Commits for angie
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v331_base to v332_preview (2016-04-11 to 2016-04-18) v332
- Changed background color to transparent (alpha) so that this will take on the background color of its container.
- src/hg/htdocs/images/homeIconSprite.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
in our dbDb tables for years, just not in these files.
- Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt.
Also added hTaxId() for looking up a db's taxId.
- src/hg/visiGene/hgVisiGene/printCaption.c - lines changed 1, context: html, text, full: html, text
- src/hg/visiGene/hgVisiGene/probePage.c - lines changed 1, context: html, text, full: html, text
- Extended jquery-ui's autocomplete by adding new options enterSelectsIdentical and enterTerm,
so that when the user hits Enter in the text input, instead of ignoring it we can select a
menu item whose value is equal to the term and/or invoke a callback (enterTerm) so the app
can react to the Enter key in its own way. There are only additions to jquery-ui's code,
no changes to existing behavior unless the new options are passed in.
- src/hg/js/jquery-ui.js - lines changed 31, context: html, text, full: html, text
- Typo fix in comments.
- src/hg/js/model/lib/cart.js - lines changed 2, context: html, text, full: html, text
- Added a flag, set by cart.debug(true/false), to turn on and off the
console.log messages.
- src/hg/js/model/lib/cart.js - lines changed 18, context: html, text, full: html, text
- Adding a NULL check before using oldVars.
- Unifying some triplicate code to print an HTTP error 400 response (Bad Request) and exit.
- src/hg/encode/hgEncodeApi/hgEncodeApi.c - lines changed 3, context: html, text, full: html, text
- src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c - lines changed 16, context: html, text, full: html, text
- src/hg/hgGtexApi/hgGtexApi.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgSuggest/hgSuggest.c - lines changed 11, context: html, text, full: html, text
- Adding a third search mode to trixSearch(), for less stringent searches such as autocomplete.
The first two modes were previously designated by a boolean expand -- now there is an enum
trixSearchMode whose first two values correspond to that (expand==FALSE = tsmExact,
expand==TRUE = tsmExpand). The third mode, tsmFirstFive, returns matches of five or more
characters even if there are many characters left in a long word. For example, "arabi" will
match "arabidopsis" in tsmFirstFive mode, but not in tsmExpand mode because that leaves six
unmatched letters after "arabi".
- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgFileSearch/hgFileSearch.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/lib/bigBedFind.c - lines changed 1, context: html, text, full: html, text
- src/hg/visiGene/hgVisiGene/fullTextExperiment.c - lines changed 1, context: html, text, full: html, text
- src/hg/visiGene/hgVisiGene/visiSearch.c - lines changed 1, context: html, text, full: html, text
- src/index/trixSearch/trixSearch.c - lines changed 1, context: html, text, full: html, text
- Adding dbDbTaxonomy.pl along with makeDb/doc instructions for generating/updating two new JS files that contain phylogenetic trees for hgwdev's and rr's species.
dbDbTaxonomy.pl uses taxIds extracted from hgcentral(test) to build a phylogenetic tree using NCBI Taxonomy database dump files.
It finds ancestors of the hgcentral species' taxIds to build a tree, and adds node names to ancestor nodes.
It assigns priorities to nodes based on a list of 'favored species' in the order we'd like to see them listed when the tree is traversed.
Then it dumps out Javascript encoding the tree as recursive Arrays. The JS output can be included as a script in HTML.
refs #15277
- src/hg/js/dbDbTaxonomy.hgwdev.js - lines changed 1087, context: html, text, full: html, text
- src/hg/js/dbDbTaxonomy.rr.js - lines changed 530, context: html, text, full: html, text
- src/hg/makeDb/doc/dbDbTaxonomy.txt - lines changed 99, context: html, text, full: html, text
- src/hg/utils/dbDbTaxonomy.pl - lines changed 360, context: html, text, full: html, text
- Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
It has icons for selecting popular species, an autocomplete input for typing in species or common names,
as well as a phylogenetic tree display that shows the relationships of the species that we host.
It has a menu for selecting the assembly of the selected species' genome and the usual assembly
description.
refs #15277
- src/hg/hgChooseDb/hgChooseDb.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgGateway/hgGateway.c - lines changed 769, context: html, text, full: html, text
- src/hg/hgGateway/hgGateway.html - lines changed 249, context: html, text, full: html, text
- src/hg/hgGateway/makefile - lines changed 11, context: html, text, full: html, text
- src/hg/htdocs/images/jWestIcons55px.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/jWestIconsAlpha65px.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/ucscHelixLogo.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/ucscLogo.svg - lines changed 3, context: html, text, full: html, text
- src/hg/htdocs/inc/jWestFooter.html - lines changed 52, context: html, text, full: html, text
- src/hg/htdocs/style/jWest.afterNiceMenu.css - lines changed 19, context: html, text, full: html, text
- src/hg/htdocs/style/jWest.css - lines changed 418, context: html, text, full: html, text
- src/hg/htdocs/style/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/inc/hubConnect.h - lines changed 13, context: html, text, full: html, text
- src/hg/js/hgGateway.js - lines changed 1537, context: html, text, full: html, text
- src/hg/lib/hubConnect.c - lines changed 49, context: html, text, full: html, text
- src/hg/lib/jWestBanner.html - lines changed 32, context: html, text, full: html, text
- Added support for removal of duplicate items from species autocomplete results.
refs #15277 (see note 142)
- src/hg/js/hgGateway.js - lines changed 49, context: html, text, full: html, text
- Change the label above the popular species icons from "MODEL SPECIES" to "POPULAR SPECIES". refs #15277
- src/hg/hgGateway/hgGateway.html - lines changed 1, context: html, text, full: html, text
- Refactored autocompleteCat options so that species autocomplete can do even more customized post-processing of results from server (insert phylo tree matches between dbDb matches and assembly hub matches). refs #15277
- src/hg/js/hgGateway.js - lines changed 104, context: html, text, full: html, text
- Species autocomplete fixes: make sure 'grch37' properly selects hg19 and make it appear before genome matches. Make genome matches appear before sciName matches. If user types hg19 and hits enter, don't mismatch on some bogus labelly value. refs #15277
- src/hg/hgGateway/hgGateway.c - lines changed 10, context: html, text, full: html, text
- Removed some code that separated assembly descriptions into 3 divs, with the middle div containing a list of links to sections in the bottom div. refs #15277
- src/hg/hgGateway/hgGateway.html - lines changed 6, context: html, text, full: html, text
- src/hg/js/hgGateway.js - lines changed 81, context: html, text, full: html, text
- Added topAlpha target for installation of top-level *.js files only.
- Keep forcing hgwdev-demo6 to use dbDbTaxonomy.rr.js (phylo tree of RR species) for testing, but use dbDbTaxonomy.hgwdev.js on other hgwdev* hosts. refs #15277
- src/hg/hgGateway/hgGateway.c - lines changed 3, context: html, text, full: html, text
- Updating icon genome and placement for dbDbTaxonomy.hgwdev.js. refs #15277
- Yikes, the new hgGateway was showing inactive dbs. refs #15277
- src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text
- Split the search refSeqComposite into two searches: refSeqCompositeAccession for short-circuit matching of NM_ and similar accessions, and refSeqCompositeName for matching gene symbols that also appear in ncbiRefSeq.name. Better to use semiShortCircuit instead of shortCircuit in general.
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 14, context: html, text, full: html, text
- Fixing buffer overflow caused by one of Hiram's hub genomes, hub_1642_GCF_000721765.1_Aureobasidium_pullulans_var._namibiae_CBS_147.97_v1.0 :)
- src/hg/lib/customTrack.c - lines changed 1, context: html, text, full: html, text
- Use hubConnectStatusListFromCart instead of hubConnectStatusListFromCartAll, which connects to hubs even if they're set to 0 (not connected) in cart.
- src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text
- Hide the Find Position section contents until they're filled in, so we don't see empty containers jumping around. refs #15277 sorta
- src/hg/hgGateway/hgGateway.html - lines changed 2, context: html, text, full: html, text
- jwSectionTitle wasn't extending quite all the way to the edge as intended. refs #15277 note 148
- src/hg/htdocs/style/jWest.css - lines changed 1, context: html, text, full: html, text
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