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Release 3.0.0#414

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Don-Isdale merged 148 commits intomasterplantinformatics/pretzel:masterfrom developplantinformatics/pretzel:developCopy head branch name to clipboardOct 22, 2024

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Commits on Feb 8, 2024

• result of npx ember-cli-update --to 3.28

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• npm install updated package-lock.json from 12 to 16. resolved merge conflicts in previous commit b650e2d - not tested

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• re-add env which was dropped in edit of merge conflict in 67f6969 environment.js

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• result of ember-cli-update --to 4, with merge conflicts resolved

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Commits on Feb 16, 2024

• start of frontend upgrade to Ember4 and Bootstrap4

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Commits on Feb 22, 2024

• Apply ember-no-implicit-this-codemod

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Commits on Feb 26, 2024

• upgrading frontend : relationship options, d3 keys,values,nest, capitalize, etc

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• update frontend/package-lock.json

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Commits on Feb 29, 2024

• bs tab fade=false. link-to route. etc

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Commits on Mar 6, 2024

• in progress : replacing sendAction() with closure actions and direct function calls. change uses of d3.event and d3.mouse

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Commits on Mar 11, 2024

• use native input in place of classic component

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Commits on Mar 12, 2024

• update frontend/package-lock.json

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• re-connect Zoom button to domain change

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Commits on Mar 13, 2024

• reduce rendering from mousewheel zoom and pan

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Commits on Mar 14, 2024

• update axis drag, feature search results display

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Commits on Mar 15, 2024

• update remaining textareas

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• update remaining d3 .on functions

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Commits on Mar 22, 2024

• updates for transitions, db edits and refreshes in groups pages

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Commits on Mar 25, 2024

• in Dockerfile update node version 12 to 18 and remove bower

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• feature search : change use of d3 nest to group for display of features blocks

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Commits on Mar 26, 2024

• update use of popover

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Commits on Mar 27, 2024

• update tab.pane and input parameters to restore layout in explore and servers list

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Commits on Mar 28, 2024

• pass closure action selectDataset down to entry-scope instead of using strings and actions defined in local js

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• update from d3.nest to d3.group requires implies in key values

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• manual update of package-lock.json ember-ajax 5.0.0 to 5.1.2

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• regenerated package-lock.json

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Commits on Apr 4, 2024

• changes to connection of adapter current request with server

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• select correct server for groups requests during connection to secondary

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• revert the change to glob in frontend/package-lock.json

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Commits on Apr 5, 2024

• minor updates

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• Change remaining inputs with class form-control from class to angle bracket so that .form-control gives the element full-width

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Commits on Apr 8, 2024

• Change Textarea param input to oninput.

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• update params for FileDropzone

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Commits on Apr 9, 2024

• log undefined levelMeta

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• update file upload drag drop to work in Chrome also

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Commits on Apr 11, 2024

• use closure action for onDelete; un-view before delete and refresh after

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• replace remaining uses of sendAction

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Commits on Apr 12, 2024

• merge into feature/upgradeFrontend from feature/ongoingGenotype

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Commits on Apr 14, 2024

• move functions binEvenLengthRound and binBoundaries to npm package interval-bins and import from there

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Commits on Apr 15, 2024

• Add a design diagram showing the calls between function defined within vcf-feature.js

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Commits on Apr 17, 2024

• Split out VCF data functions from vcf-feature.js to new repo vcf-genotype-brapi

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Commits on Apr 18, 2024

• Add design diagram showing the Genotype web API requests

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Commits on Apr 22, 2024

• import from vcf-genotype-brapi

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Commits on Apr 23, 2024

• Add DataSource BrAPI

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• change imports of vcf-genotype-brapi from local npm pack to published package

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• lb4app/package.json : replace npm link with npm install for 3 plantinformatics repos

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Commits on Apr 25, 2024

• use brapi-genotype.js

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Commits on Apr 30, 2024

• get BrAPI variantsets and references i.e. datasets and chromosomes

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Commits on May 6, 2024

• implement BrAPI samples and allelematrix

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Commits on May 8, 2024

• BrAPI result text header

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Commits on May 9, 2024

• remove whitespace before VCF result display

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Commits on May 21, 2024

• closes #374 change initial default position of right/bottom panel to right

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• closes #375 Enable Germinate Datasource, without requiring url option

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Commits on May 28, 2024

• Change plantinformatics/vcf-genotype-brapi dependency from local dev to version

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Commits on Jun 12, 2024

• add genotype-search

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• Merge branch 'develop' into feature/ongoingGenotype

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• Merge branch 'feature/workingGroup3_383_GenotypeSearch' into feature/ongoingGenotype

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Commits on Jun 13, 2024

• Collate featuresDomain of each block from result and view the blocks and brush the domain of the result features

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Commits on Jun 14, 2024

• trim whitespace from text inputs samples and features in genotype-search

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• ensure that Genotype Table is displayed when genotype-search is used

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Commits on Jun 20, 2024

• report on input Sample errors to the GUI in genotype-search

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• filter out duplicate names in Samples and SNPs in genotype-search

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• omit empty regionParams in remaining cases

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Commits on Jun 21, 2024

• resultBlocks : when blockGiven return undefined instead of an empty Map.

