https://github.com/bihealth/sodar-server - v1.1.4

Release for minor updates, maintenance and bug fixes.

• Add site app setting to disable landing zone move access cleanup
• Add CELERY_LOGLEVEL env var in Docker entrypoint
• Fix samplesheets iRODS file list modal filtering issues
• Upgrade critical dependencies

See changelog for a complete list of updates.

- Python
Published by mikkonie 10 months ago

https://github.com/bihealth/sodar-server - v1.1.3

Release for minor updates, maintenance and bug fixes.

• Add checksampleaccess management command
• Fix potential unwanted user access not unset in landing zone move flow
• Upgrade Docker image build to Debian Bookworm
• Upgrade critical dependencies

See changelog for a complete list of updates.

- Python
Published by mikkonie 11 months ago

https://github.com/bihealth/sodar-server - v1.1.2

Release for minor updates, maintenance and bug fixes.

• Add percentages in zone progress counters
• Update irodsorphans management command study table cache handling
• Fix legacy landing zone move failure due to missing iRODS owner group
• Fix incorrect file count in landing zone file moving progress counter
• Fix germline study plugin cache update crash with missing row path from assay plugin

See changelog for a complete list of updates.

- Python
Published by mikkonie about 1 year ago

https://github.com/bihealth/sodar-server - v1.1.1

Release for minor updates, maintenance and bug fixes.

• Add landing zone creation and validation limit badges in zone list UI
• Add timeline extra data for landing zone validation
• Update per-project zone validate limit to disallow unlimited validations
• Update landing zone file list modal rendering
• Fix legacy project update failure due to missing iRODS owner group

See changelog for a complete list of updates.

- Python
Published by mikkonie about 1 year ago

https://github.com/bihealth/sodar-server - v1.1.0

Feature release for landingzones updates, SODAR Core v1.1 upgrade, etc.

• Add allowed hosts support for iRODS access tickets
• Add landing zone validation and moving progress indicators
• Add landing zone file type prohibiting
• Add file list in landing zone move timeline event extra data
• Add owners and delegates read/write access to all project zones
• Add support for longer landing zone status info messages
• Add iRODS project owner/delegate group management
• Add taskflowbackend API with project lock status view
• Add project locking status display and control disabling in landing zone list view
• Add support for simultaneous validation of multiple zones in a project
• Add support for landing zone creation limit per project
• Add support for landing zone validation limit per project
• Add iRODS SHA256 checksum hashing scheme support
• Add landing zone file list modal pagination
• Update email sending and alerts to exclude inactive users
• Update iRODS access ticket creation to support path to data object in UI
• Update checksum validation to check all files before failing
• Update project landing zone list layout
• Upgrade Sample Sheets REST API version to v1.1
• Upgrade to python-irodsclient v3.1
• Upgrade to SODAR Core v1.1.6
• Replace SODARSUPPORT* settings with PROJECTROLESSUPPORTCONTACT
• Fix iRODS access ticket expiry date updating
• Remove minimum sample sheet column config editing role setting
• SODAR Core v1.1 updates: Project deletion, project leaving, paginated project list, site read-only mode, etc.

See changelog for a complete list of updates.

- Python
Published by mikkonie about 1 year ago

https://github.com/bihealth/sodar-server - v1.0.1

Release for minor updates, maintenance and bug fixes.

• Upgrade to SODAR Core v1.0.6 hotfix release
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie over 1 year ago

https://github.com/bihealth/sodar-server - v1.0.0

Release for upgrading to SODAR Core 1.0, Django 4.2 and iRODS 4.3, REST API versioning scheme update, OIDC support etc.

