Releases: cggh/panoptes
2.0.beta6
Sixth beta release of Panoptes 2.0
Features:
- #806 Add edit button to documentation to allow in-app editing of content by managers
- #720 Add new hover system to genome browser, highlighting current position in all channels
- #790
QueryResultcomponent for querying database for a value - #815 Multithreaded genotype retrieval using dask and zarr
- #163 Allow anonymous and authenticated users on the same dataset
- #816 Allow editing of YAML config from the UI, validating it before save
- #843 When navigating to a gene use the most recent
GenomeBrowser - #788 Add expanding section component
- #826 Upgrade to webpack 2 to reduce bundle size
- #36 Import tables from HDF5
- #829 Change
DataTableViewpaging to fixed page size - #615 Clicking a genotype hat opens variant
- #858 Add property description to genome browser sidebar
- #856,#811 Support GFFs with data one more level deep
Fixes:
- #864 Remove unneeded scrollbar on templates
- #865 Add italic Roboto font
- #861 Fix Genome browser channel close buttons sometimes not working
- #853 Only show
DataItemtabs if more than one tab - #850 Fix map layer toggles
- #848 Prevent layers aggregating in map layer control
- #736 Restore hover text on pivot tables
- #713 IE10 bugs
- #840 Prevent
Access Denieddue to new monetdb version - #832 Remove primary keys from map cluster hover text
- #828 Make CAS redirect dynamic based on dataset
- #823 "If" statement in handlebars should support child tables
- #821 Allow unicode in arraybuffer transfer
- #745 Allow import with out ref seq
- #813 Don't apply
LIMITbeforeSAMPLE - #803 Map histograms should be consistent
2.0.beta5
Fifth beta release of Panoptes 2.0
Features:
- #690 Sets of example genome channels can be saved and recalled
- #699 Group channels are now table specific
- #698 Colors of tracks can be picked
- #638 Sequence can be copied from ref seq channel
- #696 Add channels button at bottom of genome browser
- #712 Categorical channels can have queries, respect default query
- #616 Show info on hover over indicators on genome browser
- #716 Allow PopupButton to target new tab
- #743 Improve new popup placement
- #726 Add legend and pie charts to table map
- #47 (!) For map clusters based on a numerical, non-categorical property draw a histogram
- #727 Fetch data for tables in chunks
- #735 Expose controls for subsampling in plots and genotype rows
- #723 Make points display in numerical channels at fix point count excluding NULLs
- #625 Genotypes column header scrolls with genotypes
- #637 Reduce bundle size by half
- #679 Document expected browser compatibility
Fixes:
- #707, #709, #708 IE11 support
- #730,#640 Safari support
- #752, #722 Retina support
- #683 Firefox support
- #663 Clean up zoomed in view on numerical tracks
- #694 Fix showBar on tables
- #508 Clean up genotype controls
- #624 Genotypes don't go full width when zoomed in
- #705 Use channelColour in numerical tracks
- #711 Clean up categorical sidebar
- #728 Don't put commas in years
- #685 Standardise scroll speed across browsers
- #738 Don't line break in genome controls
- #750 Map loading indicator
- #737 Disable greyed out buttons
- #718 Remove config only reload
- #686 Prevent start page from being clobbered by links
- #760 Allow switching marker colour back to none
- #758 Show all showable columns in data tables
- #693 Remove deleted stored filters
- #763 Fix map popups
- #762 Fix map marker titles
- #770 Fix table data download
- #724 Fix flakey "zoom in" message
- #723 Make points display in numerical channels at fix point count excluding NULLs
- #719 Default to fixed scales on numerical tracks
- #774 Various map bugs
- #782 Allow disabling of subsampling
- #721 Disable animation of Y scale when summarisation window changes
- #780 Use correct lat/lng in table marker popup
- #781 Use correct map marker colours
- #779 Chrome clips map markers
- #791 Fix back button
- #744 Rename files to component name
- #796 Load map tiles from domain with https cert
- #798 Table markers load table with action sidebar
- #795 Change pie chart styling to better show corresponding map position
- #797 Show row count on all pie charts
2.0.beta4
Forth beta of Panoptes 2.0
Features:
