All File Changes

v476_preview to v476_preview2 (2024-12-16 to 2025-01-06) v476

• confs/hgwdev.hg.conf
  • lines changed 8, context: html, text, full: html, text
    21d9318c051040be09aef1eb6e258f370fb1177d Sun Dec 22 01:11:18 2024 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/agpToFa/agpToFa.c
  • lines changed 1, context: html, text, full: html, text
    7642d8f313d523d2bc7f054928a82969d2e745f8 Tue Dec 31 23:45:26 2024 -0800
    minor compilter fix for agpToFa.
• src/hg/autoSql/autoSql.c
  • lines changed 1, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/autoXml/autoXml.c
  • lines changed 2, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/cgilib/cartJson.c
  • lines changed 9, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 1, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
• src/hg/cgilib/hgSeq.c
  • lines changed 6, context: html, text, full: html, text
    3dbf0d3c66fadf0e2b0c3ce76fb3f73f7a146434 Mon Dec 30 23:09:34 2024 -0800
    fixing compiler warnings for cgilib compiling Rocky 9 hgwdev-new.
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 1, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 3, context: html, text, full: html, text
    d57ca4989c27c9ada4938b1a6c29c44a8398b17e Wed Jan 1 02:35:07 2025 -0800
    compiler fix found compiling CIRM on hgwdev-new
• src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c
  • lines changed 2, context: html, text, full: html, text
    f0bfd566e04f657b8ec144f504616067a5255b5c Tue Dec 31 21:27:20 2024 -0800
    fix hgEncodDataVersions bug found by Rocky 9 compiler on hgwdev-new
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/hg/fakeFinContigs/fakeFinContigs.c
  • lines changed 1, context: html, text, full: html, text
    eb6002e80a43afcbfb3fabfd7d9412887c7d3b3c Tue Dec 31 23:47:44 2024 -0800
    minor compilter fix for fakeFinContigs.
• src/hg/featureBits/featureBits.c
  • lines changed 2, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/gbToFaRa/gbToFaRa.c
  • lines changed 2, context: html, text, full: html, text
    b59d72e0511481a477b5a9d772c68b975bd585bc Tue Dec 31 23:51:55 2024 -0800
    minor compilter fix for gbToFaRa.
• src/hg/gsBig/gsBig.c
  • lines changed 1, context: html, text, full: html, text
    b3415b3e149e52942ef55b14077aec42fd450d1d Tue Dec 31 23:54:13 2024 -0800
    minor compilter fix for gsBig.
• src/hg/hgBlat/hgBlat.c
  • lines changed 9, context: html, text, full: html, text
    20d2f29ca6491f11c70c95e041220fe72c37a2dd Sun Dec 22 15:06:45 2024 -0800
    fix compiler warning about about restrict keywords in pthread_create.
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 2, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgGateway/hgGateway.html
  • lines changed 1, context: html, text, full: html, text
    35b0cd4c35cd7c3798437b9546e2675a9fbdf6a1 Thu Jan 2 17:40:13 2025 -0800
    Adding the assemblySearch.html link to the hgGateway page, refs #32596
• src/hg/hgGene/domains.c
  • lines changed 1, context: html, text, full: html, text
    55f6362c793e0d7cc4d2ff0ec614a5e316354b82 Thu Dec 19 21:53:29 2024 -0800
    don't install lsSnpPdbChimera.py any more
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 15, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 3, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 20, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 17, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 4, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 39, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 3, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgHubConnect/hgHubConnect.h
  • lines changed 22, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 3, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 13, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 8, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 1, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 8, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 3, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgHubConnect/hooks/hooklib.c
  • lines changed 44, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 1, context: html, text, full: html, text
    e822c92d256929cea7fc16805731c24ee8d30a83 Thu Mar 7 14:35:04 2024 -0800
    Reset umask when making a per-user directory so apache can delete files later. This is likely only to be a problem during testing where apache doesn't already own the directories/files
  • lines changed 29, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 18, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 13, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
• src/hg/hgHubConnect/hooks/hooklib.h
  • lines changed 22, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 11, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 2, context: html, text, full: html, text
    7864ddf3a6d058dbe29f706519921cd55ccc4c67 Thu May 2 09:04:45 2024 -0700
    Work in progress on building form for choosing db and hub along with files to submit
  • lines changed 10, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
• src/hg/hgHubConnect/hooks/makefile
  • lines changed 25, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 3, context: html, text, full: html, text
    b2cd11b937042bae6919758a5fa695a1d6c86426 Wed Oct 16 10:39:19 2024 -0700
    Rebuild hook scripts automatically
  • lines changed 4, context: html, text, full: html, text
    b02d071f2f6d5629bc86dfa7313f649198b91841 Tue Nov 19 12:10:33 2024 -0800
    Rename post-finish hook to pre-finish. Also restart tusd with the enabled hooks pre-create and pre-finish. This way when there is an error during the upload the error will get communicated back to the client as post-finish errors don't get sent back to the client
• src/hg/hgHubConnect/hooks/post-finish.c
  • lines changed 151, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 5, context: html, text, full: html, text
    e822c92d256929cea7fc16805731c24ee8d30a83 Thu Mar 7 14:35:04 2024 -0800
    Reset umask when making a per-user directory so apache can delete files later. This is likely only to be a problem during testing where apache doesn't already own the directories/files
  • lines changed 12, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 56, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 16, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 27, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 1, context: html, text, full: html, text
    04410cb2d7a71910ca1e0cfbfb1e66662f798467 Thu Sep 26 10:59:47 2024 -0700
    Do not leave lastModified undefined
  • lines changed 2, context: html, text, full: html, text
    a4c8987ac13d72f85a7c3adde3f867456a85516f Thu Sep 26 15:52:46 2024 -0700
    Save newly created hubs to file table, return hubs when loading the page
  • lines changed 20, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 18, context: html, text, full: html, text
    02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 Wed Nov 6 15:27:22 2024 -0800
    Start of work on optional subdir and hubName metadata for hubtools uploads
  • lines changed 16, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
  • lines changed 15, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
  • lines changed 206, context: html, text, full: html, text
    b02d071f2f6d5629bc86dfa7313f649198b91841 Tue Nov 19 12:10:33 2024 -0800
    Rename post-finish hook to pre-finish. Also restart tusd with the enabled hooks pre-create and pre-finish. This way when there is an error during the upload the error will get communicated back to the client as post-finish errors don't get sent back to the client
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 122, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 14, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 23, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 16, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 2, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 1, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 9, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 1, context: html, text, full: html, text
    b1ba2b3e4d06262be97fcce62ae422cbf6c181cb Tue Dec 31 20:01:15 2024 -0800
    fix compiler warning on hgwdev-new with Rocky 9.
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 206, context: html, text, full: html, text
    b02d071f2f6d5629bc86dfa7313f649198b91841 Tue Nov 19 12:10:33 2024 -0800
    Rename post-finish hook to pre-finish. Also restart tusd with the enabled hooks pre-create and pre-finish. This way when there is an error during the upload the error will get communicated back to the client as post-finish errors don't get sent back to the client
  • lines changed 9, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 21, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgHubConnect/hooks/testPostFinishHook.txt
  • lines changed 96, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 25, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 52, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
• src/hg/hgHubConnect/hooks/testPreCreateHook.txt
  • lines changed 44, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
• src/hg/hgHubConnect/hooks/tests/README
  • lines changed 3, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
• src/hg/hgHubConnect/makefile
  • lines changed 3, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 2, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 1, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 2, context: html, text, full: html, text
    b2cd11b937042bae6919758a5fa695a1d6c86426 Wed Oct 16 10:39:19 2024 -0700
    Rebuild hook scripts automatically
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 151, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 16, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 107, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 3, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 3, context: html, text, full: html, text
    93f43d928860a345d712a07428af3170a34facb9 Fri Apr 5 12:33:42 2024 -0700
    Make web accessible user directory link available at start time. Added a symlink to upload directory in /usr/local/apache
  • lines changed 11, context: html, text, full: html, text
    7864ddf3a6d058dbe29f706519921cd55ccc4c67 Thu May 2 09:04:45 2024 -0700
    Work in progress on building form for choosing db and hub along with files to submit
  • lines changed 74, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 55, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 12, context: html, text, full: html, text
    627b526f8ff26ebb7539a5a6ee25f515a88242da Tue Aug 6 15:10:06 2024 -0700
    Can create a directory and place a hub.txt in it, and get an email for a userName
  • lines changed 58, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 15, context: html, text, full: html, text
    a4c8987ac13d72f85a7c3adde3f867456a85516f Thu Sep 26 15:52:46 2024 -0700
    Save newly created hubs to file table, return hubs when loading the page
  • lines changed 24, context: html, text, full: html, text
    979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
    Working hub deletion
  • lines changed 16, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 52, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 6, context: html, text, full: html, text
    2dfd61094ec3e548f25f56e83379f85ec22cfab5 Thu Oct 31 16:48:26 2024 -0700
    Start using Uppy instead of my own UI
  • lines changed 2, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
  • lines changed 4, context: html, text, full: html, text
    aee603836cd555a755a72d82028e9193cebc4bf7 Mon Nov 18 17:22:43 2024 -0800
    Format dates the same as js when returning files to client, rename hub to parent dir on client when an upload is successful, add the quota used out of the max quota to the table display
  • lines changed 16, context: html, text, full: html, text
    77a1a4c6ee6c882e187f1fc80b531c0e61f957cd Tue Nov 19 15:23:59 2024 -0800
    Be more intelligent about producing default hub names, don't die when a hub exists already and we are adding another file to it
  • lines changed 10, context: html, text, full: html, text
    7b7bb68187bb42ead29a9a3b26a950205820c9ae Wed Nov 20 15:54:48 2024 -0800
    Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed. Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files Put some place holder text where the selected file information would appear so the page doesn't jump around Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads
  • lines changed 29, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 82, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    d50328647c385edc3130e6df5159548dfc8a8336 Tue Dec 31 20:03:59 2024 -0800
    fix compiler warning on hgwdev-new with Rocky 9.
• src/hg/hgMyData/hgMyData.c
  • lines changed 140, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 39, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 104, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgMyData/makefile
  • lines changed 18, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 18, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 13, context: html, text, full: html, text
    f3bb2615e7f7d1df3dc6084ab0c5694679a536e7 Wed Dec 18 14:36:01 2024 -0800
    If unable to connect to what looks like it should be a GenArk hub, don't try to write custom tracks (or else we'll get an error trying to connect to a nonexistent db).
  • lines changed 1, context: html, text, full: html, text
    fd1b0e6dff69efaea9cb93285b315fae99ff67ff Thu Dec 19 13:38:13 2024 -0800
    Changing hgdownload.gi back to hgdownload.soe, thanks Jonathan for pointing out that .soe can point to hgdownload or hgdownload2. refs #34932
  • lines changed 2, context: html, text, full: html, text
    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 1, context: html, text, full: html, text
    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/hg/hgTables/wiggle.c
  • lines changed 1, context: html, text, full: html, text
    8f28719057af0f5971729c85d7e821f58d737f84 Tue Dec 31 20:15:01 2024 -0800
    fix compiler warning on hgwdev-new with Rocky 9.
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    20d2f29ca6491f11c70c95e041220fe72c37a2dd Sun Dec 22 15:06:45 2024 -0800
    fix compiler warning about about restrict keywords in pthread_create.
• src/hg/hgTracks/searchTracks.c
  • lines changed 17, context: html, text, full: html, text
    20d2f29ca6491f11c70c95e041220fe72c37a2dd Sun Dec 22 15:06:45 2024 -0800
    fix compiler warning about about restrict keywords in pthread_create.
• src/hg/hgc/barChartClick.c
  • lines changed 0, context: html, text, full: html, text
    aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800
    fix compiler warning in hgc on hgwdev-new with Rocky 9.
• src/hg/hgc/gencodeClick.c
  • lines changed 7, context: html, text, full: html, text
    aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800
    fix compiler warning in hgc on hgwdev-new with Rocky 9.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    55f6362c793e0d7cc4d2ff0ec614a5e316354b82 Thu Dec 19 21:53:29 2024 -0800
    don't install lsSnpPdbChimera.py any more
  • lines changed 9, context: html, text, full: html, text
    aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800
    fix compiler warning in hgc on hgwdev-new with Rocky 9.
• src/hg/hgc/hgdpClick.c
  • lines changed 1, context: html, text, full: html, text
    aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800
    fix compiler warning in hgc on hgwdev-new with Rocky 9.
• src/hg/hgc/makefile
  • lines changed 9, context: html, text, full: html, text
    55f6362c793e0d7cc4d2ff0ec614a5e316354b82 Thu Dec 19 21:53:29 2024 -0800
    don't install lsSnpPdbChimera.py any more
• src/hg/hgc/vcfClick.c
  • lines changed 0, context: html, text, full: html, text
    aa05e8309dcff108120ec513b1e999c5c9fdab2c Tue Dec 31 21:03:13 2024 -0800
    fix compiler warning in hgc on hgwdev-new with Rocky 9.
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 19, context: html, text, full: html, text
    edb12b1895c6b72181ad7020eee9a6d52e49df74 Sun Jan 5 14:09:00 2025 -0800
    Adding details about chromAlias stuff to various custom track pages, refs #26360
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    edb12b1895c6b72181ad7020eee9a6d52e49df74 Sun Jan 5 14:09:00 2025 -0800
    Adding details about chromAlias stuff to various custom track pages, refs #26360
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 21, context: html, text, full: html, text
    12f89e2b40fafd9330ac50808a03cf60afc16122 Fri Dec 27 11:00:35 2024 -0800
    updating supported track types for api, refs #26350
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 1, context: html, text, full: html, text
    6a2cd2528e36139cde7d4a8881e3402ed7cf3851 Sun Jan 5 14:12:15 2025 -0800
    making samtools sort example functional
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    edb12b1895c6b72181ad7020eee9a6d52e49df74 Sun Jan 5 14:09:00 2025 -0800
    Adding details about chromAlias stuff to various custom track pages, refs #26360
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 29, context: html, text, full: html, text
    09cce8bb976575739c209813484c77126ca6a427 Mon Jan 6 13:23:47 2025 -0800
    adding note about hubClone to page, refs #25572
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 43, context: html, text, full: html, text
    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
  • lines changed 1, context: html, text, full: html, text
    f1ba4b42feca6dde2c30eeb2664ae3ac8b9d04e3 Fri Dec 20 18:08:11 2024 -0800
    Fixing the release date, refs #30262
• src/hg/htdocs/images/newsArchImages/ortholog_refSeq.png
  • lines changed 0, context: html, text, full: html, text
    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
• src/hg/htdocs/images/newsArchImages/ortholog_track.png
  • lines changed 0, context: html, text, full: html, text
    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 79, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 5, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 17, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 59, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 18, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 20, context: html, text, full: html, text
    2dfd61094ec3e548f25f56e83379f85ec22cfab5 Thu Oct 31 16:48:26 2024 -0700
    Start using Uppy instead of my own UI
  • lines changed 6, context: html, text, full: html, text
    7b7bb68187bb42ead29a9a3b26a950205820c9ae Wed Nov 20 15:54:48 2024 -0800
    Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed. Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files Put some place holder text where the selected file information would appear so the page doesn't jump around Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads
  • lines changed 9, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    0aa4ba8b9777a393f7ce83b0d51b1efbef429fd6 Wed Nov 20 15:54:16 2024 -0800
    Fix style of sessions table sort controls to make the CSS more specific to that particular table rather than just all DataTables
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 13, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 13, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
• src/hg/htdocs/style/hgMyData.css
  • lines changed 31, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 25, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
  • lines changed 8, context: html, text, full: html, text
    e5943e594934ed251a3b03deba41422ff0be68bc Fri Jan 3 14:55:48 2025 -0800
    Fix search bar and table row background color on hubspace interface
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 17, context: html, text, full: html, text
    979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
    Working hub deletion
  • lines changed 8, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
• src/hg/inc/cartJson.h
  • lines changed 3, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
• src/hg/inc/hubSpace.h
  • lines changed 89, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 2, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 2, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
• src/hg/inc/hubSpaceKeys.h
  • lines changed 69, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
• src/hg/inc/hubSpaceQuotas.h
  • lines changed 85, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
• src/hg/inc/userdata.h
  • lines changed 18, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 17, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 8, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 5, context: html, text, full: html, text
    93f43d928860a345d712a07428af3170a34facb9 Fri Apr 5 12:33:42 2024 -0700
    Make web accessible user directory link available at start time. Added a symlink to upload directory in /usr/local/apache
  • lines changed 25, context: html, text, full: html, text
    7864ddf3a6d058dbe29f706519921cd55ccc4c67 Thu May 2 09:04:45 2024 -0700
    Work in progress on building form for choosing db and hub along with files to submit
  • lines changed 3, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 3, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 4, context: html, text, full: html, text
    627b526f8ff26ebb7539a5a6ee25f515a88242da Tue Aug 6 15:10:06 2024 -0700
    Can create a directory and place a hub.txt in it, and get an email for a userName
  • lines changed 4, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 3, context: html, text, full: html, text
    979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
    Working hub deletion
  • lines changed 15, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 3, context: html, text, full: html, text
    02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 Wed Nov 6 15:27:22 2024 -0800
    Start of work on optional subdir and hubName metadata for hubtools uploads
  • lines changed 1, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
  • lines changed 4, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
  • lines changed 3, context: html, text, full: html, text
    77a1a4c6ee6c882e187f1fc80b531c0e61f957cd Tue Nov 19 15:23:59 2024 -0800
    Be more intelligent about producing default hub names, don't die when a hub exists already and we are adding another file to it
  • lines changed 10, context: html, text, full: html, text
    7b7bb68187bb42ead29a9a3b26a950205820c9ae Wed Nov 20 15:54:48 2024 -0800
    Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed. Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files Put some place holder text where the selected file information would appear so the page doesn't jump around Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads
  • lines changed 12, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
  • lines changed 4, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/js/assemblySearch.js
  • lines changed 1, context: html, text, full: html, text
    098c8fb9f6109bd1d375948bb13f3944f6869de1 Thu Dec 19 10:42:01 2024 -0800
    Making the start of the table sentence case, refs #32596
• src/hg/js/external/makefile
  • lines changed 1, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
• src/hg/js/external/tus.js
  • lines changed 4973, context: html, text, full: html, text
    1827d67ca6a757fe0ea3613763635bcf323404a9 Tue Mar 12 09:22:23 2024 -0700
    Adding unminified tus source
• src/hg/js/external/tus.min.js
  • lines changed 0, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
• src/hg/js/hgMyData.js
  • lines changed 124, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 399, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 10, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 160, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 151, context: html, text, full: html, text
    6627b1c33bdef1886f84fce4df14d0dd5c786657 Fri Mar 8 17:10:21 2024 -0800
    Make the DataTable update dynamically. Correctly use a hidden file input to keep track of submitted and unsubmitted files
  • lines changed 31, context: html, text, full: html, text
    81531bc887a5dababf08582f3408d3c50b44c126 Sun Mar 10 18:09:12 2024 -0700
    Add a link to view the uploaded files in the gb, it is a hack relying on udc.localDir and is not sustainable
  • lines changed 5, context: html, text, full: html, text
    93f43d928860a345d712a07428af3170a34facb9 Fri Apr 5 12:33:42 2024 -0700
    Make web accessible user directory link available at start time. Added a symlink to upload directory in /usr/local/apache
  • lines changed 1, context: html, text, full: html, text
    a2707301aa6d5239200eed6442e9e265091bde78 Mon Apr 8 16:35:53 2024 -0700
    Add some more file extensions to allowed extension list
  • lines changed 12, context: html, text, full: html, text
    7fcc1e23a0d728ecbd075342576d1b989829eecb Tue Apr 9 11:21:10 2024 -0700
    Make progress meter work with tus uploads, fix typo in error checks and abort functions
  • lines changed 75, context: html, text, full: html, text
    7864ddf3a6d058dbe29f706519921cd55ccc4c67 Thu May 2 09:04:45 2024 -0700
    Work in progress on building form for choosing db and hub along with files to submit
  • lines changed 81, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 67, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 50, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 63, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 77, context: html, text, full: html, text
    a4c8987ac13d72f85a7c3adde3f867456a85516f Thu Sep 26 15:52:46 2024 -0700
    Save newly created hubs to file table, return hubs when loading the page
  • lines changed 27, context: html, text, full: html, text
    979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
    Working hub deletion
  • lines changed 297, context: html, text, full: html, text
    00a364772e6004ac5d9d221c0594121063791471 Mon Oct 7 09:50:38 2024 -0700
    After meeting with QA, start small redesign to emphasize getting a track uploaded. Change the file selector to be in a modal, make the newest files sort to top and be highlighted, add a batch change file type and db, auto-detect the db from the cart
  • lines changed 127, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 277, context: html, text, full: html, text
    2dfd61094ec3e548f25f56e83379f85ec22cfab5 Thu Oct 31 16:48:26 2024 -0700
    Start using Uppy instead of my own UI
  • lines changed 1, context: html, text, full: html, text
    02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 Wed Nov 6 15:27:22 2024 -0800
    Start of work on optional subdir and hubName metadata for hubtools uploads
  • lines changed 1, context: html, text, full: html, text
    472d99a81a785956ece339852cc8a4b649d40e5d Thu Nov 7 11:10:57 2024 -0800
    Automatically open the file editor when a file is chosen
  • lines changed 16, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
  • lines changed 26, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
  • lines changed 46, context: html, text, full: html, text
    6a5052fcb442fafa62ef6800d34246a7ba631891 Thu Nov 14 12:55:15 2024 -0800
    Make file type no longer selectable, just infer from the extension and warn (correctly now) if the file type is not supported. Remove the file type batch select. TODO: add a hub name batch change and make the batch change update correctly on change
  • lines changed 104, context: html, text, full: html, text
    524d04aa83224bad2d1dcda060506694c858db0f Thu Nov 14 16:22:50 2024 -0800
    Style the batch change selectors better, add a batch change hub name input
  • lines changed 429, context: html, text, full: html, text
    6f87a0fb5dffd9f4e814e0bfe0d7b5d7693a7a0e Mon Nov 18 15:52:15 2024 -0800
    Remove a bunch of now dead code now that we are using uppy. display the quota next to the upload button
  • lines changed 3, context: html, text, full: html, text
    aee603836cd555a755a72d82028e9193cebc4bf7 Mon Nov 18 17:22:43 2024 -0800
    Format dates the same as js when returning files to client, rename hub to parent dir on client when an upload is successful, add the quota used out of the max quota to the table display
  • lines changed 1, context: html, text, full: html, text
    77a1a4c6ee6c882e187f1fc80b531c0e61f957cd Tue Nov 19 15:23:59 2024 -0800
    Be more intelligent about producing default hub names, don't die when a hub exists already and we are adding another file to it
  • lines changed 2, context: html, text, full: html, text
    c1c40e39a85c92490292c53ff209aa80b76c9b6d Tue Nov 19 15:28:54 2024 -0800
    Fix view in genome browser link to user parentDir instead of hub
  • lines changed 199, context: html, text, full: html, text
    7b7bb68187bb42ead29a9a3b26a950205820c9ae Wed Nov 20 15:54:48 2024 -0800
    Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed. Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files Put some place holder text where the selected file information would appear so the page doesn't jump around Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads
  • lines changed 57, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 308, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/hg/js/hgSearch.js
  • lines changed 97, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
• src/hg/js/makefile
  • lines changed 6, context: html, text, full: html, text
    38f09bba769d92e139b92d4bc5dde05c132a3a23 Tue Oct 17 11:46:58 2023 -0700
    Add a ctags option to js directory
  • lines changed 1, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
• src/hg/js/utils.js
  • lines changed 95, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 2, context: html, text, full: html, text
    7a4be41f979526de9de6d06aa816df9591246ddb Mon Dec 16 16:57:14 2024 -0800
    Woops fix missing braces left out during rebase somehow
• src/hg/lib/customFactory.c
  • lines changed 23, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 22, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
  • lines changed 9, context: html, text, full: html, text
    20d2f29ca6491f11c70c95e041220fe72c37a2dd Sun Dec 22 15:06:45 2024 -0800
    fix compiler warning about about restrict keywords in pthread_create.
