Release Notes - openSEEK - Version 1.2.0

New Feature

[OPSK-827] - Allow installations to disable permission summary pop-up
[OPSK-849] - Feature request: Accept sftp links
[OPSK-872] - Default license for a project
[OPSK-917] - Delete extracted samples when deleting a datafile
[OPSK-928] - Interlinking between sample types
[OPSK-940] - Generation of excel template for sample type
[OPSK-966] - Tags for samples types
[OPSK-978] - Sample types only editable by project members
[OPSK-995] - Show an overview of data usage for programme/project on admin apge

Improvement

[OPSK-725] - Handle sample type attribute name clashes
[OPSK-795] - Organisation of seed data
[OPSK-840] - Description for Sample Type
[OPSK-841] - SampleType can_edit? and can_destroy?
[OPSK-843] - Provide citation suggestion for assets and snapshots
[OPSK-855] - Support for arbitrary URL schemes for remote files
[OPSK-918] - Redefine the sample title field
[OPSK-921] - update the project browser to use jstree instead of yui
[OPSK-924] - Sample dropdown menus aren't bootstrapped
[OPSK-937] - Create an enumerator for sample attribute base types
[OPSK-951] - Index DOIs in Solr so the related thing is found when searched for
[OPSK-960] - Authorization improvements
[OPSK-975] - Don't show "Extract Samples" whilst pending
[OPSK-976] - Create Sample button on Sample Type
[OPSK-977] - Sample Type - pending template generation box
[OPSK-1000] - Allow a sample type to link to its own type
[OPSK-1001] - Investigate filtering search by project id as params
[OPSK-1004] - Sample / Sample type should be favouritable
[OPSK-1007] - Add URI attribute type
[OPSK-1017] - Model.find_each preferred over Model.all.each
[OPSK-1028] - Docker - split off delayedjob for docker compose
[OPSK-1031] - SampleDataExtractionJob should just be able to take the data file id
[OPSK-1032] - Provide some descriptive text for attribute types
[OPSK-1047] - Samples extracted from a template should be none editable
[OPSK-1055] - Sample extraction should recognise sheet with 'sample' in the name
[OPSK-1056] - Projects selector broken on "Use spreadsheet template" tab of new sample type form

Story

[OPSK-622] - Deprecation of old sample data & models
[OPSK-628] - Custom Sample Type Definitions
[OPSK-636] - Assay updated for new Sample framework
[OPSK-712] - Create Sample Type from Spreadsheet
[OPSK-713] - Populate samples from template spreadsheet

Task

[OPSK-691] - Associating samples with projects
[OPSK-692] - Sample authorization
[OPSK-693] - Sample resource list items, and related to
[OPSK-697] - Indexing of Samples for search
[OPSK-706] - Prevent sample types being changed after they have been used
[OPSK-708] - Sample#title as an attribute
[OPSK-730] - Samples framework work loose ends
[OPSK-745] - Ability to turn samples on and off
[OPSK-781] - SEEK Strain ID attribute type
[OPSK-782] - Boolean sample attribute type
[OPSK-783] - Add sample attribute types to seed data
[OPSK-784] - Simpler way of handling accessor_name
[OPSK-785] - Sample code reviewing and cleaning and documenting
[OPSK-787] - Extract samples from template as a background job
[OPSK-808] - Remove the Deprecated sample models
[OPSK-821] - Add attribute type seed data to upgrade task
[OPSK-830] - Upgrade task to add the sample attribute seed data
[OPSK-856] - SEEK4Science website needs new logo, and favicon
[OPSK-896] - Also show the number of all assets
[OPSK-915] - Resurrect Project Browser / Organiser
[OPSK-947] - Document docker
[OPSK-971] - Check if old samples related configs are needed
[OPSK-988] - Sample type selector for SEEK Sample, group by project
[OPSK-989] - Improve resource list item for sample type
[OPSK-990] - highlight title field in sample type view
[OPSK-991] - Remove text pointing to biostars forum
[OPSK-1014] - Sample type needs a better icon
[OPSK-1019] - Rake task to get the old samples & cell cultures
[OPSK-1027] - SEEK 1.2 release notes
[OPSK-1045] - Remove index view for samples
[OPSK-1046] - Extracted samples should always inheritic permissions from data file
[OPSK-1065] - Selected Strain not set when editing a sample
[OPSK-1066] - Prevent a new data file version ability being available if samples have been extracted