• Add opt-out settings for iRODS data request and zone status update emails
• Add REST API list view pagination
• Add Python v3.11 support
• Add study plugin override via ISA-Tab comments
• Add session control in Django settings and environment variables
• Add token-based iRODS/IGV basic auth support for OIDC users
• Add support for comment, performer and contact field values as list
• Add support for numeric field values as list
• Add support for UTF-8 BOM header in MD5 checksum files
• Add optional SampleDataFileExistsAPIView access restricting for users with project roles
• Update minimum supported iRODS version to v4.3.3
• Update REST API versioning
• Update REST API views for OpenAPI support
• Update lock requiring REST API views to return 503 if project is locked
• Update REST APIs to return user UUID instead of SODARUserSerializer objects
• Update landing zone creation REST API view to return 503 if no investigation or iRODS collections
• Update irodsinfo configuration download to return JSON without Zip archive if client-side cert is not set
• Upgrade to Django v4.2
• Upgrade to Postgres v16
• Upgrade to python-irodsclient v2.2.0
• Upgrade to altamISA v0.3.0
• Upgrade to SODAR Core v1.0.5
• Remove Python v3.8 support
• Remove Postgres <12 support
• Remove iRODS <4.3 support
• SODAR Core v1.0 updates: OIDC auth support, new REST API versioning, owner/delegate remote sync controls, etc

See changelog for a complete list of updates.

- Python
Published by mikkonie over 1 year ago

https://github.com/bihealth/sodar-server - v0.15.1

Release for minor updates, maintenance and bug fixes.

• Fix generic assay plugin issues
• Upgrade critical dependencies
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie almost 2 years ago

https://github.com/bihealth/sodar-server - v0.15.0

Feature release.

• Add isatemplates app for management of custom ISA-Tab templates
• Add generic assay plugin
• Add BAM/CRAM/VCF omit pattern display in study shortcut modal
• Add row links display override using assay comment
• Add iRODS checksum calculation retrying
• Add Cyberduck documentation
• Disable lock requirement for project and role update taskflows
• Make sheet template output dir field visibility optional
• Upgrade critical dependencies
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie almost 2 years ago

https://github.com/bihealth/sodar-server - v0.14.2

Release for minor updates, maintenance and bug fixes.

• Add CRAM file support for cancer/germline study links and IGV sessions
• Add path glob pattern support for IGV session BAM/VCF omit settings
• Add assay plugin shortcut collection creation in landing zones
• Add iRODS data request details in timeline events
• Add landing zone statistics in siteinfo
• Fix iRODS data request issues
• Fix IRODSROOTPATH issues
• Fix LDAP TLS settings
• Fix iRODS stats badge stuck in "updating"
• Fix landing zone status updating not working in project details card
• Fix landing zone creation crash with large amount of created collections
• Fix multiple sheet editor issues
• Minor updates and bug fixes
• Upgrade to SODAR Core v0.13.4

See changelog for a complete list of updates.

- Python
Published by mikkonie over 2 years ago

https://github.com/bihealth/sodar-server - v0.14.1

Release for minor updates, maintenance and bug fixes.

• Add iRODS v4.3 support
• Add sheet sync setting validation
• Change default IGV genome to "b37_1kg"
• Fix landing zone locking controls for non-superusers
• Fix access to new HP ontology URLs
• Fix sheet column toggle modal UI issues
• Minor updates and bug fixes
• Upgrade to SODAR Core v0.13.3

See changelog for a complete list of updates.

- Python
Published by mikkonie over 2 years ago

https://github.com/bihealth/sodar-server - v0.14.0

Major feature update.

• Add general read-only iRODS access tickets for assay collections
• Add support for additional sample sheet templates
• Add landing zone updating
• Add automated checksum calculation in landing zone validation and moving
• Add iRODS delete request REST API views
• Add iRODS delete request batch handling in UI
• Add iRODS access ticket REST API views
• Add iRODS environment retrieval REST API view
• Add cytof assay plugin
• Add "create" tag for sample sheet versions
• Add user setting for maximum sample sheet table height
• Add "normalizesheets" management command to clean up existing sample sheets
• Improve sheet template creation form
• Landingzones UI improvements
• Sample sheet table resizing and rendering improvements
• Add study table cache disabling
• Minor updates and bug fixes
• Upgrade to SODAR Core v0.13.2
• SODAR Core v0.13 updates: full role inheritance, finder role, etc.

See changelog for a complete list of updates.

- Python
Published by mikkonie over 2 years ago

https://github.com/bihealth/sodar-server - v0.13.4

Release for minor sample sheet updates, maintenance and bug fixes.

• Update ISA-Tab template dependency to cubi-isa-templates
• Allow assay tables with no materials after sample
• Fix sample sheet creation form resubmit handling
• Fix django-autocomplete-light Docker build crash

See changelog for a complete list of updates.

- Python
Published by mikkonie about 3 years ago

https://github.com/bihealth/sodar-server - v0.13.3

Release for minor updates, maintenance and bug fixes.

• Add ProjectIrodsFileListAPIView API endpoint
• Display study and assay plugin icons to contributors and above
• Remove SPECIAL_FILE_LINK_HEADERS hack
• Update URL patterns
• Upgrade dependencies, fix site for Django v3.2.19+

See changelog for a complete list of updates.

- Python
Published by mikkonie about 3 years ago

https://github.com/bihealth/sodar-server - v0.13.2

Maintenance and bug fix release.

• Improve iRODS path validation
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 3 years ago

https://github.com/bihealth/sodar-server - v0.13.1

Release for minor updates, maintenance and bug fixes.

• Allow restricting landing zone write access
• Add API examples to manual
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 3 years ago

https://github.com/bihealth/sodar-server - v0.13.0

Major feature update.

• Add project archiving support
• Add genome selecting for IGV sessions
• Add omitting IGV session BAM/VCF files by file suffix
• Add iRODS file check for material renaming in editor
• Add optional landing zone write access restriction to created collections
• Add study render table caching for sample sheets
• Add iRODS user account creation at login for users with LDAP/SODAR auth
• Update cancer study shortcut generating
• Fix iRODS connection handling issues
• Upgrade to SODAR Core v0.12.0

See changelog for a complete list of updates.

- Python
Published by mikkonie over 3 years ago

https://github.com/bihealth/sodar-server - v0.12.1

Maintenance and bug fix release.

• Fix incorrect project modify API settings in production
• Fix category member role removal
• Fix Tooz and Redis connection issue handling
• Fix unhandled project locking errors
• Optimize germline study rendering and cache updating
• Upgrade Vue app dependencies
• Minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie over 3 years ago

https://github.com/bihealth/sodar-server - v0.12.0

Release for integrating SODAR Taskflow with SODAR.

• Add Taskflowbackend app from SODAR Core
• Add Taskflow functionality from SODAR Taskflow v0.6.2
• Implement SODAR Core v0.11 project modify API
• Add hyperlink support for "external links" sample sheet columns

See changelog for a complete list of updates.

- Python
Published by mikkonie over 3 years ago

https://github.com/bihealth/sodar-server - v0.11.3

Release for minor updates, maintenance and bug fixes.

• Support for additional sample sheet templates
• Hide uneditable sheet template fields in forms
• Minor updates and general bug fixes
• Upgrade Vue app dependencies
• Upgrade to SODAR Core v0.10.13
• Update manual and remove separate dev docs

See changelog for a complete list of updates.

- Python
Published by mikkonie almost 4 years ago

https://github.com/bihealth/sodar-server - v0.11.2

Release for minor updates, maintenance and bug fixes.

• Fix known sample sheet replacing issues
• Fix iRODS file search issues
• Minor updates and general bug fixes
• Upgrade to ag-grid v27
• Upgrade to SODAR Core v0.10.10

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.11.1

Release for minor updates, maintenance and bug fixes.

• Deployment and iRODS improvements
• Upgrade Python dependencies
• Drop Python v3.7 support, add Python v3.10 support
• Minor updates and bug fixes
• Upgrade to SODAR Core v0.10.8

This release of SODAR requires SODAR Taskflow v0.6.1 or newer.

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.11.0

Major feature update.

