Recent Releases of pretzel
pretzel - Release v3.9.8 : - match sampleNames of all crops. points offset #565
Changes Implemented
ce00985d - match sampleNames of other crops in features table Genotype PCA - switch off showing overlapping points with an offset.
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.7 : - issues from workshop practice #563
Changes Implemented
from #563 'Issues and feedback from a large group test of Pretzel' - fix axis flip issues - handle duplicates in selected sample names - avoid exception after switching to Account Settings - 161d4f99 update version to 3.9.7
Branch : feature/panBARLEX
PR #564
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.6 : fix exception in QTL display - query result
Changes Implemented
e3a07b2a in blockFeaturesInterval query result also handle ObjectID in .blockId e6d0842a update version to 3.9.6
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.4
Changes Implemented
549 PanBARLEX proof of concept connectivity: Dot plot endpoint in Pretzel
- fb9c67a8 change PanBARLEX dot-plot limit 50K to 1M. update version to 3.9.4
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.3 : add feature flag options=PanBARLEX
Release v3.9.3 : add feature flag options=PanBARLEX
Pull Request #559
Changes being released
- #549 PanBARLEX connectivity: Dot plot endpoint in Pretzel f389434f add feature flag options=PanBARLEX
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.2 : ObjectIDs in API responses. Scroll bar under tables. PR #558
Release v3.9.2 : ObjectIDs in API responses. Scroll bar under tables.
Key Changes :
- change ObjectIDs in API responses : blockFeatureLimits, blockFeaturesCount and blockFeaturesInterval
- ensure space for the horizontal scroll bar in features table and genotype table
- Don't clear selectedSamplesText when selectedDatasetId is undefined.
- refresh Genotype Table display when passport data is received after user closes passport fields selection
- enable passport data to be read for large numbers of samples
Details
Details are listed in the Pull Request : - #558
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.1 : Retain dots in SNP names. Handle genotypeIds not in database.
Release v3.9.1:
Merge Pull Request #554
This change relates to : - #529 Show accession names from passport data in the column headings of the Genotype Table
- JavaScript
Published by Don-Isdale 9 months ago
pretzel - Release v3.9.0. Display of Genolink / Genesys accession data in Genotype Table headers
Introduction
This release builds on the Genolink connection functionality released in v3.8.0 via #528. The overall structure of this work is recorded in the parent issue #527, and the work in this release is recorded in #529, which documents the following added functionality :
- Show accession names from passport data in the column headings of the Genotype Table.
- Enable the user to sort/group the columns by a selected Passport data field.
- Add a modal dialog for Passport fields, providing a list for selecting fields and a separate list showing the selected fields and the order in which they will be used for sorting the samples / accessions based on Passport data from Genolink / Genesys. This list will also enable the user to customise the display order and sort priority of the fields.
- Show Passport values in multiple rows of the column header in the Genotype Table
- Enable the user to easily de-select all the Passport field which they have selected, by adding a Clear button.
- Also add an X button on each selected Passport field, to enable more selective changes.
- Column header height resizers : support individual heights per row.
- Sort by Passport fields.
- Show the text of the column header cell on mouse over, specifically for the Passport data headers.
Completed Issues included in this release
Branch : feature/genotype gui
- #529 Show accession names from passport data in the column headings of the Genotype Table
- JavaScript
Published by Don-Isdale 10 months ago
pretzel - Release v3.8.1 VCF Download of multiple chromosomes
Introduction
The focus of this patch release is GUI changes.
Completed Issues included in this release
Branch : feature/genotype gui
- #534
- #536
- #540
Branch : ui/535-genotype-accession-selection-menu
- #535 Which includes these sub-issues :
- - #536
- - #537
- - #538
- - #539
Included commits
Other commits included in this merge will be released in a following minor release, and are behind a feature flag options=new in this release. They are part of issue 529.
The branch feature/genotypeGuiRelease is created to limit the commits included in this PR.
- JavaScript
Published by Don-Isdale 10 months ago
pretzel - Release v3.8.0. Genotype enhancements from user interactions
Introduction
Interactions with AGG users via the recent Working Group and a Pretzel workshop have produced a lot of good feedback about how the application can be streamlined and improved to assist the users in their work.
This release delivers the result of the software changes suggested by users during these interactions.
The most significant of these additions are :
- #522 Enable Feature Search to match part of the given feature names.