- #534 - Tree nodes and branches can be coloured by column data
- #659 - Axis labels and titles for plots
- #509 - Download for genotype data
- #621 - Indicate query in genome browser indicator channel
- #630 - Browser track picker groups columns
- #666 - Show full chromosome when switching chromosome in browser
- #649 - Use a separate config file for the start page
- #613 - Add a colour legend to plots
- #612 - Add plot action to table side bar
Fixes:
- #678 - New tab should update title
- #662 - Use dataset colour scheme for plot points
- #665 - Annotation channel shows ID if no name for gene
- #664 - Show ID in gene component
- #622 - Make loading indicator transparent to clicks
- #648 - Don't cache docs pages
- #652 - Bring up correct data item when pie chart clicked
- #653 - Allocate colours in numerical genome tracks
- #651 - Prevent plotly stealing pointer events
- #610 - Stop sidebar sliding in on every tab change
- #626 - Give exons a minimum width so they don't disappear
- #623 - Use palette colours for genotypes
- #631 - Use header width to set deafult column width
- #635 - Fix uneditable numeric inputs
- #627 - Make gene seach case
- #617 - Remove position and chromosome from genome browser list
- #619 - Set genotypes sort from label
- #614 - Allow plot dimensions to be unset
2.0.beta3
Third beta release of Panoptes 2.0
Lots of polishing and fixing and performance improvements.
Features:
- #583 - Add click handling to genome channels
- #582 - Add click handling for genes in genome browser
- #584 - Default app state can be set by config and saved from app
- #569 - Add click handling for primary keys to related tables
- #591 - Make link button copy link
- #585 - Genome browser defaults to full chromosome
- #512 - Sort pivot table columns and rows
Fixes:
- #628 - Don't hang while drawing genotypes to offscreen buffer
- #620 - Genotypes should use default query
- #611 - Performance - Don't update all components on state change
- #605 - Genome browser is black in some browsers
- #510 - Make numeric input more usable
- #601 - Put recent genes on first tab
- #592 - Restore icons and titles
- #530 - Fix unmovable popups
- #589 - Fix 404 on favicon
- #501 - Make trees selectable in tree dropdown
- #578 - FIx map errors in ListView
- #579 - Fix find errors in ListView
- #574 - Fix errors in finder
- #586 - Fix Gene component error
- #580 - Prevent un-needed fetches in genome browser
- #522 - Preserve sort in downloaded data
- #500 - Fix add/remove on numeric track
- #523 - Stop accumulating layers on the map control
- #526 - Fix pie chart collision
2.0.beta2
Second beta release of Panoptes 2.0
Lots of polishing and fixing.
You will need to wipe $BASEDIR/monetdb before using this release.
Features:
- #507 - Query results are cached on the server and invalidated on import
- #482 - Sort tables by multiple columns
- #443 - Use default queries app-wide
- #506 - Subsampling
- #544 - Add inter-linked documentation pages
- #546 - Pivot table header supports valueColours
- #543 - Allow specific data values to display with custom content
- #536 - Cache data-derived config on import
Fixes:
- #529 - Graph points not coloured
- #557 - Dates not being handled correctly in queries and tables
- #556 - Cannot resize table columns
- #562 - Map performance issues
- #540 - Can't query for NULL values
- #552 - Boolean values shown as text when all are false and not handled properly in queries
- #495 - PieChartMap has lines when no data
- #511 - Search UI scrolls with picker columns
- #560 - Logo is missing
- #554 - Item picker column click causes error
- #538 - ListView error
- #515 - Simplify displayNames
- #532 - Genome browser has lost zoom limits
- #505 - Read distinct item values at import
2.0.beta1
First beta release of Panoptes 2.0
We're pleased to release the first beta of Panoptes 2.0. This release and the next few mainly focus on bug-fixing and polishing.
Features:
- #463 - The dataset can now be picked via the URL of the page
- #498 - Any component can now be placed in a template, and they can be arbitrarily nested
- #494 - Tile layers on maps can be transparent
- #513 - GeoTIFF and other raster data can be placed on maps (e.g. Malaria Atlas Project data)
Fixes:
2.0.alpha9
Final alpha release of the Panoptes 2.0 series.
