Feature/progressive #150
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Feature/progressive #150
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axis-2d.js : axis1d() : depend on axesPCount; dataBlocks() : use block.isData() filter in place of blocks.slice. axis-tracks.js : Change showTrackBlocks() to a CP and add it to .hbs, in place of calling it in didRender(); the CP dependencies include yDomain, zoomed and extended, thus replacing the zoomed() action. Add ComputedProperty-s : axis1d, axisS, currentPosition, yDomain, trackBlocksR. Add blocksFeaturesLengths() - used in devel trace (and initially as a dependency for tracksTree). frontend/app/ : 996d438 9412 Sep 3 17:57 components/axis-2d.js 1830a8f 24256 Sep 4 13:50 components/axis-tracks.js 5b7548e 5614 Sep 3 16:37 models/block.js 45bc1bc 12533 Sep 3 16:37 services/data/block.js 21dad47 685 Sep 4 13:38 templates/components/axis-tracks.hbs 12d01c0 69368 Aug 28 16:51 utils/stacks.js
split axes visual changes : omit (blue) rectangle around split axis region; show tracks with solid colour instead of outline : app.scss : rect.track : change fill and stroke. centre the axis title relative to the split axes : yAxisTitleTransform() : calculate and append translateText. axis-2d : give axisTitle an initial transform of width/2. Shift the Zoom / Reset button out from under the split axis region : yAxisBtnScale() : calculate and append yOffsetText. Re-apply yAxisBtnScale() to existing axes. frontend/app/ : 476c4e4 9776 Sep 5 14:25 components/axis-2d.js 2f1c7f3 223040 Sep 5 15:31 components/draw-map.js 5365f20 28422 Sep 5 15:05 styles/app.scss 8eb88ef 5823 Sep 5 15:31 utils/draw/axis.js
… handle -ve interval axis-2d.js : rename dataBlocks() to dataBlocksS() and add a new version which is based on blocks in Ember store instead of stacks Blocks. axis-tracks.js : in line with change to axis-2d:dataBlocks(), derive trackBlocks() from trackBlocksR() instead of vice versa. tracksTree() : handle -ve interval (swap) - this was causing createIntervalTree() to overflow stack. models/block.js : add axis(). data/block.js : axesBlocks() : use ensureAxis(); add dataBlocks(). draw-map.js : factor ensureAxis() and add to axisApi. The driver for this commit was to update when blocks are added in axis-tracks; that is incomplete, but the interval swap is needed as a hot-fix commit. frontend/app/ : d0f7c87 10543 Sep 6 13:29 components/axis-2d.js 0c57e6c 24562 Sep 6 16:16 components/axis-tracks.js 2312316 223195 Sep 6 16:34 components/draw-map.js 6ce4cad 6126 Sep 6 09:36 models/block.js b1d8da7 14140 Sep 6 15:57 services/data/block.js 731b006 28403 Sep 6 16:39 styles/app.scss 60ba799 1847 Sep 6 13:29 templates/components/axis-2d.hbs
axis-tracks.js : layoutWidth() : use trackBlocksR in place of trackBlocks. paths-progressive.js : requestBlockFeaturesInterval() : call getBlockFeaturesInterval() once for each blockId; see comments for background; previously the results were limited to a single block. backend/common/utilities/ : 69591ee 1288 Sep 8 13:59 block-features.js 62b68d1 28235 Sep 8 16:39 paths-aggr.js frontend/app/ : 202df14 24528 Sep 6 17:52 components/axis-tracks.js 515fde4 22795 Sep 8 16:08 services/data/paths-progressive.js
This addresses an issue of paths loading and one or more of the axes showing only tick 0, with all the paths connecting to it. This was working but a recent commit disconnected the update, as has happened several times before. Use CP dependencies to update the axis ticks and scale. draw-map.js : add to axisApi : cmNameAdd, makeMapChrName, axisIDAdd. axis-1d.js : added CPs : dataBlocksDomains, referenceBlock, blocksDomains, blocksDomain, blocksDomainEffect, domainEffect. models/block.js : add CP : featuresDomain. feature.js : add CP : valueOrdered. data/block.js : use cmNameAdd(). (viewed() may not be updating - trialling an added dependency and changed use of blockValues()). draw/axes-1d.hbs and axis-1d.hbs : commented-out display of values which may be changed during the render (refn emberjs/ember.js#13948) : axis.view, currentPosition.yDomain. Use blocksDomainEffect. utility-chromosome.js : factor copyChrData() out of chrData(); add cmNameAdd() based on draw-map.js:receiveChr(). frontend/app/ : 6e37a2f 223853 Sep 10 20:25 components/draw-map.js 62cdfc0 22369 Sep 10 21:12 components/draw/axis-1d.js 2b94ee2 24542 Sep 10 20:25 components/draw/block-adj.js 563096e 2943 Sep 10 16:51 mixins/axis-position.js 06c02ae 6638 Sep 10 18:30 models/block.js 930fc67 1021 Sep 9 16:59 models/feature.js 4e7d202 14286 Sep 10 15:14 services/data/block.js cf7716e 356 Sep 10 17:24 templates/components/draw/axes-1d.hbs ed752af 578 Sep 10 18:42 templates/components/draw/axis-1d.hbs 8c18360 3946 Sep 10 15:36 utils/utility-chromosome.js added : 998f0c9 1623 Sep 10 18:30 utils/interval-calcs.js
… are required. stacks-view and stacks.js : add stacksCount, update when Stack add / delete, showResize() when #stacks changes. data/block.js : viewed() : use blockAxis(); factor from axesBlocks() to form blockAxis() and ensureAxis(); 947cd56 224199 Sep 12 14:15 frontend/app/components/draw-map.js 6abed34 1744 Sep 11 16:26 frontend/app/components/draw/stacks-view.js b5602e5 14987 Sep 12 14:15 frontend/app/services/data/block.js e1a8a11 128 Sep 11 16:19 frontend/app/templates/components/draw/stacks-view.hbs 30564f0 5950 Sep 11 14:30 frontend/app/utils/draw/axis.js 164d095 69798 Sep 12 13:55 frontend/app/utils/stacks.js
draw-map.js : Split didRender() into CPs drawEffect() and resizeEffect(); add stacksWidthChanged(), stacksWidthChanges(). block-adj.js : updatePathsPositionDebounce(): depend on stacksWidthChanges. stacks-view.js : stacksCount(): depend on axes2d.[] frontend/app/ : 0d5612e 226488 Sep 12 20:49 components/draw-map.js e2e293c 24663 Sep 12 19:22 components/draw/block-adj.js 13c93b5 1757 Sep 12 15:09 components/draw/stacks-view.js 9cc2221 2331 Sep 12 17:38 templates/components/draw-map.hbs
axis-2d.js : add .{isViewed,hasFeatures} to dependency dataBlocks.@each
axis-tracks.js : depend on trackBlocksR.@each.featuresLength
models/block.js : add hasFeatures().
data/block.js :
Split blocksReferences(), viewReferences(), receivedBlocks() out of taskGetSummary().
blocksReferences() : don't include self-reference in the result.
loadedViewedChildBlocks() : add dependency on blockValues.@each.{isViewed,isLoaded}; use hasFeatures in place of featureCount (and enable this).
dataBlocks() : add dependency on loadedViewedChildBlocks.@each.hasFeatures.
frontend/app/ :
5340f9a 10537 Sep 13 15:37 components/axis-2d.js
713f830 24637 Sep 13 14:31 components/axis-tracks.js
03f3485 6830 Sep 13 14:31 models/block.js
2ecf573 15521 Sep 13 16:04 services/data/block.js
… and received features. request features of block initially without brush required. This is focused on displaying tracks when blocks are added to the axis, and features are received. axis-2d.js : dataBlocks() : depend on blockService.viewed.[] axis-tracks.js : merge(gpS) so that existing g.tracks are updated, and .exit().remove() for gpS and clipRectS. showTrackBlocks() : depend on axis1d.featureLength. axis-1d.js : featureLength() : depend on featuresForAxis. models/block.js : add featuresForAxis(). data/block.js : add dataAndReferences : add blockIds to blocksToView, for receivedBlocks(). paths-progressive.js : requestBlockFeaturesInterval() : there may not be a brush (handle axisBrush === null). frontend/app/ : ce195b1 10637 Sep 13 19:59 components/axis-2d.js 773885e 24888 Sep 17 10:52 components/axis-tracks.js c517d5d 22637 Sep 17 11:18 components/draw/axis-1d.js 5cadd92 1188 Sep 16 17:01 models/axis-brush.js 4b2106c 13417 Sep 16 17:01 models/block-adj.js 7564ed2 8048 Sep 16 17:01 models/block.js 50ef5be 15793 Sep 16 18:24 services/data/block.js 5e7159e 23626 Sep 17 10:31 services/data/paths-progressive.js
data/paths-progressive.js : call blocksUpdateDomain() in requestAliases(). 70b70f9 23695 Sep 17 14:52 frontend/app/services/data/paths-progressive.js
