Release v3.5.0 Dataset Collections #465

PR #478, #479

Principal addition

#465 Dataset Collections

development branch feature/datasetCollections

Sub-issues of #465, and other issues completed in this branch :

#466 group datasets by meta.Crop

#467 Display crop names as tabs in the Dataset Explorer

#471 Add Category filter for Dataset Collections

#461 Improve performance of VCF Genotype Request processing

#472 Warn if dataset upload does not define meta.Crop

#473 Generate a CSV report of datasets and export as a file download

#463 Provide GUI error message when Genotype directory is not set up

#474 Streamline the upload of Crop and Category metadata

#417 Feature Search : add a clear button to enable remove the triangle after search

#404 Feature / marker names which are numbers are being converted to numeric type instead of string

#397 Change white-space filtering in text input fields for DNA Sequence search and Feature Search

#409 Genotype request : filter out duplicate sample names entered by the user
re-tested duplicate samples and SNPs - OK, closed with a comment with commit and test description. Found an issue in 460 :

#460 Add a minus sign to remove the dataset in Dataset Explorer - beacd7c changes required by loadBlock changing to a toggle

#477 Prepare metadata for software release

Release v3.4.0

PR: #470 Release v3.4.0

Work done under sub-issues of #443 :

#444 GUI feedback when no result
#445 Blast Search : move Reference input to the top
#446 Blast Search : separate and label the Optional Inputs
#447 Show a "loading" message, particularly where searches may be long
#448 Help button with link to docs pertinent to the component
#449 VCF Genotype Search error messages when inputs don't match in the selected Dataset
#453 Reduce initial right panel width
#457 In the Dataset Explorer, wrap dataset Recent / Favourites controls in a feature flag
#458 Rename the un-filtered group selection to 'All'
#459 Feature Table : Wrap in a feature flag : Editable and Save To Database
#460 Add a minus sign to remove the dataset in Dataset Explorer

Release v3.3.0

• #431 Usability and GUI presentation improvements
• PR #450
• PR #452

This PR is the completion of #431 Usability and GUI presentation improvements, which contains these sub-issues :

• #436 Make the Datasources component less prominent because it is only used by advanced users
• #437 Hide Selected Server in the Search tab when there is only the primary server connected
• #438 Default to All Datasets after closing and re-opening the Datasets panel-container
• #439 Add the margin to VCF Genotype Search
• #441 Sort chromosome names in VCF tab of Dataset Explorer
• #428 Upload error-report in GUI : typo in JSON upload displays in GUI as [object Object]

Development branch : feature/guiChangesLeftPanel

Release v3.2.0

• PR #432 Merge Germinate update
• #435 Update Germinate connection

Release v3.1.0

PR #418 Resolve issues reported since the v3.0.0 release
PR #419 handle some exceptions
PR #420

Tracked by issues :

• #416 Items identified after release v3.0.0
• #415 Unpredictable BLAST results on AGG Pretzel

development branch feature/postReleaseIssues

Release v3.0.0

Release 3.0.0

Main work items

• upgrade of frontend frameworks
• Working Group #3 addition of Genotype Search
• BrAPI additions

Detail

The PR #414 documents the work done in this release :

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• #370 frontend upgrade
• #383 Working Group Use Case 3 : Request Genotype values for given Dataset, SNP Names, Samples
• #394 Working Group Use Case 3 Extensions
• #372 BrAPI Wittenberg Hackathon 2024 notes
• #373 Configure display of histograms to handle smaller VCF datasets
• #398 blast - errors are reported as 0 hits
• #399 Include blastServer in docker-compose yaml to enable single-command installation and startup
• #377 Standardisation of Pretzel Deployment
• #408 Pretzel server exits after Cannot set headers after they are sent to the client

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• #374 Change default position of right/bottom panel to right
• #375 Enable Germinate Datasource, without requiring url option

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PR #413
PR #414

Development branches
feature/upgradeFrontend
feature/upgradeFrontend2

Master Release v2.10.0

Display of synteny blocks.

PR #266 Master Release v2.10.0
Issue #257

Master Release v2.8.0

#248

including branches :

• #239 : FASTA / DNA sequence search API, display results in frontend . feature/backendBlast
• ? #233 : support for .xlsx upload. feature/xlsx-upload
• #249 : node server API request cache - persistent . feature/requestCachePersistent

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v2.1.0

Minor release.

Changes:

• axis track: show detail of sub-elements
• add API to get handsOnTableLicenseKey from server runtime environment to FE (afaf28f)
• add DAWN JBrowse to External Lookup (1eed2da, afae988)
• plus 2-way flow of params from url to/from the axis zoom
• fixed example maps JSON - re-upload to your pretzel instance if paths are not being displayed

v2.0

Major changes:

• view tracks as rectangles
• tracks are progressively loaded
• tracks are shown within the axis by splitting it into a rectangular space
• ...and much more! #176 #148