All File Changes
v334_preview to v334_preview2 (2016-05-31 to 2016-06-06) v334
Show details
- confs/preview.hg.conf
- lines changed 3, context: html, text, full: html, text
aa29b5728d85c55af86c16c4c6e651f140f9e4b5 Sun Jun 5 01:12:11 2016 -0700
Installing updated hg.conf files from UCSC servers
- confs/rr.hg.conf
- lines changed 3, context: html, text, full: html, text
aa29b5728d85c55af86c16c4c6e651f140f9e4b5 Sun Jun 5 01:12:11 2016 -0700
Installing updated hg.conf files from UCSC servers
- src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
- lines changed 3, context: html, text, full: html, text
918c8c17c4811996d019243a1e427d864f447328 Thu Jun 2 10:10:56 2016 -0700
fixing missing file extension when using cdwGetFile?acc=XXX
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki.htm
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load.css
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_002.css
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_002.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_003.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_004.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_005.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_006.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/load_007.php
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/Manifest file - Encode-DCC Wiki_comhaid/poweredby_mediawiki_88x31.png
- lines changed 0, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/encode3/validateManifest/oldWiki_Manifest_file.txt
- lines changed 40, context: html, text, full: html, text
ab0b882b0a5ed4a9d45961ae3ea257c6401901e5 Fri Jun 3 11:56:07 2016 -0700
adding the old wiki page about the manifest in case it disappears.
- src/hg/hgGateway/hgGateway.c
- lines changed 1, context: html, text, full: html, text
48a35fc7fbfa14fe49509ec90faf8753b584b9bc Mon Jun 6 10:00:12 2016 -0700
Enable phylogenetic tree by default so mirrors don't have to go out of their way to get it, at least for genomes that they're mirroring from us. refs #17316
- src/hg/hgIntegrator/hgIntegrator.c
- lines changed 178, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgPublicSessions/hgPublicSessions.c
- lines changed 22, context: html, text, full: html, text
7f2c71980d90f22204d7aa2ca39cc09eaaf47d97 Fri Jun 3 19:20:38 2016 -0700
Added session details button, plus code review changes refs #15312, #17439
- src/hg/hgSession/hgSession.c
- lines changed 348, context: html, text, full: html, text
7f2c71980d90f22204d7aa2ca39cc09eaaf47d97 Fri Jun 3 19:20:38 2016 -0700
Added session details button, plus code review changes refs #15312, #17439
- src/hg/hgSession/hgSession.h
- lines changed 1, context: html, text, full: html, text
7f2c71980d90f22204d7aa2ca39cc09eaaf47d97 Fri Jun 3 19:20:38 2016 -0700
Added session details button, plus code review changes refs #15312, #17439
- src/hg/hgTables/correlate.c
- lines changed 20, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/filterFields.c
- lines changed 26, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/hgTables.c
- lines changed 17, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/hgTables.h
- lines changed 13, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/intersect.c
- lines changed 5, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/mainPage.c
- lines changed 70, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/pal.c
- lines changed 1, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTables/schema.c
- lines changed 4, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/hgTracks/bedTrack.c
- lines changed 1, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/hg/hgTracks/longRangeTrack.c
- lines changed 4, context: html, text, full: html, text
b3660684338a45c565fb79c89a72479941b7b2bd Thu Jun 2 14:31:26 2016 -0700
some tweaks to longRange support #15232
- src/hg/hgTracks/simpleTracks.c
- lines changed 2, context: html, text, full: html, text
e9850e19c91eb247cec5ab3204b2ac000dcbecaf Wed Jun 1 09:42:35 2016 -0700
Don't load oreganno info when track isn't on; it hurts the RR, refs #17278
- lines changed 2, context: html, text, full: html, text
052ade22f38b6c1d1bc9fd943a00e63cb6f24dc3 Wed Jun 1 11:05:45 2016 -0700
Removing extraneous hgcentral connection, refs #17278
