File Changes for angie

v378_base to v379_preview (2019-02-25 to 2019-03-04) v379

• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 11, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 6, context: html, text, full: html, text
    be389dc72daedc439d8a00cf2b09acfa8d41c38d Wed Feb 27 14:24:12 2019 -0800
    Yikes, hgIntegrator was not setting up udc! htslib was using its own network code.
  • lines changed 2, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 61, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgTracks/extTools.c
  • lines changed 2, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgTracks/hgTracks.c
  • lines changed 73, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 30, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgVai/libifyMe.c
  • lines changed 55, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/hgVai/libifyMe.h
  • lines changed 11, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 59, context: html, text, full: html, text
    585ec51f88290d195b72e671bd30d55aace3bc70 Tue Feb 26 09:53:55 2019 -0800
    Reworded ncbiRefSeq section. Also updated TOC and uppercased GENCODE. refs #22970
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 4, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/inc/hgFind.h
  • lines changed 17, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/lib/cart.c
  • lines changed 19, context: html, text, full: html, text
    4ccf33da61239996702db7af0d93018806b2d38e Fri Feb 22 14:04:22 2019 -0800
    lastPosition is set by cartHtmlShell* -- but not by other cart openers e.g. cartAndCookie or cartEmptyShell. CGIs that use the latter must set lastPosition after determining db and position. refs #22945
  • lines changed 30, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
  • lines changed 4, context: html, text, full: html, text
    0283f0d3e96fe85f11241197f477611680c01186 Mon Mar 4 09:58:59 2019 -0800
    cartWebStart adds a hidden <input> to set db on every page. However, some CGIs pass in NULL for db, so db is set to '(null)'. Don't make the <input> unless a value is passed in.
• src/hg/lib/hgFind.c
  • lines changed 233, context: html, text, full: html, text
    4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5 Fri Feb 15 14:02:58 2019 -0800
    Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945 hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results). In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards. Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter. The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    3f661bcfef779274a734a4d31637c0df55a48102 Wed Feb 27 16:28:06 2019 -0800
    Only hgVai uses webStart() and does not need the old logo .jpg, so call webStartWrapper withLogo=FALSE. sorta refs #22945
• src/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    49a9e46f48bc7872a655527694e027e51aa46f38 Wed Feb 27 12:19:38 2019 -0800
    Oops, forgot to check for NULL in a corner case: VCF file has records only in chromosomes preceding the query region chrom.
• src/lib/cheapcgi.c
  • lines changed 2, context: html, text, full: html, text
    6ad610566091450adc69bf9f321ac57f38a3d9d2 Wed Feb 27 12:18:03 2019 -0800
    Add more info to 'Short POST input' error message.
  • lines changed 2, context: html, text, full: html, text
    0714ad987fb4018da001e4ec75a9288207f902cf Fri Mar 1 14:14:45 2019 -0800
    Revert "When hgTables gets multiple search results, hgFind calls webEnd and then hgTables needs to do cartWebEnd, so jsInlineFinish is called twice. Until the webStart/webEnd can be factored out of hgFind.c, prevent the jsInlineFinish warning from bothering the user. refs #22945" webStart/webEnd has been factored out of hgFind, so hgTables can open and close the page cleanly and there's no warning to hide from the user. This reverts commit ee3659b05d0af22a52207792b8deaf836a727fe5.