- #524 Add option for samples to match if their genotype pattern at the inspected SNPs is heterozygous
- #528 Connect from Pretzel to the Genolink web site and populate the search box with selected Accession IDs
Each of these issues shows screenshots of the result of these changes, which illustrate the changes, and the issues contain text identifying the context, motivation, requirements and design of the suggested changes.
There are also a number of detail points which are itemised in the corresponding issues for each of these user interaction events, listed in the following comment.
- PRs #533 #530
- JavaScript
Published by Don-Isdale 11 months ago
pretzel - Release v3.7.4
507
- Improve handling of a new Genotype dataset viewed on the same chromosome when SNPs are selected for defining a haplotype. Merge selected SNPs from other datasets on the same reference.
509
Trim genotype value from last sample when filtering samples by defined haplotype. Trim the genotype value off the last sample in vcfGenotypeSamplesFiltered.
Increase default number of rows which are requested for Genotype Table. Change rowLimit 100 to 300.
- JavaScript
Published by Don-Isdale about 1 year ago
pretzel - Release v3.7.2. Genotype Table : Filtered Samples update for multiple chromosomes
Release v3.7.2
- PR #506
Genotype Table : Filtered Samples update for multiple chromosomes
- #505 d2571a62 update after user edits to Selected Samples, without requiring Enter 2c605444 Enable featureNameListInputKey in genotype-search
- #495 bc79a03d ensure that genotypeSamplesFilteredByHaplotypes is updated and filtered samples are requested for all brushed blocks with selected SNPs
- JavaScript
Published by Don-Isdale about 1 year ago
pretzel - Release v3.7.1
Release v3.7.1
Genotype Table Column sorting : multiple chromosomes
Extend Sample column sorting by selected SNPs Alt/Ref / defined haplotype to handle multiple chromosomes of a dataset.
501
PR #504
- JavaScript
Published by Don-Isdale about 1 year ago
pretzel - Release v3.7.0
Samples filter by Haplotype : add support for filtering multiple chromosomes of a dataset.
GUI Changes : Documentation Links and Genotype Table
Head Issue #492
Sub-issues
- #491
- #493
- #494
- #495
- #496
499
PR #503 branch : feature/snpSamples
- JavaScript
Published by Don-Isdale about 1 year ago
pretzel - Release v3.6.0
Release v3.6.0 Search Sample by Genotype of selected SNPs #482 PR #490
Issues Completed
Principal issue for this branch and release : - [x] #482
Sub-Issues : - [x] #483 - [x] #484 - [x] #485 - [x] #486 - [x] #487 - [x] #488
Other issues : - [x] #481
410
- [x] 352f3b36 Re-enable VCF Download by changing from file-anchor to fileDownloadBlob and fileDownloadAsCSV
- [x] 529ed45f Discard comment columns of AddMetadata sheets
Branch
feature/snp samples
- JavaScript
Published by Don-Isdale about 1 year ago
pretzel - 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
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - 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
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - 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
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - Release v3.2.0
- PR #432 Merge Germinate update
- #435 Update Germinate connection
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - 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
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - 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.
- JavaScript
Published by Don-Isdale over 1 year ago
pretzel - Master Release v2.10.0
Display of synteny blocks.
PR #266 Master Release v2.10.0 Issue #257
- JavaScript
Published by Don-Isdale almost 5 years ago
pretzel - Master Release v2.8.0
248
including branches :
- [x] #239 : FASTA / DNA sequence search API, display results in frontend . feature/backendBlast
- [ ] ? #233 : support for .xlsx upload. feature/xlsx-upload
- [x] #249 : node server API request cache - persistent . feature/requestCachePersistent
- JavaScript
Published by Don-Isdale almost 5 years ago
pretzel - v2.1.0
Minor release.
Changes:
- axis track: show detail of sub-elements
- add API to get
handsOnTableLicenseKeyfrom 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
- JavaScript
Published by rsuchecki about 6 years ago
pretzel - v1.2.0
Production release
- Progressive loading to enable faster and smoother rendering of larger data sets
- Hierarchical browsing of data sets by data type and chromosome, with filtering/grouping and feature search to streamline finding relevant data among a rapidly growing list of data sets
- Mouse-wheel zoom/pan and configurable path/feature density
- and much more!
- JavaScript
Published by rsuchecki over 6 years ago