We decided to have a final alpha release for the last major change in 2.0 - removing MySQL in favour of MonetDB (https://www.monetdb.org/Home). MonetDB is a column-store database more suited to the analytical workload of Panoptes. It allows summary tracks to be calculated on-demand, saving expensive pre-calculations at import-time and allows them to be dynamic parametrised. Several columns of a billion rows can be queried and summarised in seconds on a decent machine.
This release also sees signifcant improvements to maps.
Breaking changes:
- MonetDB needs to be installed, see http://panoptes.readthedocs.io/en/2.0.alpha9/manual_install.html
- Property dataTypes have changed to (Float | Double | Boolean | Int8 | Int16 | Int32 | GeoLatitude | GeoLongitude | Date)
- The following config keys have been removed: readData, maxLen, maxDecimDigits, canUpdate, connectLines, order, summaryValues, blockSizeMin, blockSizeMax, channelColor, maxDensity, refSequenceSumm, columnIndexField, autoScanProperties, browserTrackHeightFactor, genomeMaxViewportSizeX, allowSubSampling
Features:
- #482 - MonetDB and associated work:
- Remove MySQL, replacing with MonetDB
- Change column DataTypes
- New arraybuffer based query method with support for SQL aggregations
- Remove all import-time summarising
- Import reference sequence as a table
- Import reference data as a table
- Rewrite genome tracks to use new query method and dynamic summarising
- Switch genome browser to canvas as it make more sense with the arraybuffer data.
- #487 - Export template code from a map
- #486 - Allow selection of map tiles in maps
Fixes:
- #395 - Reference sequence channel error
- #490 - Pivot table errors when column is same prop as row
- #480 - Remove unneeded server-side routines
- #485 - Fix map highlighting
- #476 - Performance regression in genome browser
Known issues:
- Trees cannot be accessed.
- Per-row summaries are not bought over to monet
- Chromsome switching in genome browser causes error
2.0.alpha8
Eighth alpha release of the Panoptes 2.0 series.
This release adds genotypes and flexible maps, completing the the major components. We expect to move to beta for the next release.
Breaking changes:
Reference summaries are now only supported in the "combined" format. This is in preparation for them to become full tables at a later date.
This release includes:
Features:
- #384 - Genotypes channel, with new drawing technique ~20x faster than 1.6.2.
- #430 - Leaflet based maps, supports flexible map creation in templates and raster layers such as prevalence data
- #454 - Reinstate ref genome summaries, supporting only the combined data format
Fixes:
None, feature-focused release.
Known issues:
Trees cannot be accessed.
2.0.alpha7
Seventh alpha release of the Panoptes 2.0 series.
This release introduces pivot tables - a way of summarising data tables.
Work on maps and genotypes are progressing well but are not ready to merge till next release.
Breaking changes:
Queries are no longer base64 encoded except on the wire - allowing them to be edited in config and specified in templates.
This release includes:
Features:
- #456 - Prototype Pivot table
- #379 - Warn if screen too small
- #464 - Only encode queries on the wire
- #438 - Key handling in Query Picker
- #462 - Auto set API endpoint
- #471 - Allow remote development
Fixes:
2.0.alpha6
Sixth alpha release of the Panoptes 2.0 series.
This release features a large-scale refactoring of how an instance is configured. This allows deployment managers and users to change settings on the fly from the application, such as text, colours, stored queries and views. Previously such operations required editing the files on disk, then re-importing the dataset.
Breaking changes:
The config specification has changed - a migration tool is at https://github.com/cggh/panoptes/blob/2.0.alpha6/scripts/migrate-settings.py
This release includes:
Features:
- #447 - Instead of storing instance config in MYSQL, serve a JSON config object that closely reflects the YAML on disk.
- #452 - Allow arbitrary editing of the JSON config, which is persisted to the YAML.
- #442 - Popup sizing and positioning is responsive to window size
- #441 - Query edit buttons are "add filter" if current filter is "all"
Fixes: