File Changes for angie

v332_preview to v332_preview2 (2016-04-18 to 2016-05-25) v332

• src/hg/hgGateway/hgGateway.c
  • lines changed 32, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 4, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/dbDbTaxonomy.hgwdev.js
  • lines changed 1087, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/dbDbTaxonomy.js
  • lines changed 1089, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/dbDbTaxonomy.rr.js
  • lines changed 530, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/hgGateway.js
  • lines changed 60, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/hg/lib/cartJson.c
  • lines changed 13, context: html, text, full: html, text
    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/hg/makeDb/doc/dbDbTaxonomy.txt
  • lines changed 60, context: html, text, full: html, text
    915f56e3f34f66d58bf6573dc4dfddd068bd4090 Tue Apr 19 13:36:48 2016 -0700
    Simplify the generation of hgGateway's dbDbTaxonomy tree info and support mirrors better: new hg.conf setting hgGateway.dbDbTaxonomy enables tree display and specifies relative URL to file. Instead of dbDbTaxonomy.{hgwdev,rr}.js, there is only one dbDbTaxonomy.js, built from hgcentraltest (hgwdev). hgGateway.c's HTML output includes JS encoding the set of active genomes+taxIds. hgGateway.js uses that to prune the tree so it contains only active genomes; now we can use the hgwdev tree on the RR and see only RR species. Also updated dbDbTaxonomy.js to get the latest hgwdev species as of 4/18/16.
    refs #15277
    
• src/inc/jsonWrite.h
  • lines changed 13, context: html, text, full: html, text
    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/lib/asParse.c
  • lines changed 2, context: html, text, full: html, text
    1e6566439ca544eb838a2247ade0dd2d08c6b762 Wed Apr 20 09:54:01 2016 -0700
    Adding special case to asTypeNameFromSqlType: sometimes a field is declared as string in .as but then in .sql it's changed to date (e.g. gbCdnaInfo.moddate), so treat sql type date as string.
    
• src/lib/jsonWrite.c
  • lines changed 32, context: html, text, full: html, text
    a4311d22ec503f936c0b624c13b1349c590a01ea Wed Apr 20 12:01:26 2016 -0700
    Added an errCatch to cartJsonExecute so that instead of returning invalid JSON where there's an errAbort, we can close out the JSON-in-progress (if any) and add an error message to the JSON response -- then the user will at least see the error message instead of a parser error alert. This required extending jsonWrite's objStack so that in addition to tracking whether a comma is needed, it now tracks whether each stack item is an object or a list. Then, when necessary we can tell jsonWrite to pop up to a certain level (in this case, level 1 so we can include an error string in the response object) by closing out any lists or objects that are deeper than that level. The new flag also allows us to test for errors like ending a list when we need to end an object or vice versa.
    
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    30056ddd2a71593a731606f5c6bb81b17965b717 Wed Apr 20 09:35:59 2016 -0700
    Adding documentation of new setting hgGateway.dbDbTaxonomy to src/product/ex.hg.conf, should have been part of 915f56e3f. refs #15277