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- lines changed 16, context: html, text, full: html, text
b3660684338a45c565fb79c89a72479941b7b2bd Thu Jun 2 14:31:26 2016 -0700
some tweaks to longRange support #15232
- lines changed 10, context: html, text, full: html, text
42aede31678764a07bac578f3a810685b7c9340e Thu Jun 2 15:00:11 2016 -0700
more tweaks to the longRange hgc page
- src/hg/htdocs/goldenPath/help/hgSessionHelp.html
- lines changed 6, context: html, text, full: html, text
e340e89030b958cee1255703438a679ea773cdce Fri Jun 3 10:39:46 2016 -0700
Updating policy regarding custom tracks in saved sessions, refs #14724
- src/hg/htdocs/goldenPath/help/sessions.html
- lines changed 33, context: html, text, full: html, text
d0cb21a3024311b2ca11fc827a58d3a3014a83ac Fri Jun 3 15:38:11 2016 -0700
added HR tags between sessions and expanded the explanation associated with the first two
- lines changed 13, context: html, text, full: html, text
5310554ddf9e3f1caa4df9171c110f01b662470e Fri Jun 3 17:06:04 2016 -0700
moved the link to hg38 inside the paragrpah where it belongs
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 28, context: html, text, full: html, text
29d8156c530a7b28618003d89a090c99af49751e Wed Jun 1 15:58:31 2016 -0700
Adding news release announcement for density graph refs #952
- lines changed 2, context: html, text, full: html, text
3578b0fd7aa87e7b776c8d980bc037b7abe22a4e Wed Jun 1 16:52:59 2016 -0700
Adding Braney as credit on news about density graph refs #952
- lines changed 1, context: html, text, full: html, text
db851cdb62108c634277bdb60a4ac31896073326 Thu Jun 2 10:18:43 2016 -0700
Updating newsarch to have right archive link refs #952
- lines changed 28, context: html, text, full: html, text
c630206cc0394b0488375ac306f84f6d8a4ecbce Fri Jun 3 14:14:55 2016 -0700
adding files for new video09 about exon-only mode, including staging announcement. refs #17462
- src/hg/htdocs/images/Orcinus_orca.jpg
- lines changed 0, context: html, text, full: html, text
49feb41a341d3ae6f20c18a744e6dfee86d8ae22 Tue May 31 13:56:53 2016 -0700
photo from Robert Pitman NOAA https://upload.wikimedia.org/wikipedia/commons/3/37/Killerwhales_jumping.jpg refs #17425
- src/hg/htdocs/images/training/thumbGateway.jpg
- lines changed 0, context: html, text, full: html, text
9ad16186791fa5b625aec17b485273c45b55f8a8 Thu May 12 11:33:16 2016 -0700
adding gateway vid to training pages. replacing a thumbnail with properly small version. dropping stockholm and adding CRG and ASBMR workshops
- src/hg/htdocs/images/training/vidTitle08.jpg
- lines changed 0, context: html, text, full: html, text
9ad16186791fa5b625aec17b485273c45b55f8a8 Thu May 12 11:33:16 2016 -0700
adding gateway vid to training pages. replacing a thumbnail with properly small version. dropping stockholm and adding CRG and ASBMR workshops
- src/hg/htdocs/images/training/vidTitle09.jpg
- lines changed 0, context: html, text, full: html, text
c630206cc0394b0488375ac306f84f6d8a4ecbce Fri Jun 3 14:14:55 2016 -0700
adding files for new video09 about exon-only mode, including staging announcement. refs #17462
- src/hg/htdocs/indexNews.html
- lines changed 40, context: html, text, full: html, text
29d8156c530a7b28618003d89a090c99af49751e Wed Jun 1 15:58:31 2016 -0700
Adding news release announcement for density graph refs #952
- lines changed 2, context: html, text, full: html, text
3578b0fd7aa87e7b776c8d980bc037b7abe22a4e Wed Jun 1 16:52:59 2016 -0700
Adding Braney as credit on news about density graph refs #952
- lines changed 38, context: html, text, full: html, text
c630206cc0394b0488375ac306f84f6d8a4ecbce Fri Jun 3 14:14:55 2016 -0700
adding files for new video09 about exon-only mode, including staging announcement. refs #17462
- lines changed 2, context: html, text, full: html, text
f2f2019254aee115c15c6ce473419feb04e6b73e Fri Jun 3 14:31:44 2016 -0700
had to move the exclusion tag. forgot to rehide the short version of announcements after testing them. refs
- lines changed 1, context: html, text, full: html, text
fceb4a4cb6bacebe1a4ade04ca1fa470862d0db0 Fri Jun 3 14:33:47 2016 -0700
dang. had to add HR tag between news items. refs #17462
- src/hg/htdocs/mirror.html
- lines changed 19, context: html, text, full: html, text
993f99bbaed4e16e8cafa59d7a3d91061d1ad5cc Wed Jun 1 15:18:20 2016 -0700
