.. -*- coding: utf-8 -*- Project cubicweb-brainomics =========================== :creation date: 2013/01/23 :homepage: http://www.brainomics.net/ Cube for the Brainomics application. .. vcsinclude:: README Version 0.12.0 -------------- :publication date: 2014/10/24 :expected date: n/a Ticket #4045032 Add standard scores and scales ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Eg. ECOG (http://en.wikipedia.org/wiki/Performance_status#Lansky_score), ... Ticket #4046276 Update importer with clinipath data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending Ticket #4045184 Updat e importer with new genomics entities ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending Ticket #4045114 Update random import with new medical data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending Version 0.11.5 -------------- :publication date: 2014/11/25 :expected date: n/a Ticket #4627755 zip export: handle cases where there are multiple labels ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.250 :state: validation pending Version 0.11.4 -------------- Focused improvements with respect to 0.11.3 :publication date: 2014/09/24 :expected date: n/a Ticket #4142557 Allow to hide relations with uninstantiated subjects / objects ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending Ticket https://www.cubicweb.org/ticket/4094581 addressed the issue of hiding attributes with undefined values. Now, relations with uninstantiated subjects / objects are to be hidden as well. Ticket #4142552 Enable CSS customization on out of context views ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending Version 0.11.3 -------------- :publication date: 2014/07/04 :expected date: n/a Ticket #4094581 Add an option to hide undefined value, even with edit permissions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Version 0.11.2 -------------- :publication date: 2014/07/04 :expected date: n/a Ticket #4084898 Add an access point to add additional data for subjects in timeline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #4084902 Add survival data in timeline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #4084897 Hide protocols in TechnicalAnalysis table view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Version 0.11.1 -------------- :publication date: 2014/07/03 :expected date: n/a Ticket #4071209 Do not show filter for BiopsySample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #4071181 Dynamic facets should appears below the combobox ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #4071173 Fix first column for genetic results ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #4052951 Slickgrid files are missing. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Version 0.11.0 -------------- :publication date: 2014/06/26 :expected date: n/a Ticket #4035949 Add support for slickgrid ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 2.000 :state: validation pending Ticket #4035950 Implement dynamic facets (e.g. for Cgh ratio) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 2.000 :state: open Version 0.10.0 -------------- :publication date: 2014/06/26 :expected date: n/a Ticket #3912385 Add dependency to the clinipath cube. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending Update the schema accordingly. Ticket #3896262 Allow for updating the wiki of an entity once it exists ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.100 :state: validation pending Indeed, currently a new wiki is created via the "Update wiki" action. Instead, one would like to be able to update the wiki if it exists, and to create a new wiki only if no wiki exists for the entity. Ticket #3924898 Fix the files box ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending It is based on deprecated schema relations Ticket #3912393 Wiki and documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated Allow for updating the wiki of an entity if it exists instead of creating a new wiki each time Version 0.9.0 ------------- :publication date: 2014/04/30 :expected date: n/a Ticket #3705525 Add container ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 1.000 :state: validation pending It may be interesting to add container cube to Brainomics to deal with the security: * a container for the subject and its related elements: * Scorevalue; * Diagnostic; * Therapy; * Admission/AdmissionStep; * DrugTake; * a container for each assessment and its related elements: * Measure; * ScoreValue; * Files Ticket #3489099 Backport secondary views ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Secondary views of the different cubes (medicalexp, genomics, questionnaire, neuroimaging) should be backported into Brainomics, to use the BrainomicsAbstractOutOfContextView from https://www.cubicweb.org/ticket/3489083 Ticket #3694374 "browse" dropdown menu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending Add a "browse" dropdown menu in the navbar, for selecting subjects using a file. Ticket #3446604 get rid of identifier, use cwuri instead ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.000 :state: deprecated While discussing with Vincent the use of identifier in Brainomics, it appeared the current situation is far from ideal: * if required, identifier should be unique, * identifier is currently required, but some projects do not need it. The idea is to get rid of identifier from (most?) entities in brainomics and its direct dependencies (use cwuri instead?) Comments :: On 2014/01/16 21:05 - dimitri wrote : Additionally, views should be modified so that identifier is not needed and so that entities without any useful attribute left to view, display their relations instead to provide meaningful information in views that require it. On 2014/01/28 12:44 - dimitri wrote : After further discussions "cwuri" shouldn't be used for that. Otherwise it looks like most identifiers that were supposed to be removed have been removed. Close this ticket? > On 2014/01/28 13:49 - vmichel wrote : > I will close this ticket after publishing the code. Ticket #3489083 Out of context view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Brainomics should provide a cleaner and more easier way to define OutOfContext view. Ticket #3314076 Remove identifier ? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending There are too much identifiers attributes that are not useful. They should be removed for most of the subject's specific entity types (assessment, questionnaire run, ...) Comments :: On 2013/11/22 13:55 - dimitri wrote : I tend to agree. Ticket #3020514 Remove reference to Localizer from the title/startup view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: validation pending Comments :: On 2013/07/19 13:53 - dimitri wrote : Hasn't this be closed by the following patch? [postcreate] Change site title Unable to find the patch in the list. > On 2013/12/09 08:40 - vmichel wrote : > The startup cards still exist, and should be removed. Ticket #3702349 Update timeline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending The timeline of an author should include Therapy, Diagnostic, DrugTake, ... Ticket #3280244 Cleanup of the code ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.000 :state: deprecated Cleaning up the code, especially the views; Add docstring + some tests if necessary; Reorganize a bit the different views (e.g. moving the "detailled assessments" of a subject in a separated tab); Create a generic PrimaryView for AnyEntity following the design of Brainomics UI, in order to have an homogenous design even for less important Etype. Comments :: On 2014/03/31 14:52 - vmichel wrote : This has been done in different tickets, e.g. #3489097 Ticket #3316345 Fix mix between filepath and results_file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated We should only use on simple way to deal with all the different type of files (stored or not) in Brainomics Comments :: On 2014/03/31 14:54 - vmichel wrote : This is related to #3694093 and #3446640 Version 0.8.0 ------------- :publication date: 2014/02/17 :expected date: n/a Ticket #3501793 Add a button to download data as Json ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending We should add a button in the download box to download data as json. Ticket #3501794 Facets CSS ~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending The facets CSS should be modified to have a cleaner display. Ticket #3007544 genetics files should not be read by subject ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.000 :state: deprecated In neuroimaging, each subject comes with its own set of files. Nothing like that in genomics: there is a single set of BED/BIM/FAM files per dataset, not per subject. Fix all importers/schema accordingly. More specifically, in the localizer importer, information should be extracted from a global BED/BIM/FAM file: - one should probably check for the presence of subject identifier in the FAM file, - the "filepath" attribute coould point to the global BED file. Fix cubicweb-genomics schema accordingly: - the "filepath" does not really make sense as is : maybe "filepath" could point to the BED file common to all subjects, or maybe a GenomicsDataset entity should be created, - an additional attribute could contain the identifier of the subject in the BED file, in case the identifier is different from the identifier in the Subject entity. Comments :: On 2013/07/12 14:55 - dimitri wrote : I've pushed a patch that attempts to fix the Localizer importer, without modifying the schema. The schema could be modified to accomodate a global BED/BIM/FAM triplet. But then all importers will have to be fixed accordingly. > On 2013/07/12 14:56 - dimitri wrote : > Here is the documentation I've used to understand the BED/BIM/FAM format: > http://www.shapeit.fr/pages/m02_formats/bedbimfam.html On 2014/01/21 08:19 - dimitri wrote : This was related to the Localizer importer. Since the importer has been removed from the brainomics cube, shouldn't this ticket be closed? > On 2014/01/21 08:31 - vmichel wrote : > Yes. I depreciate this ticket. Ticket #3486042 Remove got rhythm action. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #3489097 Uicfg ~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Brainomics should provide some tools based on uicfg to add a specific rset into the attributes/relations sections of the primary view. Ticket #3175888 zip file ~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Large zip files are not properly created for download. It could be that the Zip file generation fails for files larger than 2 Gb. While we need a more robust way to download files, let's fix this 2 Gb for now. Comments :: On 2014/01/21 08:55 - dimitri wrote : I think the attached patch has already been applied to brainomics 0.4.0. Should the patch be completed or should we close this ticket? > On 2014/01/21 09:41 - vmichel wrote : > Indeed, it should be closed. Version 0.7.1 ------------- :publication date: 2014/01/30 :expected date: n/a Ticket #3309078 bullets for Bootstrap'ed lists ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated HTML lists lack bullets under the current Bootstrap style of Brainomics. Could you bring bullets back? I guess this could wait resolution of ticket #3306560 (Use bootstrap 0.3.0). Comments :: On 2014/01/29 13:52 - vmichel wrote : Using bootstrap 0.3.0 should be enough. > On 2014/02/11 10:07 - dimitri wrote : > I'm not certain it has been fixed with recent versions. For example which > version is used by the Brainomics site? See: http://www.brainomics.net/ Ticket #3486137 cube brainomics depends on ... but constraint badly formatted ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :state: validation pending Error messages when running cubicweb-ctl with brainomics in the CW_CUBES_PATH: * cube brainomics depends on neuroimaging but constraint badly formatted: >=0.5.0 * cube brainomics depends on questionnaire but constraint badly formatted: >=0.5.0 Ticket #3486002 Drop leftover bootstrap css in uiprops ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Css should be correctly dropped in Uiprops. Ticket #3486252 Fix outofcontext views CSS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated With the new bootstrap, the outofcontext view with the "thumbnail" class should be adpated. Ticket #3493322 Jqplot is broken ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.200 :state: validation pending Jqplot graph (e.g. for Answer) is broken after using bootstrap 0.3.0 Ticket #3493389 Remove call to unknown attributes in AbstractMutationTableView ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #3486004 Some CSS fixes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated The navbar should be narrower. Ticket #3493387 TableView is broken for AnswerOutOfContextTableView ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #3493388 Update random importer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Random importer should be updated using the new genetics entities. Ticket #3493366 Update to last changes in squareui ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: validation pending Update to squareui 0.2.0 Ticket #3486022 Use bootstrap monkey patched search boxe ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Ticket #3360790 Update brainomics website ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Version 0.7.0 ------------- :publication date: 2014/01/20 :expected date: n/a Ticket #3383893 Composite relations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending We should add composite relations (and associated tests) for all measures/assessment/entities related to a subject. Ticket #3439002 Discard aggregate data table from Subject primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending The aggregate data table is redundant with the data listing just below. Ticket #3175940 fix use of cubicweb-registration ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated Register link is missing in Brainomics applications. Also the link should be boostrap'ified. Ticket #3127316 IndexError: tuple index out of range ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated Erreur en visualisant un questionnaire quelconque associé à un sujet: une erreur est survenue IndexError: tuple index out of range tuple index out of range File /usr/lib/python2.7/dist-packages/cubicweb/web/application.py, line 456, function core_handle: result = controller.publish(rset=rset) [+] File /usr/lib/python2.7/dist-packages/cubicweb/web/views/basecontrollers.py, line 134, function publish: rset=rset, view=view) [+] File /usr/lib/python2.7/dist-packages/cubicweb/cwvreg.py, line 398, function main_template: res = obj.render(**kwargs) [+] File /usr/lib/python2.7/dist-packages/cubicweb/view.py, line 137, function render: view_func(**context) [+] File /home/cl239099/cubicweb/cubes/brainomics/views/basetemplates.py, line 46, function call: view.render(w=w) [+] File /usr/lib/python2.7/dist-packages/cubicweb/view.py, line 137, function render: view_func(**context) [+] File /home/cl239099/cubicweb/cubes/brainomics/views/primary.py, line 93, function call: self.display_header(entity) [+] File /home/cl239099/cubicweb/cubes/brainomics/views/primary.py, line 60, function display_header: for label, attribute in self.iterate_attributes(entity): [+] File /home/cl239099/cubicweb/cubes/brainomics/views/primary.py, line 424, function iterate_attributes: assessment = entity.reverse_generates[0] [+] CubicWeb version: 3.17.2 