• Add simple link support to string cells in sample sheets
• Add generic raw data assay plugin
• Add assay plugin override via ISA-Tab comments
• Add default ontology column value
• Add user alerts and member emails for landing zone actions
• Add user alerts for sample sheet iRODS cache updates
• Add user message to landing zones upon successful moving
• Add "finished" parameter to LandingZoneListAPIView to access finished zones
• Add locked status info to landingzones UI and LandingZoneRetrieveAPIView
• Add descriptions and batch deletion for sample sheet versions
• Add automatic study/assay table filtering from search results
• Add collections to iRODS file list modals for landing zons
• Manual clearing of finished landing zones in UI no longer needed
• Upgrade to SODAR Core v0.10.7

This release of SODAR requires SODAR Taskflow v0.6.0 or newer.

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.10.1

Maintenance and bug fix release.

• Docker setup fixes and improvements
• Site settings improvements
• Upgrade Vue app dependencies
• Minor updates and bug fixes
• Upgrade to SODAR Core v0.10.3

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.10.0

Release for multiple new features and major SODAR Core upgrade.

• iRODS delete requests for data objects and collections
• Diff comparison for sample sheet versions
• Sample sheet creation from templates using cubi-tk
• Sample sheet read-only mirroring from another project or site
• Per-project restriction of column configuration updates
• Support for project public guest access
• Optional automated creation of expected landing zone collections
• Allow sheet export and version viewing for guest users
• Upgrade to SODAR Core v0.10

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.9.0

Major update for ontology editing, UCSC Genome Browser integration and other new features.

• Ontology editing and lookup support
• iRODS ticket and track hub support for UCSC Genome Browser integration
• iRODS data administration features
• Microarray assay support
• Support for missing column types in sample sheet editor
• Multi-term search support
• File status query REST API endpoint
• Landing zone UUID copying
• Major samplesheets vue app refactoring and testing
• Upgrade to SODAR Core v0.9.0

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.8.0

Major release for row editing and other editor improvements.

• Sample sheet row insertion
• Sample sheet row deletion
• Improved cell editing support
• Sheet display config saving
• Sheet config versioning and updating
• Landing zone validation triggering with uploaded file
• API improvements

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.7.1

Release for API updates, minor features and maintenance.

• Add tokens app from django-sodar-core
• Upgrade to django-sodar-core v0.8.1
• Add samplesheets REST API views for iRODS collection creation and sheet import
• Add REST API documentation in manual
• Minor features and fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.7.0

Major release for sample sheet editor, API and small files updates

• Add initial sample sheet editor for modifying basic cell values
• Add column configuring for sample sheet editor
• Add sample sheet version browsing, restoring, export and deletion
• Add initial REST API for landing zones and sample sheets
• Add shortcut columns to project list
• Move small files to iRODS, remove filesfolders app
• Refactor iRODS connections in irodsbackend
• Improve inline file linking for metabolomics assay apps
• Upgrade to django-sodar-core v0.7.2 and altamISA
• Numerous minor updates and bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.6.1

Release for iRODS updates and maintenance.

• Enable supplying optional iRODS environment files for connections
• iRODS logging improvements
• Minor bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.6.0

Relase for ISAtab exporting, ISAtab handling updates and sample sheet rendering improvements.

• Add ISAtab exporting
• Upgrade to altamISA v0.2.5, refactor importing for full ISA model support
• Add rendering for multiple missing columns
• Add saving of original ISAtab data into the SODAR database
• Add IGV merge shortcuts
• Add multi-file ISAtab importing
• Enforce row order in studies
• Replace TSV table export with Excel export
• Add support for panel sequencing and metabolite profiling in assays
• Upgrade to django-sodar-core v0.7.0
• Fix major issues with multi-cell copying
• Numerous minor updates and fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.5.1

ISAtab parser update and sample sheet viewer improvements.

• Upgrade to altamISA v0.1 for importing sample sheets
• Update models, parsing and rendering for the new parser API
• Add displaying of parser warnings
• Various sample sheet rendering improvements and fixes
• Upgrade to SODAR Core v0.6.2

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.5.0

Release for a major sample sheet viewer update.