removing Australian mirror from list. refs #17205
- src/hg/htdocs/style/HGStyle.css
- lines changed 4, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/htdocs/training/index.html
- lines changed 35, context: html, text, full: html, text
9ad16186791fa5b625aec17b485273c45b55f8a8 Thu May 12 11:33:16 2016 -0700
adding gateway vid to training pages. replacing a thumbnail with properly small version. dropping stockholm and adding CRG and ASBMR workshops
- lines changed 17, context: html, text, full: html, text
b8bd23d3898aa627421777f6f4aebd9a9aaa617a Wed Jun 1 14:39:01 2016 -0700
removing completed workshops in Spain. adding Denver in September
- lines changed 2, context: html, text, full: html, text
c630206cc0394b0488375ac306f84f6d8a4ecbce Fri Jun 3 14:14:55 2016 -0700
adding files for new video09 about exon-only mode, including staging announcement. refs #17462
- src/hg/htdocs/training/vids/index.html
- lines changed 29, context: html, text, full: html, text
9ad16186791fa5b625aec17b485273c45b55f8a8 Thu May 12 11:33:16 2016 -0700
adding gateway vid to training pages. replacing a thumbnail with properly small version. dropping stockholm and adding CRG and ASBMR workshops
- lines changed 57, context: html, text, full: html, text
c630206cc0394b0488375ac306f84f6d8a4ecbce Fri Jun 3 14:14:55 2016 -0700
adding files for new video09 about exon-only mode, including staging announcement. refs #17462
- src/hg/inc/cartTrackDb.h
- lines changed 3, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/inc/jsHelper.h
- lines changed 5, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/inc/sessionThumbnail.h
- lines changed 9, context: html, text, full: html, text
7f2c71980d90f22204d7aa2ca39cc09eaaf47d97 Fri Jun 3 19:20:38 2016 -0700
Added session details button, plus code review changes refs #15312, #17439
- src/hg/js/d3.dendrograms.js
- lines changed 32, context: html, text, full: html, text
fbf528b0c682bbb8a11f7c275b973a220d8bb49b Tue May 17 10:07:46 2016 -0700
Committing some old work, fixing up run speed and some other refactoring, refs #16341
- src/hg/js/model/hgIntegrator/hgIntegratorModel.js
- lines changed 156, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/js/react/hgIntegrator/hgIntegrator.jsx
- lines changed 9, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/lib/annoStreamDb.c
- lines changed 5, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/lib/cart.c
- lines changed 4, context: html, text, full: html, text
c393b2f6fa265761873dc9222bc8ba83015b3d5d Fri Jun 3 13:04:17 2016 -0700
Custom tracks in sessions no longer expire. Changing cart message when session with custom tracks is saved. Reminds users to keep a local back-up of their session contents and custom tracks, refs #14724
- src/hg/lib/cartJson.c
- lines changed 8, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/lib/cartTrackDb.c
- lines changed 121, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/lib/customFactory.c
- lines changed 1, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/hg/lib/customTrack.c
- lines changed 7, context: html, text, full: html, text
ad6d30584193b3be7dc7ca66a01456ac599acb40 Thu Jun 2 10:56:19 2016 -0700
fixing custom tracks bigBed auto-detect to ignore the ? part in the URL, refs #17423
- src/hg/lib/hAnno.c
- lines changed 6, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/hg/lib/jsHelper.c
- lines changed 13, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/hg/lib/longRange.c
- lines changed 19, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/hg/lib/oreganno.c
- lines changed 1, context: html, text, full: html, text
e9850e19c91eb247cec5ab3204b2ac000dcbecaf Wed Jun 1 09:42:35 2016 -0700
Don't load oreganno info when track isn't on; it hurts the RR, refs #17278
- src/hg/makeDb/doc/bosTau8.txt
- lines changed 56, context: html, text, full: html, text
ba24048d3f5ab41c8f8ad127ac67b908535c8097 Fri Jun 3 10:07:00 2016 -0700
lastz chain net to orcOrc1 per user request refs #17425
- src/hg/makeDb/doc/orcOrc1/initialBuild.txt
- lines changed 636, context: html, text, full: html, text
3e4c7799848278c6c3d10c85ef6b5dcc486d66a4 Tue May 31 16:09:56 2016 -0700
initial build for orcOrc1 underway refs #17425
- lines changed 124, context: html, text, full: html, text
8b91241691f366e826cf701fd58e485aa09e094a Thu Jun 2 13:47:47 2016 -0700
