a PSCID at a given snp + that snp's annotations. * CNV: A table where each row is a PSCID's observed variation, its location and additional information about that variation. * Methylation: A table where each row is the beta value of a PSCID at a given cpg + annotations of that cpg * Files: A list of files uploaded with that module For most of theses tabs, it is possible to display more columns in the table by selecting "All fields" in the Display drop down. "I tried to upload a csv file but the system gives an file format error" I will need a more specific error message to help. There might be limitations in the file size and/or type due to apache configurations. (see the README for a list of susceptible options) I hope this shed some light Please contact me for any questions, comments and/or request. - Xavier Lecours LORIS Developer ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ousmane Diallo Sent: April 25, 2018 8:43 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] LORIS first steps Hi, I have installed LORIS and want to see how it can help in manasing our samples. My aim is to analyse SNP, CNV from GWAS data. First, to understand the LORIS web interface I tried to use the Demo, but I don't understand much about it. I don't know which files are used and which data are compareted to what? I tried to upload a csv file but the system gives an file format error. I wan't to know what kind of file format are used to upload in LORIS? Is there a readme which help to understand the Demo. Is there a specific team that I can contact for support? -- Ousmane Diallo Bioinformatics specialist Guy Rouleau laboratory MNI - McGill University 514-398-6761 ousmane.diallo3 at mcgill.ca _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev Loris-dev -- LORIS Developers - McConnell Brain Imaging Centre www.bic.mni.mcgill.ca A forum for LORIS developers to exchange ideas. To see the collection of prior postings to the list, visit the Loris-dev Archives.. Using Loris-dev: To post a message to all the list members, send email to loris-dev at bic.mni.mcgill.ca. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cardillo at med.umich.edu Wed Apr 25 08:51:31 2018 From: cardillo at med.umich.edu (Cardillo, Garry) Date: Wed, 25 Apr 2018 12:51:31 +0000 Subject: [Loris-dev] incorporating javascript into php instrument forms Message-ID: Hello All, I am new to Loris development and I'm trying to figure out how to incorporate javascript, jquery, html and css elements into php instrument forms (class.inc files). These files seem to only want to accept php. I'm trying to figure out how to exert more control over the look/feel of instrument forms, as well as incorporate some conditional logic on which fields are displayed. It seems like there is something simple that I'm missing. Thanks for any input! Garry Cardillo [1523292633747_image001.png] Database Analyst/Programmer Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domino?s Farms Lobby B Suite 1000 24 Frank Lloyd Wright Dr PO BOX 362 Ann Arbor, MI 48106 t: 734-936-0630 f: 734-998-8403 e: cardillo at umich.edu ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues -------------- next part -------------- An HTML attachment was scrubbed... URL: From dblader.mcin at gmail.com Wed Apr 25 13:12:02 2018 From: dblader.mcin at gmail.com (David Blader) Date: Wed, 25 Apr 2018 13:12:02 -0400 Subject: [Loris-dev] incorporating javascript into php instrument forms In-Reply-To: References: Message-ID: Hey Garry, Thanks for reaching out to us. Adding your own customized JS & CSS for instruments can be done pretty simply by extending the NDB_BVL_Instrument class in your project/libraries directory. Within your new child class, you can then override the methods "getJSDependencies()" and "getCSSDependencies()" (defined in NDB_Page). In these overridden methods, you can then merge the dependencies defined in the inherited method implementation with the paths to the customized JS & CSS files of your choice. Once you've done this, it is just a matter of making sure your instrument forms are extending the new child class. Attached is an image of an example of what one of these overridden methods might look like. I hope it helps. Cheers, David On Wed, Apr 25, 2018 at 8:51 AM, Cardillo, Garry wrote: > Hello All, > > > I am new to Loris development and I'm trying to figure out how to > incorporate javascript, jquery, html and css elements into php instrument > forms (class.inc files). These files seem to only want to accept php. I'm > trying to figure out how to exert more control over the look/feel of > instrument forms, as well as incorporate some conditional logic on which > fields are displayed. It seems like there is something simple that I'm > missing. > > > Thanks for any input! > > > Garry Cardillo > [image: 1523292633747_image001.png] > > Database Analyst/Programmer Intermediate > > Department of Radiology > > Functional Neuroimaging, Cognitive and Mobility Laboratory > > Domino?s Farms Lobby B Suite 1000 > > 24 Frank Lloyd Wright Dr PO BOX 362 > > Ann Arbor, MI 48106 > > t: 734-936-0630 > > f: 734-998-8403 > > e: cardillo at umich.edu > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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