• New sample sheet viewer built from scratch on vue.js and ag-grid
• New design for study shortcuts
• Multi-cell selection and clipboard copying
• Table column selection
• Table column resizing
• iRODS file information caching
• iRODS collection list filtering
• Numerous smaller additions, changes and fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.6

Hotfix and maintenance release.

• Fix crash for sample sheets replacement with duplicate study names
• Upgrade site for SODAR Core v0.5.1

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.5

Maintenance release.

• Fix hard coded WebDAV URL in study app IGV links
• Add missing SODAR Core v0.5 settings variables

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.4

Minor maintenance release. The last expected release of the v0.4.x branch, unless critical bugs are discovered.

• Add copying of HPO term IDs to clipboard
• Upgrade to SODAR Core v0.5.0
• Bug fixes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.3

Release for iRODS query optimization, sample sheet rendering improvements and user management improvements.

• Add iRODS linking support for transcription profiling
• Add performer and perform date rendering
• Render multiple ontology links within sample sheet cell
• Fix problems with iRODS button updating and timeouts
• Security updates for Landing Zones
• Upgrade to SODAR Core v0.4.5
• User management improvements from SODAR Core v0.4.5

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.2

Release for iRODS UI improvements, catching up with SODAR Core and minor fixes.

• Client-side updating of iRODS links
• Reduce unnecessary iRODS connections
• Upgrade project and requirements for SODAR Core v0.4.3
• Cleanup and refactoring to match SODAR Core v0.4.3
• Remove most local JS/CSS includes
• Reformat using Black

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.1

Minor update and bug fix release.

• Upgrade site to SODAR Core v0.4.0
• Remove local filesfolders app, import from SODAR Core
• Improve alternative material name search
• Optimize iRODS file search
• Secure SODAR Taskflow API views
• Bug fixes and minor updates

NOTE: Requires SODAR Taskflow v0.3.1

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.4.0

Update for integrating SODAR with SODAR Core.

• Site now based on SODAR Core v0.3.0
• Add remote project metadata synchronization from SODAR Core
• Remove formerly local apps now provided by SODAR Core (most notably projectroles and timeline)
• Finalize rebranding project to SODAR
• Only minor front-end changes

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.3.3

Update adding an app for cancer study shortcuts in samplesheets.

• Add cancer study app
• Refactor germline study app
• Add general samplesheets helpers and utilities

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.3.2

Minor bug fix and documentation update.

• Add BIH Proteomics data transfer docs (from Mathias Kuhring)
• Fix ISAtab replacing failure if encountering an error in the investigation file
• Fix dropdown menu overflow issue in certain tables

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.3.1

Release for app ui/functionality updates and fixes for v0.3.0.

• Optional automated unpacking for zip archives in Small Files
• Option for validating landing zone files without moving
• Major improvements in iRODS file querying and irodsbackend API
• Redesigned search view
• Search for iRODS files
• External ID display and annotation for samples
• Samplesheets layout improvements
• Enable using content apps for multiple assay types
• Proof-of-concept ID querying API

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.3.0

Release for milestone %"Omics Data Management v0.3". * Rebrand site as SODAR * Separate config apps into study and sample sub-apps in samplesheets * Add special configuration sub-apps to landingzones * Improve iRODS links and file navigation * Add a Sphinx-based user manual * Add IGV session creation for germline projects

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.3.0b

Beta release for milestone %"Omics Data Management v0.3".

• iRODS integration (with omics_taskflow v0.2.0b)
• Landing Zones app added for managing file uploads in iRODS
• Add sample sheet configuration specific sub-apps, bih_germline as a demo case
• Irodsinfo app for configuring iRODS connection

See changelog for a complete list of updates.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.2.0

Release for milestone %"Omics Data Management v0.2".

• Add new samplesheets app with ISAtab support
• New URL scheme using object UUIDs
• Remove "project staff" role

See changelog for a complete list of changes.

- Python
Published by mikkonie about 4 years ago

https://github.com/bihealth/sodar-server - v0.1

Release for milestone %"Omics Data Management v0.1". see changelog for details.

- Python
Published by mikkonie about 4 years ago