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