• src/hg/lib/customTrack.c
  • lines changed 43, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 37, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
• src/hg/lib/hubSpace.as
  • lines changed 13, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 1, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 4, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
• src/hg/lib/hubSpace.c
  • lines changed 291, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 21, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 4, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 2, context: html, text, full: html, text
    02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 Wed Nov 6 15:27:22 2024 -0800
    Start of work on optional subdir and hubName metadata for hubtools uploads
  • lines changed 34, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
  • lines changed 2, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
• src/hg/lib/hubSpace.sql
  • lines changed 26, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 3, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
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    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 1, context: html, text, full: html, text
    626a31bd940b062fe05a16053d72c23e139e9b49 Wed Nov 6 15:26:05 2024 -0800
    Make primary key length on the fileName field to be long enough to make them unique
  • lines changed 8, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
• src/hg/lib/hubSpaceKeys.as
  • lines changed 6, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
• src/hg/lib/hubSpaceKeys.c
  • lines changed 136, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
• src/hg/lib/hubSpaceKeys.sql
  • lines changed 13, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
• src/hg/lib/hubSpaceQuotas.as
  • lines changed 6, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/lib/hubSpaceQuotas.c
  • lines changed 193, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/lib/hubSpaceQuotas.sql
  • lines changed 12, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
• src/hg/lib/jsHelper.c
  • lines changed 2, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
• src/hg/lib/liftOver.c
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    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/hg/lib/makefile
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    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 1, context: html, text, full: html, text
    65d4e214bd753220cd3f1b9700f107ef1ae648da Fri May 24 09:36:42 2024 -0700
    Make hubSpace autoSql files, haven't created the table yet
  • lines changed 1, context: html, text, full: html, text
    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 1, context: html, text, full: html, text
    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/lib/qaSeq.c
  • lines changed 2, context: html, text, full: html, text
    bc6bf7b8c9b952dd6434acbb09b99f25b46a9ab3 Mon Dec 30 21:07:43 2024 -0800
    Fixing compiler warngins compiling on hgwdev-new with Rocky 9
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    bc6bf7b8c9b952dd6434acbb09b99f25b46a9ab3 Mon Dec 30 21:07:43 2024 -0800
    Fixing compiler warngins compiling on hgwdev-new with Rocky 9
• src/hg/lib/userdata.c
  • lines changed 57, context: html, text, full: html, text
    c79deb301511fcf0de0ed376c7746e4902804472 Fri May 5 16:59:33 2023 -0700
    Experiment number one, can succesfully upload a file and store it via hgCustom. New userdata library for managing where to store the files Get skeleton structure of new cgi together More work in progress, mostly stubbing out the CGI More work in progress, mostly stubbing out the html page
  • lines changed 41, context: html, text, full: html, text
    dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
    Start on trackHubWizard module
  • lines changed 36, context: html, text, full: html, text
    1c9352a7c5c2550a52b1d9fb2bae806b6aaed1be Thu Jan 18 13:28:56 2024 -0800
    Starting on pre-create hook for tusd
  • lines changed 18, context: html, text, full: html, text
    8f2e6dbc0e250e934382477cea73e60624ccfe32 Fri Feb 16 11:45:42 2024 -0800
    Start of populating a list of files to the UI
  • lines changed 16, context: html, text, full: html, text
    93f43d928860a345d712a07428af3170a34facb9 Fri Apr 5 12:33:42 2024 -0700
    Make web accessible user directory link available at start time. Added a symlink to upload directory in /usr/local/apache
  • lines changed 40, context: html, text, full: html, text
    7864ddf3a6d058dbe29f706519921cd55ccc4c67 Thu May 2 09:04:45 2024 -0700
    Work in progress on building form for choosing db and hub along with files to submit
  • lines changed 6, context: html, text, full: html, text
    0f349359a8bebbd67c7bd7bb732285dee71905fc Tue May 7 08:43:51 2024 -0700
    Start of requiring hub,genome,and file type with each file submission
  • lines changed 42, context: html, text, full: html, text
    3a88c02326aadbb1df3436cd519f7b8a4df6ae5b Thu Jun 6 15:32:15 2024 -0700
    Work in progress using the mysql table for hubSpace on client side
  • lines changed 12, context: html, text, full: html, text
    627b526f8ff26ebb7539a5a6ee25f515a88242da Tue Aug 6 15:10:06 2024 -0700
    Can create a directory and place a hub.txt in it, and get an email for a userName
  • lines changed 34, context: html, text, full: html, text
    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
  • lines changed 25, context: html, text, full: html, text
    979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
    Working hub deletion
  • lines changed 105, context: html, text, full: html, text
    2f0d3fa3d2bcbf3e23e834ca68565c470f73939d Mon Oct 21 12:32:08 2024 -0700
    Back end for auto-generating a hub with every user upload done
  • lines changed 18, context: html, text, full: html, text
    02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 Wed Nov 6 15:27:22 2024 -0800
    Start of work on optional subdir and hubName metadata for hubtools uploads
  • lines changed 17, context: html, text, full: html, text
    d2800e10690b66bf2ab04804e124958459f0ff0d Thu Nov 7 11:11:15 2024 -0800
    Add a parentDir field to the hubSpace table and make an index on it
