Release v3.4.0 #470
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Release v3.4.0 #470
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…en genotype-search is inserted because navigateGenotypeTableP() increases right panel width (rightSplitInstance.setSizes([35, 65])), and this was happening when the app started; now it happens when the user inputs to genotype-search e.g. select dataset. Closes #453 genotype-search.hbs : drop use of didInsertElement_. genotype-search.js : drop didInsertElement_(), which formerly called this.navigateGenotypeTable(). lookupMessage() : add dependency manageGenotype. vcfGenotypeSearch() : refer to userSettings via this.args instead of manageGenotype.args, which could (unlikely) be undefined or .isDestroying because of resultP.finally(() => later() ).
genotype-search.hbs : display .resultCounts.blocks and .features. genotype-search.js : add class ResultCounts. add @Tracked resultCounts. vcfGenotypeSearch() : share userSettings.resultCounts = this.resultCounts; clear counts .blocks and .features. manage-genotype.js : vcfGenotypeReceiveResult() : resultCounts : .blocks++ and .features += added.createdFeatures.length, i.e. count the result
part of #444 (as was previous commit aac5b89) goto-feature-list.js : matchAliasesChanged() : set .matchAliases = value, which is now target.checked not event. manage-genotype.js : vcfGenotypeReceiveResult() : resultCounts : log createdFeatures.length blast-results-view.js : showTable() : after promise is resolved, don't continue loop waiting for result. goto-feature-list.hbs : <input checkbox matchAliases : pass value='target.checked' to matchAliasesChanged (default arg wasxo event) instead of displaying .blocksOfFeatures.length when non-zero, display it when not .loading, and also display .aliases.length
Closes #445 sequence-search.hbs : Move from <ul config-list to top of <tab.pane sequence-search-input, above DNA Sequence Input : <select .selectedParent ... <option #each this.datasetsToSearch ...
Closes #446 sequence-search.hbs : prepend <hr> <ul class=config-list and insert <li> <label>Optional Inputs ...
part of #447 genotype-search.hbs : if .vcfGenotypeSearchTask.isRunning, display Loading ... genotype-search.js : vcfGenotypeSearchDisabled() : add vcfGenotypeSearchTask.isRunning vcfGenotypeSearch() rename to vcfGenotypeSearchP(), return resultP, and wrap with vcfGenotypeSearch() -> vcfGenotypeSearchTask().
goto-feature-list.hbs : .loading message : prepend Searching ... to Alarm Clock unicode
closes #448 Added links are <a class=margin-left-help ...><i class=glyphicon glyphicon-question-sign></i></a> with href based in https://docs.plantinformatics.io/Basic-Functions/Search-tab/ genotype-search.hbs : {{panel-heading }} VCF Genotype Search : add link to #vcf-genotype-search <label>Samples input : add link to #vcf-genotype-search-inputs <label>Features input : add link to #vcf-genotype-search-inputs manage-search.hbs : {{panel-heading }} Feature Search : add link to #feature-search sequence-search.hbs : {{panel-heading }} DNA Sequence Blast Search : add link to #dna-sequence-blast-search <label>Reference to search : add link to #blast-search-inputs <label>Optional Inputs : add link to #optional-inputs
... this was broken by #370 which included d3 update; b7e2ae2 converted from d3.nest() to d3.group(), but additional changes were required. d3.nest() result is [{key, values}, ..] d3.group() result is Map key->value (related note in manage-explorer.js : parentAndScope()). Instead of maintaining the nested structure, this commit changes nested to grouped. Closes #454 grouping.js : in blocksParentAndScope2() and throughout : rename nested to grouped, including these 2 function names : fromNestedMulti() -> fromGroupedMulti() fromNestedParentAndScope() -> fromGroupedParentAndScope() fromGroupedMulti() : change recursion check to : values instanceof Map. if (typeof values !== object) don't call levelMeta.set(values ) (WeakMap.set() only valid for object value).
These changes are part of the frontend framework upgrade #370. manage-explorer.js : historyViewChanged() historyBlocksChanged() and showHierarchyChanged() : set the object attribute, which was previously done implicitly for the {{input}} name or checked attribute; this was changed to <input> in 004fabf. use Ember_set() for .controlOptions.{historyView,historyBlocks,showHierarchy} because they are tracked by a tracking context. entry-blocks-array.js : dataFiltered() : if data is an (Array) Proxy (e.g. ManyArray), convert it to an Array, to avoid error re. mutateSortRelatedRecords. manage-explorer.hbs : pass value=target.checked to the checkbox actions historyBlocksChanged and showHierarchyChanged
…et Explorer manage-explorer.hbs : wrap in #if this.urlOptions.historyFilters : historyView radio-button-s and historyBlocks checkbox
Closes #459 table-brushed.js : add urlOptions alias. table-brushed.hbs : wrap in #if this.urlOptions.featuresEditable : <input checkbox > .editable and .saveToDatabase
Closes #458 groups.js : noGroup : change .name '' to 'All'
Closes #460. stacks-view.js : stacksAdjustY() : check axis1d.isDestroying to avoid exception : Attempted to access the computed .portion on a destroyed object in axisScaleChanged -> yAxisTicksScale -> yAxisTextScale mapview.js : loadBlock() : change to be a toggle, enabling +/- in the Dataset Explorer. block.js : add viewToggleIcon() : icon name plus or minus to represent toggling the current value of this.isViewed. view.js : add axisSiblings() viewRelatedBlocks() : add param view i.e. handle un-view also. factor to form viewFn(). don't call setViewed() if ! view. toView : unshift instead of push if ! view, so that child blocks are not viewed without their reference / parents. also determine parentBlock via .unviewFor(); push parentBlock{,2} to related before handling related; if ! view use axisSiblings(block, related) to check that referenceBlock can be unviewed. This is not designed to handle the possibility of a parent block having multiple viewed child datablocks; the next iteration might filter for other dataBlocks on block.axis which have the same .parentBlock. Tested OK with dataBlocks such as Alignments on a reference, and QTLs whose parent is a Genetic Map or Alignment. axesForViewedBlocks() : pass additional arg view=true to viewRelatedBlocks(). Make loadBlock icon dynamic in these entry-block*.hbs : entry-block-add-button.hbs : entry-block-add.hbs : entry-block.hbs : button-base loadBlock : show regardless of this.entry.isViewed (i.e. drop #unless / #if #else); icon : change plus to this.entry.viewToggleIcon
Closes #462 This also addresses [object Object] shown when upload does not connect to server. Show network error message text via headsUp.tipText data-base.js : uploadData() : if ! err.responseJSON and err.statusText, construct text errmsg from fnName, err: .statusText .state() .status; api-server.js : blocksAnnotateWithFCStatus() : handle undefined .datasetsBlocks, seen after datasets refresh after server exit. mapview.js : model() : getDatasets .catch() : show err via headsUp. auth.js : _ajax() : add config.error : show textStatus via headsUp. $.ajax().catch : construct a text errmsg from route, err: .statusText .state() .status, and show via headsUp app.scss : #headsUp : adjust margin-left : -20px -> 10px so that left edge of text is not obscured
{,frontend/}package.json : version : 3.3.0 -> 3.4.0
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Work done under sub-issues of #443 :