just about ready for pushQ entry refs #17425
- src/hg/makeDb/doc/orcOrc1/lastzRuns.txt
- lines changed 129, context: html, text, full: html, text
1d50150f86e036e6573adc2489cb423e9d916d1e Fri Jun 3 13:22:26 2016 -0700
catching up on previous lastz runs refs #17425
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
0e7a9b03acb884c21c65228faec2efe6df6eaf11 Thu Jun 2 13:10:56 2016 -0700
Added orcOrc1 - killer whale - Orcinus orca - refs #17425
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 22, context: html, text, full: html, text
b4064bac1906917d049c19ac0734e3246e5daff8 Wed Jun 1 11:31:44 2016 -0700
Added orcOrc - Orcinus orca (killer whale) refs #17425
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
0e7a9b03acb884c21c65228faec2efe6df6eaf11 Thu Jun 2 13:10:56 2016 -0700
Added orcOrc1 - killer whale - Orcinus orca - refs #17425
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- lines changed 2, context: html, text, full: html, text
b4064bac1906917d049c19ac0734e3246e5daff8 Wed Jun 1 11:31:44 2016 -0700
Added orcOrc - Orcinus orca (killer whale) refs #17425
- src/hg/makeDb/schema/all.joiner
- lines changed 11, context: html, text, full: html, text
786076aa72e112e87ca704002fd9548033511d08 Wed Jun 1 15:43:01 2016 -0700
adding rules for orcOrc1 refs #17425
- src/hg/makeDb/trackDb/cow/bosTau8/trackDb.chainNet.ra
- lines changed 29, context: html, text, full: html, text
c01c5bbd37ac611d306b36c2754d1927ea6986dd Thu Jun 2 13:07:21 2016 -0700
adding orcOrc1 chain net refs #17425
- lines changed 2, context: html, text, full: html, text
cbd881859024572ff079cb0890b07fe7accdc49c Fri Jun 3 09:58:05 2016 -0700
fixup release tags to avoid errors in tdbQuery refs #17425
- src/hg/makeDb/trackDb/cow/bosTau8/trackDb.ra
- lines changed 1, context: html, text, full: html, text
c01c5bbd37ac611d306b36c2754d1927ea6986dd Thu Jun 2 13:07:21 2016 -0700
adding orcOrc1 chain net refs #17425
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 37, context: html, text, full: html, text
0f071c122e550f72b077b13dd0e891d9c4159235 Fri Jun 3 14:56:26 2016 -0700
add comparison track for refGene to ncbiRefSeq refs #13673
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 3, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- lines changed 39, context: html, text, full: html, text
3ca5cfe792e283cc838c020a544b0889be1787f8 Fri Jun 3 11:57:53 2016 -0700
Don't let 'tableBrowser noGenome' sneak out ahead of v334 -- keep 'tableBrower off' until then. refs #4458
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700
adding orcOrc1 to the build refs #17425
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
9511c5128086eb5992e71329dca36e58bf71ee0b Tue May 31 21:01:50 2016 -0700
Temporary addition of alpha release tag to ORegAnno track with v333 release issue
- src/hg/makeDb/trackDb/whale/orcOrc1/description.html
- lines changed 64, context: html, text, full: html, text
8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700
adding orcOrc1 to the build refs #17425
- src/hg/makeDb/trackDb/whale/orcOrc1/gap.html
- lines changed 30, context: html, text, full: html, text
8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700
adding orcOrc1 to the build refs #17425
- src/hg/makeDb/trackDb/whale/orcOrc1/gold.html
- lines changed 34, context: html, text, full: html, text
8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700
adding orcOrc1 to the build refs #17425
- src/hg/makeDb/trackDb/whale/orcOrc1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700
adding orcOrc1 to the build refs #17425
- lines changed 5, context: html, text, full: html, text
f92e2279b961c6c264c0efeef674583a40f8171f Thu Jun 2 13:46:49 2016 -0700
adding search rule for gold/assembly track refs #17425
- src/hg/utils/automation/makeDownloads.pl
- lines changed 4, context: html, text, full: html, text
1cdb96fce1eadd6476ebf2dfbe11642c5ec9042c Fri Jun 3 10:27:05 2016 -0700
allow ncbiBioSample in the config.ra file refs #17425
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 7, context: html, text, full: html, text
3db1bd39e85a02a999d436459703f0fe8d99add7 Tue May 31 15:17:22 2016 -0700
allow ncbiBioSample variable in the config.ra file refs #17425
- src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
- lines changed 53, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/hg/utils/gff3ToGenePred/tests/expected/nameAttrIdTest.gp