Sub-task

[OPSK-623] - rename Sample -> DeprecatedSamples
[OPSK-624] - rename Specimen -> DeprecatedSpecimens
[OPSK-625] - rename SampleAsset -> DeprecatedSampleAssets
[OPSK-626] - rename SopSpecimen -> DeprecatedSpecimenSop
[OPSK-627] - rename Treatment -> DeprecatedTreatments
[OPSK-629] - Create bare Sample model
[OPSK-630] - Create SampleType model
[OPSK-631] - Ability to define sample type for a sample and store values
[OPSK-632] - A pre-defined list of supported attribute types
[OPSK-633] - Page for defining sample types
[OPSK-634] - Simple page for adding a new Sample
[OPSK-635] - Add support for required fields
[OPSK-637] - Define 0 or more incoming samples
[OPSK-638] - Define 0 or more “outgoing” samples
[OPSK-641] - Remove Biosamples browser
[OPSK-642] - Remove biosamples_enabled config
[OPSK-644] - Remove Sample & Specimen views and controllers
[OPSK-663] - Remove Biosample search fields
[OPSK-685] - Support units for sample attribute
[OPSK-686] - Support for controlled vocabulary sample attribute type
[OPSK-705] - Index page for sample types
[OPSK-714] - Ability to upload a spreadsheet and associate with a new sample type
[OPSK-715] - Defined sample type attributes from columns in spreadsheet
[OPSK-716] - Submit new sample type for template
[OPSK-717] - After uploading data file, identify whether it matches a sample type
[OPSK-718] - Provide option to extract samples
[OPSK-719] - Handle problematic sample entries
[OPSK-720] - Ability to download template associated with a sample type
[OPSK-724] - SampleAttributes not destroyed when SampleType is
[OPSK-731] - Samples in Browse Menu
[OPSK-732] - Add Sample Type to Create Menu
[OPSK-733] - Creating sample type manually or from template in separate tabs
[OPSK-734] - Sample Type is missing required * next to title
[OPSK-735] - Hide Add Attribute button when defining from a template
[OPSK-736] - Javascript for title constraints in sample type form
[OPSK-737] - Put extract samples button in proper menu
[OPSK-738] - Add confirmation step, and select sample type if > 1, when extracting samples
[OPSK-739] - Summary of extracted samples after extraction
[OPSK-740] - Show samples linked to Data File
[OPSK-741] - Show originating data file for sample
[OPSK-742] - Add a attribute type for Date (in addition to date time)
[OPSK-744] - Dependant destroy for sampe_type#content_blob
[OPSK-746] - Authorise the sample extraction action
[OPSK-748] - Integers should be accepted as a valid Float
[OPSK-749] - Show page for Sample Type
[OPSK-750] - Searchable sample types
[OPSK-751] - Better error reporting for uploading a none valid template
[OPSK-752] - Default attribute type to String when creating sample type
[OPSK-753] - Weblink types should be shown as a link
[OPSK-754] - Sample type link from sample page can now go to sample type show page
[OPSK-755] - Table view for samples under a data file/sample type
[OPSK-780] - Update ISA graph to show inputs and outputs rather than just links
[OPSK-929] - Define Sample Type attribute type
[OPSK-930] - Allow selection of Sample Type attribute type, along with sample type in the form
[OPSK-931] - Allow selection of sample when creating a sample linked to a sample type
[OPSK-932] - Prevent a sample type being deleted when used as an interlinked sample type
[OPSK-933] - Handle samples defined in a spreadsheet
[OPSK-934] - Display sample as a link when showing parent sample
[OPSK-935] - Include interlinked sample in related items list
[OPSK-939] - Show the sample type in attributes for SEEK Sample
[OPSK-941] - Small java apache poi library to generate spreadsheet
[OPSK-942] - Generate spreadsheet include CV data validations
[OPSK-943] - Include sample and strain list as a dropdown
[OPSK-944] - Determine when the template needs regenerating
[OPSK-945] - Bundle up as a ruby gem and integrate with SEEK
[OPSK-946] - Concider whether the template could be generated as a back ground process
[OPSK-961] - More efficient auth lookup refresh
[OPSK-962] - Re-structure "is_authorized?" method
[OPSK-968] - Cluster sample types by tag

Bug

[OPSK-747] - Can extract samples multiple times
[OPSK-758] - "Remove" sample attribute broken
[OPSK-792] - Replace tooltip plugin with more modern one
[OPSK-809] - Sample extraction fails if no matching samples
[OPSK-819] - Title of sample not linked for source datafile
[OPSK-822] - Floats ending in 0 are not accepted in samples extraction
[OPSK-825] - References to Specimens still appear in assets_creators
[OPSK-826] - Samples and SampleType are not correctly using the grouped pagination
[OPSK-829] - SampleTypes must be paginated
[OPSK-833] - Cytoscape visualisation
[OPSK-851] - Split up contributors and creators
[OPSK-853] - XSS on sample type show page
[OPSK-862] - First user is no longer added to the default project and institution
[OPSK-882] - Check and Fix Gemfile env seperation
[OPSK-886] - there is an extra 'add' icon at admin avatar, when it is the contributor of an asset
[OPSK-887] - New study but on edit page
[OPSK-888] - db:setup shows the entries seeded in the log, but no entries in database
[OPSK-894] - file_path points to the filestore/tmp/image_assets/
[OPSK-895] - when 'view content', it is counted as download, but not when 'explore'
[OPSK-912] - On the sandboxed SEEK I can't create a strain (also problem on test SEEK)
[OPSK-914] - Error when clicking link to a scale
[OPSK-926] - Samples creators always 'None' in resource list item
[OPSK-927] - Samples are not included in person related items
[OPSK-938] - Asset Creator not behaving correctly for sample
[OPSK-949] - Problem with creators box
[OPSK-957] - XSS in JStree
[OPSK-964] - inconsistent writing of SOP/sop
[OPSK-969] - Associate sample type with a project
[OPSK-970] - Document samples
[OPSK-992] - Match all tags option for sample type selection not working as expected
[OPSK-998] - auth lookup task seems to be not triggered when removing a permission
[OPSK-999] - search turned off after an upgrade 1.1 -> 1.2
[OPSK-1002] - Update message for why you can't delete a sample type
[OPSK-1005] - Sample type edit - some drop downs become incorrectly visible
[OPSK-1009] - Error generating sample template with a CV for apples
[OPSK-1010] - Error when trying to change type from CV
[OPSK-1011] - Sample Text attribute didn't like new line
[OPSK-1015] - should only be able to delete sample type if a member of the project
[OPSK-1016] - Limit sample type creation and editing to project administrators
[OPSK-1042] - error when trying to create a sample type with project missing
[OPSK-1043] - When Strain is not required, there is not a blank default option
[OPSK-1044] - Strain linked to samples doesn't show samples as related items
[OPSK-1050] - content_blob_id on SampleType is unused
[OPSK-1071] - The Sample Type administer menu button always appears
[OPSK-1072] - Error when creating sample with the title set to a SEEK entity
[OPSK-1079] - Not clear how to edit controlled vocabulary