File Changes for angie

v313_preview2 to v313_base (2015-03-02 to 2015-03-09) v313

• src/hg/hgAi/hgAi.c
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
  • lines changed 15, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 39, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 18, context: html, text, full: html, text
    Added a link to chrom.sizes file (on hgdownload) at the end of the sequence size table on the chromInfo page.
    refs #14870
    
• src/hg/inc/cartJson.h
  • lines changed 3, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 15, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/external/lodash.2.4.1.compat.min.js
  • lines changed 61, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/js/external/lodash.3.3.1.compat.min.js
  • lines changed 91, context: html, text, full: html, text
    Updating lodash library to latest version.
    
• src/hg/js/external/makefile
  • lines changed 1, context: html, text, full: html, text
    Updating lodash library to latest version.
    
  • lines changed 1, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/js/install.mk
  • lines changed 1, context: html, text, full: html, text
    Make output less verbose
    
• src/hg/js/model/hgAi/hgAiModel.js
  • lines changed 431, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 21, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
  • lines changed 15, context: html, text, full: html, text
    Don't fetch the top 2 levels of groupedTrackDb after all because the
    partial groupedTrackDb was causing subtrack dataSources to be pruned
    because they weren't found there. It made things a little jumpy anyway.
    refs #14579
    
  • lines changed 10, context: html, text, full: html, text
    Since groupedTrackDb is so large for hg19, it can actually arrive after
    the user has already switched to a different database and received the
    groupTrackDb for the new database. Prevent clobbering by including the
    database to which this particular groupedTrackDb belongs.
    
• src/hg/js/model/lib/CladeOrgDbMixin.js
  • lines changed 9, context: html, text, full: html, text
    Use _.capitalize instead of writing own; use _.last instead of pop so we don't mutate path.
    
  • lines changed 4, context: html, text, full: html, text
    oops! CladeOrgDbMixin.js had a little out-of-place, no-op code.
    
  • lines changed 141, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/model/lib/ImModel.js
  • lines changed 6, context: html, text, full: html, text
    Make sure that the handler function passed into register* is really a function.
    
  • lines changed 1, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/model/lib/PositionSearchMixin.js
  • lines changed 1, context: html, text, full: html, text
    oops! CladeOrgDbMixin.js had a little out-of-place, no-op code.
    
  • lines changed 7, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 232, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
• src/hg/js/react/lib/LabeledSelect.jsx
  • lines changed 4, context: html, text, full: html, text
    Added support for disabling an option.
    
• src/hg/js/react/react.mk
  • lines changed 3, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/js/subdirs.mk
  • lines changed 5, context: html, text, full: html, text
    Added recursive jshint target to all subdirs.
    
• src/hg/lib/cartJson.c
  • lines changed 163, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
  • lines changed 159, context: html, text, full: html, text
    Moved the smarts about changing clade/org/db out of cartJson.c & hgAi.c and
    into CladeOrgDbMixin.js & hgAiModel.js. Now the CGI sends the full tree of
    clades, genomes and dbs, and the model instantaneously updates when the user
    changes clade, org or db, and tells the CGI exactly what info it needs instead
    of relying on the CGI to send a special mix.
    refs #14579
    
  • lines changed 6, context: html, text, full: html, text
    Since groupedTrackDb is so large for hg19, it can actually arrive after
    the user has already switched to a different database and received the
    groupTrackDb for the new database. Prevent clobbering by including the
    database to which this particular groupedTrackDb belongs.
    
• src/inc/jsonWrite.h
  • lines changed 3, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).
    
• src/lib/jsonWrite.c
  • lines changed 8, context: html, text, full: html, text
    Several major changes in the way data sources are represented:
    1. Instead of the CGI sending menus for group, track and table, make it send
    the whole tree of groups, tracks, views, subtracks -- "groupedTrackDb".
    Now the client-side model can make menus that reflect the tree structure.
    This also gives us flexibility to tweak labels easily.
    2. Instead of hardcoding group, track and table into elements of
    hgai_querySpec.dataSources, make each data source a proper object with
    a trackPath (path through groupedTrackDb), and for the UI, other attributes
    like label and URL for hgTables schema page. When the CGI unpacks
    hgai_querySpec.dataSources, it now uses trackPath and gets table from the
    leaf track or subtrack (the last item in trackPath).
    Note: this doesn't work for old Conservation tracks that don't have
    views/subtracks -- need to figure out how to fudge subtracks for those.
    3. Limit the number of data sources to 5, don't let the user add the same
    data source twice, and remember which track the user most recently selected
    in the "Add Data Source" section.
    Also, in hgAi.jsx, I separated out a bunch of things that were rendered in
    the top-level AppComponent into subcomponents to add some granularity to
    "Loading..." sections (instead of making the whole page saying "Loading..."
    until everything is in place).