Cube brainomics version: 0.3.0 Cube bootstrap version: 0.1.0 Cube card version: 0.4.0 Cube comment version: 1.8.2 Cube genomics version: 0.2.0 Cube jqplot version: 0.3.0 Cube medicalexp version: 0.3.0 Cube neuroimaging version: 0.3.0 Cube questionnaire version: 0.3.0 Cube registration version: 0.4.2 Comments :: On 2013/09/23 08:44 - cl239099 wrote : Il semblerait que l'"index out of range" prenne la valeur 1 dans une liste vide, ceci dû a une relation non renseignée dans la base (liens entre entités manquants) Sans explication concrète, en recommençant l'insertion d'individu sur une base de données vierge, l'erreur n'apparaît plus Ticket #3326417 Remove detailled assessments ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Detailled assessments for subject should go to a tab. Comments :: On 2013/12/09 08:41 - vmichel wrote : See https://www.cubicweb.org/ticket/3340591 Ticket #3400781 Remove the abide, mindboogle and openfmri importers, as they are no longer maintained ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending Ticket #3400780 Remove the remake-uuid command ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending The functionality provided by this command is superseded by more recent developments. Ticket #3438979 Stop displaying the Assessments in the Study primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending The Assessments are redundant with the detailed measures. Ticket #3439001 Swap disease and therapy in Subject primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.200 :state: validation pending The therapy comes after the disease. Ticket #3323338 Table view for scorevalues and questions/answers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending We should add a score value for questions/answers and scorevalues. Ticket #3455656 Use squareui ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending It should be possible to use squareui and remove the specific template of Brainomics. Ticket #3348088 Make the startup page load with bootstrap 3.0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending Currently, the startup page is not accessible when using bootstrap 3.0. Ticket #3306560 Use bootstrap 0.3.0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 2.000 :state: validation pending We should upgrade to bootstrap 0.3.0. Ticket #3340591 Use CW primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 2.000 :state: validation pending Modify the primary views logic of Brainomics to be able to use UICFG. Version 0.6.1 ------------- Packaging :publication date: 2013/12/11 :expected date: n/a Version 0.6.0 ------------- :publication date: 2013/12/10 :expected date: n/a Ticket #2639551 Search bar does not show current RQL request anymore ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 1.000 :state: validation pending The search bar at the top of the web page used to show the RQL request corresponding to the selected filters. It is no more the case in the last version. Is it a choice or a bug ? I found this feature was very practical. Comments :: On 2013/01/30 14:51 - vmichel wrote : The RQL bar has been removed as, now, we use the current facets system from CubicWeb that does not dynamically change the RQL according to the applied facets. The search form in the top navigation bar can still execute RQL. However, we are planning to change (for the 0.2.0 version) the facets for the simplefacet system. And, in this case, will we be indeed interesting to add a large RQL bar. So yes, it is a choice to remove it from now, but it will be back soon ! > On 2013/01/30 15:58 - dominique.geffroy wrote : > Ok, perfect ! Ticket #3341091 Add a therapy outofcontext view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending Ticket #3341081 Add table view for drug take ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending Ticket #3341030 Add therapy and disease in subject primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: validation pending Ticket #3344757 Update Gene primary view so that several chromosomes are displayed for translocated genes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: validation pending Version 0.5.0 ------------- :publication date: 2013/11/26 :expected date: n/a Ticket #3323323 Add GenomicRegion view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Add a genomicregion view, according to the change in genomics cube, see #3323185 Ticket #3323386 Add protocol primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Ticket #3028907 age should not be an attribute of Subject ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :state: resolved See ticket #2818501 for cubicweb-medicalexp. Comments :: On 2013/07/20 15:00 - dimitri wrote : The imagen importer should be fixed in addition to the localizer importer. On 2013/07/20 16:19 - dimitri wrote : Facets associated to measures must use the Assessment attribute 'age_for_assessment' instead of the obsolete attribute 'age' in Subject. Ticket #3023130 bootstrap: strange resizes of the entity list when playing with facets ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :state: resolved After moving brainomics from orbui to boostrap, when playing