v387

Code changes:

• Added style for pressed buttons on hgTracks for multi-region, reverse modes (#23922). Kate
• Various improvements to blatServersCheck including continuing checking other servers after a connection failure, and reporting obsolete entries and mismatches between targetDb.seqFile and gfServer filename. Galt
• hubCheck reports multiWigs with only one subtrack (#13428). ChrisL
• Ongoing hubCheck user interface work (#18870). ChrisL
• Fix broken hgGene/hgc links to MuPIT (#22953). ChrisL
• Ongoing work for multi-region link on interact track details page (#24037). Kate
• Blat / patch support: generate altsAndFixes file for blat's new -perSeqMax arg (#23112). Angie
• Jim has been doing work to import data from GEO into the HCA metadata format, which is an excel spreadsheet with up to 500 fields and 27 tabs. He has stood up a relational database, called hcat for HCA Tracker, and wrapped a Django based web site around it, completing all the work in such a way as to make as many of the components reusable in other projects:
  • Strex - a string expression language. Please see src/lib/strex.doc for info on how to use it.
  • tabToTabDir - Convert a giant table to a bunch of smaller normalized tables. You can map fields straight up or use strex to split apart overloaded ones. Tables are all in tsv format.
  • geoToTagStorm - polished it a bit, moving the sample.characteristics_* family of fields to lab.* instead. This is the bit where the user is able to add their own tag/value pairs past the ones GEO has defined.
  • hcatTabUpdate - this is HCA specific, it converts the import started by geoToTagStorm, and put through a few other simple already existing steps into something we can patch the hcat relational database with in the next tool.
  • sqlUpdateRelated - this takes as input tab separated files that may include foreign key and multiple-multiple relationship fields, and adds them to the database making sure all these exotic fields are handled right. Also is set up so that it can only add a record if it doesn't already exist.
  • Django python which lives in kent/src/hca/hcat/mysite
• Fix a problem in hgConvert that made it think inactive db's were perfect for conversions. Brian
• Moved bottleneck server check to the very beginning of hgTracks and hgRenderTracks before any SQL activity (#23217). Hiram
• Added bottleneck penalty for each custom track loaded via customText URL (#23217). Hiram

Data changes: