File Changes for chmalee

v498_preview2 to v498_base (2026-05-04 to 2026-05-11) v498

• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 21, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
  • lines changed 5, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 3, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/hgTables/bedList.c
  • lines changed 5, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTables/custom.c
  • lines changed 2, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 36, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 2, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/joining.c
  • lines changed 2, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 33, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 1, context: html, text, full: html, text
    bd0d63cb1a33174b6f43b32a48fddad7850d0acc Mon May 4 14:05:56 2026 -0700
    Remove em-dashes and fix myVariants custom tracks to use encoded usernames in their track names and trash files instead of raw usernames, refs #33808
  • lines changed 104, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgc/myVariantsClick.c
  • lines changed 3, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 87, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/myVariantsDesc.html
  • lines changed 51, context: html, text, full: html, text
    fa0ff693583dbd90241f3bd3b2dce6eafd974d6a Mon May 4 14:17:20 2026 -0700
    Add a basic description page for myVariants tracks, refs #38808
• src/hg/inc/myVariants.h
  • lines changed 29, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/userdata.h
  • lines changed 10, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/js/hgMyData.js
  • lines changed 101, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
  • lines changed 30, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/js/hgTracks.js
  • lines changed 11, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 4, context: html, text, full: html, text
    c6c395f3e8c38023107bab00507ee605f140ecf8 Thu May 7 11:00:09 2026 -0700
    More variant|item to annotation labeling changes. One 'item' is left in because it seems more appropriate as the placeholder text, refs #33808
  • lines changed 1, context: html, text, full: html, text
    6eaa03a52d1610050bcacf6e3a56c3086677574d Thu May 7 11:02:34 2026 -0700
    Change create to add in the highlight menu for creating a myVariants item, refs #33808
  • lines changed 3, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    8cdfd0efc540471112f850be74da7b87a8bd9b1e Fri May 8 13:48:54 2026 -0700
    Fix zoom to exon/codon option not appearing for genePreds/bigGenePreds/bigBeds. This broke because of tooltip code that now moves tooltip text into a data-tooltip attribute instead of leaving the text in the title attribute, refs #37521
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    8cdfd0efc540471112f850be74da7b87a8bd9b1e Fri May 8 13:48:54 2026 -0700
    Fix zoom to exon/codon option not appearing for genePreds/bigGenePreds/bigBeds. This broke because of tooltip code that now moves tooltip text into a data-tooltip attribute instead of leaving the text in the title attribute, refs #37521
• src/hg/lib/customFactory.c
  • lines changed 7, context: html, text, full: html, text
    fa0ff693583dbd90241f3bd3b2dce6eafd974d6a Mon May 4 14:17:20 2026 -0700
    Add a basic description page for myVariants tracks, refs #38808
• src/hg/lib/myVariants.c
  • lines changed 27, context: html, text, full: html, text
    bd0d63cb1a33174b6f43b32a48fddad7850d0acc Mon May 4 14:05:56 2026 -0700
    Remove em-dashes and fix myVariants custom tracks to use encoded usernames in their track names and trash files instead of raw usernames, refs #33808
  • lines changed 2, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 167, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/inc/cheapcgi.h
  • lines changed 6, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/lib/cheapcgi.c
  • lines changed 13, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/lib/jsonParse.c
  • lines changed 7, context: html, text, full: html, text
    1da15f230f81e48dd030f04649f186688cefd933 Thu May 7 11:58:06 2026 -0700
    Fix incorrect strncpy call in jsonParse with a better snippage of the input string that avoids a strncpy altogether, refs #37500