with facets, I experience strange resizes of entity lists. Can be reproduced when displaying Subjects, Images or Questionnaires - Genetics have no facets. Cannot send screenshots on a public Web site because the data is confidential. Will send them on request but it should be pretty straightforward to reproduce on Ubuntu 12.04 with Firefox of Google Chrome. Just click on Subject and modify any of the facets in the left column. The width of the entity list will shrink. Is it a brainomics or bootstrap bug? Comments :: On 2013/07/18 07:16 - vmichel wrote : This seems to be a bootstrap bug. I will take a look on it, it is due to the monkey patched AjaxFunction. > On 2013/07/19 08:56 - dimitri wrote : > Works for me after applying patch 3027056 to bootstrap. Thank you! Ticket #3296292 Brainomics primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved We should redefine the primary view of CW in order to have the defaut primary view that follows the Brainomics UI/design. Ticket #3323398 Drop brainoviz ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Brainoviz cube is not necessary and not even published. Drop it from __pkginfo__ Ticket #3314075 register_user ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved The register_user is monkey patch to register users as guests for security reason (only readability). This should be moved to applicative cubes. Comments :: On 2013/11/22 14:07 - dimitri wrote : * In Brainomics/Localizer we stick to a previous version of brainomics, so we don't mind removing this code from current versions. * Can you help us push this monkey patch to Brainomics/Imagen? > On 2013/11/22 17:40 - vmichel wrote : > Ok, we will backport this to Brainomics/Imagen and I will remove it from > Brainomics (see also https://www.cubicweb.org/ticket/3316348) Ticket #3299721 Registrer cube ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Register cube (and forgotpwd cube) should not be mandatory, as well as the license acceptance logic attached to the registration process. Ticket #3316348 Remove download while register logic, used only for BrainomicsLocalizer ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved There is a part of the code that limit the downloading of data to register users only. This behavior may be configured in the all-in-one but should be removed anyway and be implemented through permissions. Ticket #3323446 Table and filters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved We should add some filters/facets on table view for measures. Ticket #3296293 Vid in primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending The function _build_data of the primary view of Brainomics should allow a vid as argument for the build_url function. Version 0.4.6 ------------- :publication date: 2014/04/30 :expected date: n/a Ticket #3699203 Update pkginfo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Operator < not supported Version 0.4.5 ------------- :publication date: 2014/03/13 :expected date: n/a Ticket #3564508 Discard the whole login/registration machinery. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: validation pending This is not needed anymore for the demo website. Version 0.4.4 ------------- :publication date: 2014/01/20 :expected date: n/a Ticket #3292512 external resources should be downloadable ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.000 :state: deprecated Comments :: On 2013/12/09 08:29 - vmichel wrote : I think this is related to https://www.cubicweb.org/ticket/3316345 I deprecate this ticket for now. Ticket #3455866 Fix bootstrap version ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.100 :state: validation pending Version 0.4.3 ------------- :publication date: 2013/11/26 :expected date: n/a Ticket #3323447 Action for csv export ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved The __regid__ of the action for the csv export should be 'csvexport' as it is used as vid. Version 0.4.2 ------------- :publication date: 2013/11/25 :expected date: n/a Ticket #3323449 Packaging issue ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Version 0.4.1 ------------- Fix for Localizer's website :publication date: 2013/11/14 :expected date: n/a Ticket #3282158 "View" should not be displayed when brainoviz cube is missing ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved I don't know how easily it is feasible, bu the "View" button should not be visible unless the brainoviz cube is available. The error message "The brainoviz cube is required" is not informative for users because the cube is not even publicly available. Ticket #3295939 Bootstrap registration link ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Bootstrap break the registration link. Ticket #3295982 Examples card ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved Update examples card following the schema evolutions (e.g.remove age). Ticket #3295942 Missing DATA_URL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved The hhml header of the template should define the DATA_URL js variable, required for facets. Ticket #3295977 Remove hard dependency for vtimeline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved The vtimeline cube should not be a hard dependency. Ticket #3295979 UI components and recommended cubes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved We should add safety belt on recommended cubes UI components. Ticket #3295949 XML escape in primary view ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved There should be XML escape for dc_title in primary view. Ticket #3295966 Zip download ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 0.500 :state: resolved We should use the ZIP_DOWNLOADABLE variable for the selector of the DataZipAbstractView. Version 0.4.0 ------------- :publication date: 2013/11/07 :expected date: n/a Ticket #3280234 Add a timeline ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: resolved Add a timeline for assessments Ticket #3280233 Importer ~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: resolved Update importer according to schema changes Version 0.3.0 ------------- :publication date: 2013/11/07 :expected date: n/a Ticket #3016694 Allow to request data from a list of identifiers. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :state: resolved It should be interesting to allow the user to request subjects, scans, ... using a file of identifiers. Thus, we should create: - a view (startup view), calling a form. - a form that allows to browse/select a file, and to select the concerned etype. - a controller, that reads the file after the form submission, and redirect to a "list" view with the RQL "Any X WHERE X is ???, X identifier IN (...)" Ticket #3020518 Register ~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: resolved For the register form: * add "affiliation" and "infos" on CWUSer. * add these two fields in the register form. * add a checkbox to accept the license. * check if the email adress does not already exist. Comments :: On 2013/07/17 22:26 - dimitri wrote : Doesn't work anymore. I get an error just after clicking on "sign in": Exception: select ambiguity: [, ] (args: (,), kwargs: ['id', 'rset', 'klass']) I'l try to attach as screenshot, but I'm afraid it won't work as usual. > On 2013/07/18 07:19 - vmichel wrote : > I can't reproduce the issue here. Have you removed the orbui code from your > PYTHONPATH, from /etc/cubicweb.d//bootstrap_cubes, and use > "remove_cube('orbui')" ? Ticket #3020519 Security ~~~~~~~~~~~~~~~~~~~~~~~~ :type: enhancement :load: 0.500 :state: resolved Create a group for users that are just allow to download data. Remove the possibility to create/modify/delete data. Version 0.2.0 ------------- :publication date: 2013/07/05 :expected date: n/a Ticket #2818437 ask for mail/lab before letting download ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 2.000 :state: done P. Pinel suggests we require minimal information before download. No strong security against hackers, just ask users to provide : - mail - lab - short description of project This may imply some sort of session based on cookies and initialized by a form. Check email address is correct? Comments :: On 2013/06/04 09:54 - vmichel wrote : We should keep a track of who download some data (and why). Ticket #2791942 no login ~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved Add an option to disable login by default. This application provides read-only data to the general public. A login prompt can be seen an inconsiderate risk. See attached patch. Comments :: On 2013/04/12 11:18 - dimitri wrote : This line must be removed from the patch: vreg.unregister(JSonController) It generates such warnings in /var/log/cubicweb/localizer-all-in-one.log: 2013-04-12 10:52:12 - (registry) WARNING: can't remove cubicweb.web.views.basecontrollers.JSonController, no id json in the registry On 2013/04/12 12:16 - dimitri wrote : This line must also be removed: vreg.unregister(AjaxController) It seems to be killing evrything AJAX, including facets. Removing it does not seem to be re-enbling login in any way. On 2013/06/06 13:59 - dimitri wrote : The logic of this patch should be reverted: * keep login by default, * disable login if option set in all-in-one.conf. On 2013/07/02 08:59 - dimitri wrote : Use new "nologin" cube instead - not yet in review. Ticket #2920274 Schema documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: open Provide a schema documenation in the web interface. Ticket #2755948 schema missing from demo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved On the `Brainomics demo`_ home page, the link `schema page to see the structure of the data !`_ points to ``brainomics.net`` instead of ``www.brainomics.net``. You probably need to change variables ``host`` or ``base-url`` in ``all-in-one.conf``. Also I've attempted to change the URL manually by entering ``http://www.brainomics.net/demo/schema`` in my Firefox navigator. The ``diagramme`` tab doesn't display anything. .. _`Brainomics demo`: http://www.brainomics.net/demo/ .. _`schema page to see the structure of the data !