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• add required space in bash condition

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• change authSource admin to database to reflect change of pretzelUser

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• ensure / between rootURL and apiNamespace

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• Dockerfile : update PRETZEL_VERSION, drop const ROOT_URL=/pretzelUpdate

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Commits on Jun 24, 2024

• Don't use 0 value of colHeaderHeight. Exclude INFO from featureSampleMAF

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Commits on Jun 25, 2024

• Set selected samples for the dataset searched in genotype-search

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• Set the Genotype Table width to be set for genotype-search.

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Commits on Jun 26, 2024

• disable filtering out of soft links in vcf status for genotype search

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• Genotype Search : set array in selected samples.

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Commits on Jul 2, 2024

• handling of some exceptions and errors

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• prevent exception - don't ensureAxisBrush until block.axis1d is defined

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Commits on Jul 3, 2024

• handle undefined vcfGenotypeSamplesSelectedAll

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Commits on Jul 4, 2024

• include the Python Flask blastServer.py in a docker-compose yaml

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• add .dockerignore

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Commits on Jul 18, 2024

• add to docker-compose environment mntData, handsOnTableLicenseKey

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• define vcfDir using mntData in vcfGenotypeLookup.bash

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• define vcfDir using mntData in vcfGenotypeLookup.bash

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• include the Python Flask blastServer.py in a docker-compose yaml

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• use mntData for blastDir and vcfDir

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Commits on Jul 22, 2024

• Merge remote-tracking branch 'origin/feature/composeDirs' into feature/workingGroup3_383_GenotypeSearch

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• closes #398 : display blast errors in GUI to distinguish errors from empty results

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Commits on Jul 24, 2024

• add request header accept json and parse message from html response

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• update version -> v2.18.1

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Commits on Jul 25, 2024

• Set initial tab in left panel to Dataset Explorer

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• catch exception from loading landingPageContent

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Commits on Aug 9, 2024

• Exclude Feature .INFO from calculations on sample values

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• enable datasets in groups to display in Dataset Explorer

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• don't expose the blastserver port 4000

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Commits on Aug 13, 2024

• adjust paths configuration for blastserver

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• add glob and rollup. ensure ROOT_URL has a trailing slash.

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• change source of package ember-cli-build-date

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Commits on Aug 14, 2024

• include a copy of ensureTrailingString to work around module error

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Commits on Aug 16, 2024

• use github Facilecomm for ember-local-storage

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• adjust frontend dependency vcf-genotype-brapi

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• import ember-local-storage from @Facilecomm

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• increase base font size to match previous

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• Enable configuration of ROOT_URL in container image build

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Commits on Aug 20, 2024

• fix initial width of axis track rectangles

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• adjust mousewheel zoom at top of axis

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• change default extraOutsideMargin to 0

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Commits on Aug 21, 2024

• show right edge when axis with QTLs is split

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• resize height of right axis edge when window resizes

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Commits on Aug 26, 2024

• Merge remote-tracking branch 'origin/feature/workingGroup3_383_GenotypeSearch' into feature/upgradeFrontend2

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• show error message from vcfGenotypeLookup

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• direct dependency on serve-favicon is not required

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• handle connection failures when requesting ontology tree

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• change form of github path of interval-bins in package.json

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Commits on Sep 3, 2024

• in Publication Mode disable the axis drag/drop target zones

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Commits on Sep 5, 2024

• genotype-search : show triangles for features found

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Commits on Sep 11, 2024

• copy blastn from ncbi/blast image into blastserver image

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• increment BLASTSERVER_VERSION to 1.0.5

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Commits on Sep 12, 2024

• genotype-search show HTML error text, ensure vcfGenotypeSamplesSelectedAll is defined, handle undefined lookupBlock.

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Commits on Sep 13, 2024

• genotype-search handle undefined vcfGenotypeSamplesSelectedAll

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Commits on Sep 17, 2024

• add configuration to handle links for non-container blastserver

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• update the action for file input in file-drop-zone

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Commits on Sep 18, 2024

• handle errors from numeric ontologyId

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Commits on Sep 19, 2024

• ensure brushedDomain is exact so that outside SNPs are not filtered out of table

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Commits on Sep 30, 2024

• handle undefined feature.values

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Commits on Oct 3, 2024

• add .nvmrc in frontend and lb4app

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• factor sample filter from Genotype Table to Genotype Search

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Commits on Oct 7, 2024

• get and display samples in genotype-search when user selects dataset

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• disable adding a block of selectedDataset to viewedVCFBlocks

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Commits on Oct 8, 2024

• in Genotype Search don't show checkbox Common samplesIntersection and remove replaced Textarea .selectedSamplesInput

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• re-render selectedFeatures when their number changes

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• disable some trace

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Commits on Oct 11, 2024

• order the Genotype Table first on chromosome, then position

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Commits on Oct 14, 2024

• add button Show Samples

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• ensure manageGenotype is shown before setting selectedSamplesText

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• initialise body class tablesPanelRight

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• clear QTL hover in top-right of graph after 5sec

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• Don't switch to the dataset tab if the Genotype Table is displayed

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• show active initial dataset tab in Genotype Table controls

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• update frontend/package re. vcf-genotype-brapi

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• preserve Genotype Search selectedDatasetId

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• enable Search button when manage-genotype is not shown

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• clean up after previous commit commit 03dce1c

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Commits on Oct 22, 2024

• solve exception caused by click in header row of LD Block column

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• add to blastserver image binaries parallel and vmtouch used by blastn

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• disable CSV Download button so that paths are shown in table

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• update version 2.18.1 -> 3.0.0

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• update blastserver image version to 1.0.6

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• Merge pull request #413 from plantinformatics/feature/upgradeFrontend2

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