- lines changed 1, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/hg/utils/gff3ToGenePred/tests/expected/nameAttrNameTest.gp
- lines changed 1, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/hg/utils/gff3ToGenePred/tests/expected/useNameTest.gp
- lines changed 1, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/hg/utils/gff3ToGenePred/tests/makefile
- lines changed 14, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/inc/annoStreamTabix.h
- lines changed 11, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/inc/aveStats.h
- lines changed 2, context: html, text, full: html, text
6374e6fcfd6b6234d3f6c30ef1eb9ec4eaa80a41 Wed Jun 1 13:48:05 2016 -0700
fix up the way that the aveStats library calculates the median and
quartiles
- src/inc/bedTabix.h
- lines changed 3, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/inc/cheapcgi.h
- lines changed 3, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/inc/gff3.h
- lines changed 0, context: html, text, full: html, text
1e461577c8619bed4fb82335523ef3eb0726a158 Wed Jun 1 14:29:05 2016 -0700
added options to control the createion of the genePred name and name2 fields
- src/lib/annoStreamTabix.c
- lines changed 228, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/lib/aveStats.c
- lines changed 76, context: html, text, full: html, text
6374e6fcfd6b6234d3f6c30ef1eb9ec4eaa80a41 Wed Jun 1 13:48:05 2016 -0700
fix up the way that the aveStats library calculates the median and
quartiles
- lines changed 1, context: html, text, full: html, text
41fd2ae8614ea0c952d3c96ae4f158ceb7e37a8b Wed Jun 1 15:40:04 2016 -0700
oops... an uninitialized variable in aveStats
- src/lib/bedTabix.c
- lines changed 3, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/lib/cheapcgi.c
- lines changed 6, context: html, text, full: html, text
1a2011f25ac0bd4ce02ed0eb093ff169724f9047 Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables. The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.
See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.
hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts). As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists. 'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome(). The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.
hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks. When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb. If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.
In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled. On the main page, JS code controls whether options are disabled
depending on the current region. When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled. If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored. If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.
hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.
refs #4458
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
68315931f4a9ec4272a8df76e6a881339717ac16 Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator
- src/product/installer/README.md
- lines changed 1, context: html, text, full: html, text
9ca7dba1476e9770e7b6cba562dd5fa8ae54eebf Tue May 31 15:22:08 2016 -0700
fixing tiny typo in gbic readme file
- lines changed 7, context: html, text, full: html, text
0dbb3442ab7fcd9d144458f778e0e0710c3da311 Fri Jun 3 13:18:30 2016 -0700
Minor changes to install script readme, refs #14399
- lines changed 9, context: html, text, full: html, text
dd3d4457ebb990cb2cefefcfd79294fc23a6c225 Fri Jun 3 14:13:44 2016 -0700
Fixing minor typo and trying to encode email address in README, refs #14399
- src/product/installer/browserSetup.sh
- lines changed 3, context: html, text, full: html, text
d71f836fae46bc6fdc7f15cab8ee244d8588ffec Tue May 31 15:54:12 2016 -0700
trying to fix the "clean" command of the gbic installer, refs #14399
- src/product/mirrorDocs/staticPage.lua
- lines changed 26, context: html, text, full: html, text
5e8cab2138a26c17ffd3eca5d02b24ba098e0890 Fri Jun 3 22:13:46 2016 -0700
obfuscating email address like Hiram in lua, refs #14399
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
168d1ae1702ea8b5da03e31531dcf47379a82e57 Mon Jun 6 10:16:11 2016 -0700
v334 preview2 refs #17457
- lines changed: 3246
- files changed: 120