`: http://brainomics.net/demo/schema Ticket #2920258 Wiki and labels ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 2.000 :state: done We should be able to add documentation and annotation of the data based on some wiki-like cards. Ticket #2940242 genetics should not be downloadable ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :state: resolved Go the page of a genomics measure, for example genomic_measure_BH070095. There are three buttons in the left column: 1. Download Xcede 2. Download Zip 3. Download CSV Button 2 (Zip) is a serious security problem: it gives access to the genetics. This is totally prohibited on a public server. Please remove button 2 and make sure there is no way to download the genetics files. By the way, the Zip button doesn't work right now, because it adds the ".bed" extension to the ".bim" extension: une erreur est survenue OSError: [Errno 2] No such file or directory: '/opt/localizer/data/genetics/sprintBack/bysubj/BH070095.bim.bed' [Errno 2] No such file or directory: '/opt/localizer/data/genetics/sprintBack/bysubj/BH070095.bim.bed' Otherwise the view itself and buttons 1 (Xcede) and 3 (CSV) are OK because they only give access to metadata. Comments :: On 2013/07/05 09:44 - vmichel wrote : The logic should be: - unallow download for unregister user (see #2818437). - add some security for genetics, but this should be done in an application cube (e.g. localizer), e.g. by adding in schema.py:: def post_build_callback(schema): # Add security on genomic measure, see #2940242 rs = schema['filepath'].rdef('GenomicMeasure', 'String') rs.permissions = {'read': ('managers',), 'update': ('managers',)} > On 2013/07/12 10:31 - dimitri wrote : > Indeed the application cube looks like the proper place to disallow > downloading genetics because this really depends on the project/dataset: * In > the case of the Localizer dataset, genetics should not be downloaded because > the server is public. * In the case of the Imagen dataset, genetics should be > downloadable. On 2013/07/12 15:27 - dimitri wrote : I've pushed a patch that specifically handles this issue: By the way, the Zip button doesn't work right now, because it adds the ".bed" extension to the ".bim" extension. Ticket #2925973 Localizer importer: re-encode the Subject ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :type: bug :load: 1.000 :state: resolved The Subject identifier must be re-encoded. I think you just need to add a global in-memory map to translate each incoming 'nip' into a random output 'nip' that will be inserted instead in the CubicWeb database. Use something like this to generate a random 'nip': import random import string c1 = random.choice(string.ascii_lowercase) c2 = random.choice(string.ascii_lowercase) n6 = random.randint(0, 999999) nip = '%c%c%06d' % (c1, c2, n6) Discard the map as soon as the script is finished, do not keep it! Comments :: On 2013/06/21 08:37 - vmichel wrote : The main idea is to re-encoded the "identifier" attribute for all entities having it. This could be done: - using "system_sql" with a specific "make uuid" function. - using "RQL" with a binding to a SQL function. This should be included in a cw-ctl command, with an option to also rencode the names of the file. In this case, for each entity having a filepath, we should change the filepath to an "uuid" filepath, and copy the file using this new name. See: http://stackoverflow.com/questions/3831481/how-to-generate-uuid-with-postgresql-8-4-4-on-ubuntu-10-04 On 2013/06/28 11:46 - dimitri wrote : After some brainstorming, the rencoding should be read from an external file. The rencoding rules are to be handled outside of CubicWeb - at least as an option. On 2013/07/11 14:31 - dimitri wrote : I've added a patch for the external UID file. This option just wouldn't work as is. It might be worth to add unit tests for this one. On 2013/07/11 14:41 - dimitri wrote : Anonymization doesn't work properly, not all occurrences of old UID are erased. See attached screenshot after running: cubicweb-ctl remake-uid localizer -l -d -u ~/reencode.csv where the CSV file maps old UIDs to new UIDs such as: bru3303 -> S75 The CubicWeb log files shows errors that point to a missing piece of code such as: os.path.join(ROOT_DIR, file) See attached log extract. On 2013/07/11 14:47 - dimitri wrote : I'm unable to attach files. I'll send an email to you instead. On 2013/07/11 14:55 - dimitri wrote : Both file and directory names should be renamed: any file/directory containing "bru3303" and such must disappear from the directory containing the data. > On 2013/07/11 15:08 - dimitri wrote : > Indeed the problem is in update_ident_fpath() with: copy_file(concerned_fpath, > new_filepath, logger) os.remove(concerned_fpath) > > Filenames concerned_fpath and new_filepath are relative paths (relative to the > subject directory!), not absolute paths. On 2013/07/12 14:23 - dimitri wrote : Do not forget to anonymize the contents of the FAM genetics file. It's easy to read/write the file as a CSV file but one has to scan the data directory and find FAM files because there's no link to it the database. Version 0.1.0 ------------- First release of Brainomics: * Merge schemas from medicalexp, genomics, neuroimaging, questionnaire. * Start views and export components. * Add import for OpenFmri, Abide, MindBoogle. * Add Xcede export. :publication date: 2013/07/05 :expected date: n/a