Commits for angie

74720ae3a83557093fcf0373528b24ad1d96f932 Tue Nov 14 11:33:38 2017 -0800

hgTablesTest's countNoncommentLines was skipping blank lines which caused it to get the wrong row count when querying a field that is sometimes empty. skipLeadingSpaces skips '\n' due to isspace; check for '\n' before calling it. refs #20534
- src/hg/hgTablesTest/hgTablesTest.c - lines changed 7, context: html, text, full: html, text

ee4177fbf667f2eafeba46e4352075cf93e36983 Wed Nov 15 14:37:14 2017 -0800

Using Braney's unicode em-/en-dash replacement trick in react TextInput module. refs #20517
- src/hg/js/react/lib/TextInput.jsx - lines changed 1, context: html, text, full: html, text

b9dffc597ef24b8fe28b4f1104f85d6016ef9446 Fri Nov 17 09:34:29 2017 -0800

Updated dbNcbiRefSeq.pl to extract genomic "rna" sequence if NCBI doesn't provide rna sequence for genes on chrM. (For human and mouse, NCBI provides only protein accessions in the GFF3.) Re-ran on hg38 and mm10. refs #18997 notes 84-88, 90-92, 96-102
- src/hg/makeDb/doc/hg38/ncbiRefSeq.txt - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/doc/mm10.txt - lines changed 6, context: html, text, full: html, text
- src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 19, context: html, text, full: html, text

06a011cb7b2170db0747a30281c2ee972286c220 Fri Nov 17 10:49:20 2017 -0800

Fixed search specs for ncbiRefSeqCurated and ncbiRefSeqPredicted and moved them into refSeqComposite.ra. refs #18997 note 108
- src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 16, context: html, text, full: html, text

29e1c55f50ef906b4d553446ae1f1b42d10fe92e Fri Nov 17 12:06:30 2017 -0800

Bring ncbiRefSeq name2 and protAcc searches up from human/hg38/trackDb.ra to top-level refSeqComposite.ra and add search on product. hgFind's formatting of results is not as nice as for refGene, but at least searching works. refs #18997
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 74, context: html, text, full: html, text
- src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 56, context: html, text, full: html, text

b56aaf37a70d531c514f7ba88f3c6a73888b527e Mon Nov 20 11:59:22 2017 -0800

hgTracks/simpleTracks.c's lookupRefNames ignores subtrack-level label settings, so don't display the refGene label settings when it's a subtrack. Also fixed up omim-detection logic for ncbiRefSeqLink. refs #19318
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 21, context: html, text, full: html, text

be368a5841d9104cd9957cdb8325ae5d4ed25456 Tue Nov 21 10:26:45 2017 -0800

tdbQuery was ignoring databases that did not have their own trackDb.ra file, in order to exclude non-assembly subdirs like cv/* and human/encodeTest. Since legit assemblies always have a description.html file, make it accept subdirs that have a description.html file even if they don't have a trackDb.ra.
- src/hg/utils/tdbQuery/tdbQuery.c - lines changed 4, context: html, text, full: html, text

19e706ca643a4229087fb53d97e40dc165afc9df Wed Nov 22 16:43:28 2017 -0800

Added dataVersion (from file) setting to refSeqComposite for all subtracks but refGene since that's updated by the genbank process. This setting will be ignored by v357 code because it uses hgFixed.trackVersion preferentially. I'm going to change it to prefer dataVersion, because dataVersion with a file is much easier to push out to hgwbeta and RR than rows of the hgFixed.trackVersion table. refs #18997 note 141
- src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 2, context: html, text, full: html, text

45b4b52a4727e9aeedabcd39e011d4408f35b7e8 Wed Nov 22 16:48:32 2017 -0800

In printDataVersion, instead of preferring hgFixed.trackVersion to trackDb setting dataVersion, prefer dataVersion because it is easier to manage pushes with a dataVersion file vs. with rows of the trackVersion table. refs #18997 note-141
- src/hg/lib/hui.c - lines changed 39, context: html, text, full: html, text

6adb58474d7cf1e4669c788e417a4e28a8c20a06 Wed Nov 22 16:50:02 2017 -0800

Store version in a file /gbdb/<db>/ncbiRefSeq/ncbiRefSeqVersion.txt instead of inserting a row into hgFixed.trackVersion -- easier to manage pushes. refs #18997 note-141
- src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 19, context: html, text, full: html, text