axis-tracks.js : add gpM, to distinguish from gp which is enter / append (fixes duplicate g clip-path). c71a660 24902 Sep 17 15:06 frontend/app/components/axis-tracks.js
axis-tracks.js : use Identity key function for blocks in layoutAndDrawTracks(). block.js : filter out .obj === null from dataAndReferences. frontend/app/ : 0d41efc 25051 Sep 17 06:47 components/axis-tracks.js 9b9e9de 15901 Sep 17 06:14 services/data/block.js
draw-map.js : axisTitleFamily() : use block.getId() as key function for block subtitles. 09cc7d1 226514 Sep 17 18:12 frontend/app/components/draw-map.js
This synchronises title and tracks colours. Add a per-axis mapping from blockId to an index for axisTitleColour(). axis-tracks.js : replace blockIndexes() (which based blockIndex on DOM element sequence). draw-map.js : use block.axisTitleColour(). axis-1d.js : add blockIndexes() (derives blockIndex mapping from dataBlocks). stacks.js : add Block : axisTitleColour(). frontend/app/ : 81149af 24755 Sep 18 12:32 components/axis-tracks.js fe26b41 226965 Sep 19 11:13 components/draw-map.js be9e2f1 23328 Sep 18 16:33 components/draw/axis-1d.js 189f30b 6357 Sep 19 14:28 utils/draw/axis.js c128dc3 70664 Sep 19 14:15 utils/stacks.js
…ute function. draw-map.js : move axisTitleColour() to become Block.axisTitleColour() and use that in axis-tracks also. (this change was intended in the previous commit). frontend/app/ : 00e9a92 226612 Sep 19 05:26 components/draw-map.js 436a881 6482 Sep 19 05:26 utils/draw/axis.js ea812eb 71078 Sep 19 06:00 utils/stacks.js
axis-1d.js: factor out axisTitleFamily(); add updateAxisTitleSize() (uses axisApi.updateAxisTitleSize) and use in extended(). frontend/app/ : 80ef04e 226653 Sep 20 07:50 components/draw-map.js 1a013f6 23715 Sep 19 21:36 components/draw/axis-1d.js
entry-tab.js : add autoAllActive, calculated using leafCount(values). value-tree.js : add leafCount(), to count the blocks in the filtered values. entry-expander.js : allActive() : depend on entryTab.autoAllActive. frontend/app/ : f4c7ca9 3270 Sep 23 11:05 components/record/entry-expander.js 4566daa 2098 Sep 23 10:43 components/record/entry-tab.js 44a3b71 3977 Sep 23 10:43 utils/value-tree.js
value-tree.js : leafCount() add param levelMeta to distinguish a Blocks array value; rename count -> count0, dc -> count1. fc49e80 2152 Sep 23 17:07 frontend/app/components/record/entry-tab.js 44a1b29 4802 Sep 23 17:25 frontend/app/utils/value-tree.js
…which don't increase the domain.
blocks.js : rename featuresDomain{,Update}; add setDomain(), featuresDomainValue, featuresDomain().
99aa5f8 9233 Sep 25 00:37 frontend/app/models/block.js
c10157b 952 Sep 4 13:32 from dev:~/scripts/mongo_admin.2019Sep04.bash (only part is staged) resources/tools/mongo_admin.bash
-z not required in tar because added --gzip to mongodump (recorded in previous commit). 4595257 951 Sep 5 14:05 from dev:~/scripts/mongo_admin.bash, where these edits were done. (edit main->dev is not staged) resources/tools/mongo_admin.bash
mongo_admin.bash : use SERVER_NAME, default to main; factor checkDIM() out of dbCollections(); add signupList(), signupReport(). b63f54b1 2432 Sep 26 09:16 UTC dev:~/pretzel/resources/tools/mongo_admin.bash
654611f 830 Oct 1 14:41 frontend/bower.json
Updated various urls and config info. Based on a Windows build done a while back; will later step through this process again to check it. ee260b9 6411 Oct 3 12:13 README.windows.md
…dded new note from https://github.com/spriggsy83/pretzel branch windowsSetup1019 commit 212d049 Author: Andrew Spriggs <spriggsy83@yahoo.com.au> Date: Wed Oct 2 15:52:34 2019 +1000 README.md : add section : Installation on MS Windows using WSL (almost a direct copy from the pull request; rephrased the section heading and removed trailing spaces). f7c8720 13243 Oct 3 16:15 README.md
…in .gitignore from https://github.com/spriggsy83/pretzel branch windowsSetup1019 commit 50912ee Author: Andrew Spriggs <spriggsy83@yahoo.com.au> Date: Wed Oct 2 15:29:26 2019 +1000 dc81e81 435 Oct 3 16:19 .gitignore
… pretzel-data repo instead.
README{,.windows}.md : Inserting data : change to refer to example dataset files in pretzel-data repo instead of resources/example_map?.json.
delete resources/example_map{1,2,3,4,5}.json because they are in the old (json upload) format and they have already been converted to the new format in pretzel-data/my*.json and aliases.json.
5375bf1 13910 Oct 3 19:59 README.md
eea9dc2 6377 Oct 3 19:54 README.windows.md
…ilter-group model out of component. filter-group.js : split a model out of the component; move from component to model : patterns(), patternsRE(), defined(), match(); drop didRender() - no longer needed; add applyDataset, applyBlock - the GUI additions to access these 2 will be in a following commit. filter-group.hbs : use prefix data. to refer to fields which are now in model. filter-groups.js : move contents of initialFilterGroup to model. manage-explorer.js : rename useFilterGroup to definedFilterGroups, return an array instead of just [0]; add datasetFilterGroup(), blockFilterGroup(), isDatasetFilter() frontend/app/ : 7a1dccf 870 Oct 2 14:46 components/panel/filter-group.js 2f863de 823 Oct 2 15:13 components/panel/filter-groups.js c235df2 41944 Oct 2 16:47 components/panel/manage-explorer.js 8648108 2968 Oct 2 15:21 templates/components/panel/filter-group.hbs
the styling is just a starting point. frontend/app/ 27f64a6 28617 Oct 4 16:41 styles/app.scss 15ce906 3527 Oct 4 16:41 templates/components/panel/filter-group.hbs 41ae110 726 Oct 4 16:41 templates/components/panel/filter-groups.hbs 7593068 563 Oct 4 16:41 templates/components/record/entry-tab.hbs
2a84d1b 6724 Oct 4 18:21 README.windows.md
7d0b742 23439 Nov 19 18:50 frontend/app/services/data/block.js
block-features.js : add blockFeatureLimits(). backend/common/models/block.js : Add blockFeatureLimits. change nBins to number/false. access.js : add blockFeatureLimits auth.js : add getBlockFeatureLimits(). data/block.js : add taskGetLimits() (based on taskGetSummary), getLimits() (based on getSummary()), getBlocksLimits(). frontend/app/models/block.js : featuresDomain() : use featureLimits in place of featuresDomainUpdate (unrelated, minor changes : ) axis-chart.js : blockFeatures() : don't draw features of block if ! block.isChartable backend/ : b23efda 29139 Nov 20 16:03 common/models/block.js d24c4bd 4308 Nov 20 16:46 common/utilities/block-features.js 3c76613 3714 Nov 18 17:04 server/boot/access.js frontend/app/ : 8b91567 19916 Nov 20 09:46 components/axis-chart.js 51c1bb6 9609 Nov 20 16:22 models/block.js ffeb54f 4845 Nov 20 14:10 routes/mapview.js fd8002b 11164 Nov 18 17:04 services/auth.js ec97e07 25060 Nov 20 16:46 services/data/block.js
1. Dataset fetch task to dataset list is handled only on Mapview controller and passed down as required to child components. 2. Manage-explorer and Upload-data-csv no longer call fetch task again themselves. 3. Upload-data-csv Selectors populated in template rather than in controller.
view-controls.js : reduce initial pathSample : 1000 -> 400. models/block-adj.js : domainChange() : add ppDiff() : include pathsDensityParams in comparison. change taskGetPaths () from maxConcurrency(2).restartable() to drop() and simplify : drop the time calculations : now, lastStarted, elapsed, timeoutResult. paths-filter.js : pathInDomain() : dataLocation() : handle value being a CP. frontend/app/ : 801121d 27022 Nov 22 11:24 components/draw/block-adj.js eb2e049 5603 Nov 22 11:27 components/panel/view-controls.js db3730b 13788 Nov 21 19:33 models/block-adj.js a8d4efa 25254 Nov 21 19:48 services/data/paths-progressive.js 29f8a1b 5052 Nov 22 11:09 utils/draw/paths-filter.js
feature in returned path data is now converted from json data to a store reference so use .get() to access blockId if defined. this change applies in : path-data.js : add feature2BlockId(), and paths-progressive.js frontend/app/ : (Nov 22 16:22, applied from dev edit 04:26,41) 53b8457 4344 components/draw/path-data.js 041ff99 25336 services/data/paths-progressive.js
…se shared functionality vs json or csv upload-type specific
… feature/progressive
resetBrushes() : add > g[clip-path] to selector, since the d3 brush is on that not the parent g.brush. showResize() : heightChanged : set height of > clipPath > rect; add > g[clip-path] to selector for calling the brush. Drop use of maybeFlipExtent(..., a.flipped) for brush .extent(). frontend/app/ d8c3058 228940 Nov 26 19:22 components/draw-map.js e65031b 2501 Nov 26 19:04 utils/stacksLayout.js
Add getBrushedRegions(), axisBrushShowSelection(), 121eaf9 231387 Nov 27 14:48 frontend/app/components/draw-map.js
pathsAliases(): append a match to pipeline. e85005c 28698 Nov 28 16:56 backend/common/utilities/paths-aggr.js
frontend/app/ : a95d540 231765 Nov 28 18:10 components/draw-map.js 3c2b32d 26854 Nov 28 17:40 components/draw/axis-1d.js
This is used when e.g. flipRegion Add combinedId as id of circles. 7331caa 232505 Nov 28 19:49 frontend/app/components/draw-map.js
…for features which are not previously loaded goto-feature-list.js : blocksUnique() : handle changed form of input argument - was JSON result, now has ember store object references; data is no longer in subfield features.features; use .get() for .blockId, .id. block.js : add pushFeatureSearchResults() : convert feature / block / dataset data in JSON result into ember store object references. feature-lookup.js : storeFeature() : use cmNameAdd(); set oa.z[axisID] from chrData() draw-map.js : verification expression was inverted. frontend/app/ ef48d52 232505 Dec 2 12:36 components/draw-map.js 90f70fd 6012 Dec 2 15:29 components/goto-feature-list.js 82b2615 26444 Nov 29 15:39 services/data/block.js 5938ae5 5821 Dec 2 15:19 utils/feature-lookup.js
value-tree.js : leafCount() : handle valueType Dataset (possibly caused by test data). 6a99855 5260 Dec 3 14:48 frontend/app/utils/value-tree.js
add axisScaleEffect() and move renderTicksThrottle call into it, from zoomedAxis(). frontend/app/ : 8ebafb6 3614 Dec 3 15:53 components/draw/axis-ticks-selected.js 3ecdeab 73 Dec 3 16:01 templates/components/draw/axis-ticks-selected.hbs
… feature/progressive
Add reRenderLater(). 686d7c8 3937 Dec 3 19:40 frontend/app/components/draw/axis-ticks-selected.js
axis-1d.js : add scaleChanged(). block-adj.js : updatePathsPositionDebounce() : depend on axis1d scaleChanged in place of .axesDomains, i.e. after the domain changes the scale is updated then can draw; don't get dependency stacksWidthChanges because that causes multiple dependency updates in one render cycle. block.js : stacksCount() : depend on stacks.stacksCount in place of stacksAxes.size. stacks.js : Stack() move stacksCount.increment to after stack changes are complete (otherwise verify error etc). frontend/app/ : 2d09479 27237 Dec 4 14:10 components/draw/axis-1d.js 889fedf 26454 Dec 5 17:26 components/draw/block-adj.js 11e2137 26856 Dec 4 15:55 services/data/block.js c406f81 71563 Dec 4 16:14 utils/stacks.js
…upload failed leaving orphan record
stacks.js : Stacked : getDomain() : combine domainCalc result with blocksDomain. 4137d12 71747 Dec 5 18:29 frontend/app/utils/stacks.js (original edit on dev server : 621ca2e 71599 Dec 4 01:08, + comment)
… feature/progressive
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There are further commits coming to prepare this branch for merge.
(notes from discussion 2019Oct31 4:30pm ) :
use feature flags to disable features which are not ready :
dataset explorer : switch off 1 of the 2 genome tabs
alias paths result currently includes direct paths : check if this can easily be excluded in the mongo query; if not excluded it in the BE or FE whichever is easier.
feature search : check - there may be issues around the matched feature not being loaded due to progressive (partial) load. (Also the timing of setting block.isViewed).