File Changes for max

v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297

• src/hg/hgBlat/hgBlat.c
  • lines changed 13, context: html, text, full: html, text
    fixing hgBlat not working in browserbox if hg19.2bit does not exist,refs #11957
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/hgGene/rnaStructure.c
  • lines changed 26, context: html, text, full: html, text
    Fixing RNAplot problem with newer versions, refs #11957, note 178 andrefs #6382
    
• src/hg/hgMirror/hgMirror
  • lines changed 12, context: html, text, full: html, text
    adding basic security of CGI parameters to hgMirror
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 8, context: html, text, full: html, text
    changing documentation to reflect previous code commit
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 16, context: html, text, full: html, text
    better gbib help file, refs #11957
• src/hg/inc/cgiApoptosis.h
  • lines changed 19, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/inc/customTrack.h
  • lines changed 8, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 3, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 12, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
  • lines changed 4, context: html, text, full: html, text
    woke up at night and suddenly remembered that url string should be on the stack,not on the heap.
    
• src/hg/lib/cgiApoptosis.c
  • lines changed 130, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/customPp.c
  • lines changed 31, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/lib/customTrack.c
  • lines changed 24, context: html, text, full: html, text
    Adding possibility to paste URLs of bam/bigWig/bigbed, without acustom track header line, into the hgCustom upload box (refs #12813)
    
• src/hg/lib/hdb.c
  • lines changed 8, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
  • lines changed 16, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/hg/lib/jksql.c
  • lines changed 165, context: html, text, full: html, text
    browserbox changes: In refs #11957, refs #12524 and refs #12615, it wasnoted that a jksql connection can move from a db that is present only
    remotely to a db that is present again locally (main) and remotely
    (slow). QA found that this happens in the table browser. Moving existing
    code into sqlUnconnectedConn and sqlMustUseFailover. This simplifies
    sqlChangeDb, which has now two clear codepaths browserbox versus normal
    site. Also handling the case that a DB is only remote upon connect. In
    this case do connect, but with a NULL db (mysql accepts that).
    Because we accept remote-only DBs now, not enforcing a table cache anymore.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/web.c
  • lines changed 10, context: html, text, full: html, text
    fixing crash at first startup of new mirror by phoneHome, refs #148
  • lines changed 137, context: html, text, full: html, text
    moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
    cgiApoptosisSetup (originally: phoneHome) will be called after mysql
    connections are opened. This leads to "mysql server has gone away" if
    any CGI is not faster than the child process forked here. The child will
    close all mysql connections of the parent process. With the new setup,
    the childi is forked before any mysql connections are opened. Ideally
    this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
    part of the code.
    
• src/hg/lib/wikiLink.c
  • lines changed 8, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957
    
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    Fixing RNAplot problem with newer versions, refs #11957, note 178 andrefs #6382
    
  • lines changed 6, context: html, text, full: html, text
    Allow special value HTTPHOST for central.domain and wiki.host, so aserver can be reached under multiple names. Might be a good default
    value for our example hg.conf? refs #11957