  • lines changed 75, context: html, text, full: html, text
    a4ec09b5bbfbaf7c4f40053b24f42f075a5b6b85 Tue Nov 12 14:23:32 2024 -0800
    Lots of changes after meeting, mostly to accomadate hubtools uploads: allow parentDir in upload request, make batch change dropdowns have the right options. TODO: remove type selection all together from UI, make hub name generation not be hardcoded in ui
  • lines changed 1, context: html, text, full: html, text
    aee603836cd555a755a72d82028e9193cebc4bf7 Mon Nov 18 17:22:43 2024 -0800
    Format dates the same as js when returning files to client, rename hub to parent dir on client when an upload is successful, add the quota used out of the max quota to the table display
  • lines changed 52, context: html, text, full: html, text
    77a1a4c6ee6c882e187f1fc80b531c0e61f957cd Tue Nov 19 15:23:59 2024 -0800
    Be more intelligent about producing default hub names, don't die when a hub exists already and we are adding another file to it
  • lines changed 35, context: html, text, full: html, text
    7b7bb68187bb42ead29a9a3b26a950205820c9ae Wed Nov 20 15:54:48 2024 -0800
    Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed. Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files Put some place holder text where the selected file information would appear so the page doesn't jump around Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads
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    e8ffc5e45bd8e8de9f1c78347ea6b11fd4817a40 Mon Dec 2 12:37:53 2024 -0800
    Generate api keys for each user and store them in hgcentral.hubSpaceKeys
  • lines changed 118, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
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    759368142eec396d7b54ad72dc94a38459d1e3bf Tue Dec 17 16:57:35 2024 -0800
    Add a table with userName,quota to hgcentral so hubspace can have user-defined quotas, refs #31058
• src/hg/liftUp/liftUp.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/doc/asmHubs/cladeListings.sh
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    9ed9912f5703b6ba1c660fc9702b0d8d61358ee6 Thu Dec 19 14:20:13 2024 -0800
    helper script to manage clades refs #34370
• src/hg/makeDb/doc/hg38/hg38.txt
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    8fb72c8da4d09c44c56388251370428af1868adf Thu Dec 19 15:59:42 2024 -0800
    Adding the ENCODE 4 TF track, refs #34930
• src/hg/makeDb/doc/mm39/initialBuild.txt
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    8dea55f517c6b7ebfd2e39e93a8294d65b270f47 Mon Dec 30 06:06:04 2024 -0800
    adding official cytoBand from NCBI refs #35007
• src/hg/makeDb/doc/splicevardb.txt
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    9923b0d727379c208d267d367c59ca69829a0b94 Tue Dec 17 04:21:56 2024 -0800
    adding spliceImpact super track and splicevardb track under it, refs #34424
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
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    fd35b9a0e11c4bd917246480cc542e1b58e60ebe Thu Dec 19 14:22:23 2024 -0800
    fixup a common name refs #34370
• src/hg/makeDb/hgClonePos/hgClonePos.c
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    e505f514d7b741bb400ac03d81cd5ce4b778a00c Tue Dec 31 23:56:47 2024 -0800
    minor compiler fix for hgClonePos.
• src/hg/makeDb/hgGcPercent/hgGcPercent.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/hgGoldGapGl/hgLoadGap.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
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    b2747f670ec8572868679259f88196674ca6e32a Tue Dec 31 21:32:32 2024 -0800
    fix hgLoadMaf found by Rocky 9 compiler on hgwdev-new
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/hgNibSeq/hgNibSeq.c
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    c9ad13b92e344edb3df4cef62781b2c7ecff1de5 Tue Dec 31 23:59:02 2024 -0800
    minor compiler fix for hgNibSeq.
• src/hg/makeDb/outside/hgGtex/hgGtex.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/makeDb/trackDb/human/decipher.ra
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    24db022dbc78ce9ad4bc6ec97ef754d4175672ae Thu Dec 26 12:17:25 2024 -0800
    Adding priority values to keep CNV and SNV tracks next to each other. Removing the group settings since it is defined in the parent stanza, refs #34968
• src/hg/makeDb/trackDb/human/decipherContainer.html
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    496a6aa93c0c492f6901ae6e01698f85f2e3d488 Mon Dec 30 13:59:16 2024 -0800
    Removing the Table Browser, downloads, and Data Integrator section from the Data Access section, refs #35009
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    ea458a5d4f7e2dd216b35aeabd648030197f4be9 Thu Jan 2 10:20:44 2025 -0800
    clarifying decipher ddgp downloads after question from decipher Julia Foreman
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.html
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    5465f9bdee909f2f3dd602296ca9ab1f019197a7 Tue Dec 17 04:43:22 2024 -0800
    small docs change to variant scores track, refs #27766
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.ra
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    cb252fbfa607515d4e3ed94ee512726b4837186f Tue Dec 17 03:08:20 2024 -0800
    renaming prediction scores track, refs #27766
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
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    8fb72c8da4d09c44c56388251370428af1868adf Thu Dec 19 15:59:42 2024 -0800
    Adding the ENCODE 4 TF track, refs #34930
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    8fb72c8da4d09c44c56388251370428af1868adf Thu Dec 19 15:59:42 2024 -0800
    Adding the ENCODE 4 TF track, refs #34930
• src/hg/makeDb/trackDb/human/refSeqComposite.html
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    7a7f7a92a1f0b41c59cf266efddd36a5202b4324 Fri Dec 20 15:57:50 2024 -0800
    Adding a link to the description page on how NCBI calculates orthologs, refs #30262
• src/hg/makeDb/trackDb/human/revel.html
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    ffa700c5d2138c455b25e736178ce963ef01a1ef Fri Dec 20 13:44:49 2024 -0800
    Adding an archive link for the old overlap.bb file, refs #34947
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
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    9923b0d727379c208d267d367c59ca69829a0b94 Tue Dec 17 04:21:56 2024 -0800
    adding spliceImpact super track and splicevardb track under it, refs #34424
• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
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    9923b0d727379c208d267d367c59ca69829a0b94 Tue Dec 17 04:21:56 2024 -0800
    adding spliceImpact super track and splicevardb track under it, refs #34424
• src/hg/makeDb/trackDb/human/splicevardb.ra
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    9923b0d727379c208d267d367c59ca69829a0b94 Tue Dec 17 04:21:56 2024 -0800
    adding spliceImpact super track and splicevardb track under it, refs #34424
• src/hg/makeDb/trackDb/human/trackDb.ra
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    9923b0d727379c208d267d367c59ca69829a0b94 Tue Dec 17 04:21:56 2024 -0800
    adding spliceImpact super track and splicevardb track under it, refs #34424
• src/hg/makeDb/trackDb/mouse/mm39/cytoBand.ra
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    8dea55f517c6b7ebfd2e39e93a8294d65b270f47 Mon Dec 30 06:06:04 2024 -0800
    adding official cytoBand from NCBI refs #35007
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    b86a64d107e037d0af2f13748f591a6e746c5e6d Sun Jan 5 11:51:55 2025 -0800
    trying a cytoBand track with index - does not seem to index refs #35007
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
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    7a7f7a92a1f0b41c59cf266efddd36a5202b4324 Fri Dec 20 15:57:50 2024 -0800
    Adding a link to the description page on how NCBI calculates orthologs, refs #30262
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    8dea55f517c6b7ebfd2e39e93a8294d65b270f47 Mon Dec 30 06:06:04 2024 -0800
    adding official cytoBand from NCBI refs #35007
• src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
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    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
• src/hg/makeDb/trackDb/refSeqComposite.html
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    7a7f7a92a1f0b41c59cf266efddd36a5202b4324 Fri Dec 20 15:57:50 2024 -0800
    Adding a link to the description page on how NCBI calculates orthologs, refs #30262
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    0967c36677fccbce9d80eb6e2aa21eed04759ebe Fri Dec 20 17:42:53 2024 -0800
    Announcing the release of the NCBI Gene Orthologs track, refs #30262
• src/hg/mouseStuff/knownVsBlat/kvsSummary.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/mouseStuff/phToPsl/phToPsl.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/nci60/findStanAlignments.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/pslGlue/pslGlue.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/pslSort/pslSort.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/ratStuff/mafSplit/mafSplit.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/ratStuff/stageMultiz/stageMultiz.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/semiNorm/semiNorm.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
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    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/hg/splitFaIntoContigs/splitFaIntoContigs.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/trfBig/trfBig.c
  • lines changed 3, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/uniqSize/uniqSize.c
  • lines changed 1, context: html, text, full: html, text
    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/utils/automation/asmHubTrackDb.sh
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    1891633f3daf8ca3fb2342cb421b46bcdb68feec Fri Dec 13 11:46:42 2024 -0800
    fix spelling of trackDb variable refs #34370
• src/hg/utils/otto/dengue/buildTree.sh
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    5cd81d78c5261be06e848e33cf17c76dfc26ae6b Fri Dec 20 15:33:55 2024 -0800
    Add nextclade-assigned lineages to metadata; install hgPhyloPlace files in /gbdb instead of cgi-bin.
• src/hg/utils/otto/dengue/getNcbiDengue.sh
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    265430be8faea69b3c41caa789e9a58a0ac4ebb8 Fri Dec 20 15:25:04 2024 -0800
    Suppress progressbar when downloading, clean up when done.
• src/hg/utils/otto/fluA/buildConcatTree.sh
  • lines changed 302, context: html, text, full: html, text
    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/buildTree.sh
  • lines changed 373, context: html, text, full: html, text
    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/concat.config.json
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/dms_annotate_pb2.py
  • lines changed 200, context: html, text, full: html, text
    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/dms_annotate_wigeon.py
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/getNcbiFluA.sh
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    7c4c221a4d2aac593173c70826731ae0aa621aab Fri Dec 20 14:57:16 2024 -0800
    Include serotype and segment in metadata, suppress the progressbar output when downloading.
• src/hg/utils/otto/fluA/h5n1_ha.config.json
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/joinSegments.py
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/pb2.config.json
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/processMetadata.pl
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    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/runDms.sh
  • lines changed 38, context: html, text, full: html, text
    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/runDmsPb2.sh
  • lines changed 39, context: html, text, full: html, text
    01859939a397ed998e752ad25c54cdd22742a49c Fri Dec 20 15:00:05 2024 -0800
    Lots of additions for H5N1 outbreak work. * Add Andersen Lab's assemblies of USDA SRA data from 2024 H5N1 outbreak * Add Bloom Lab metadata from Deep Mutational Scanning (DMS) experiments on H5N1 HA (referenced to American Wigeon 2021 vaccine strain) and PB2 * Add build of concatenated segments from the 2024 H5N1 outbreak * Better handling of serotype and segment in INSDC metadata
• src/hg/utils/otto/fluA/updateAndersenLab.sh
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    86e5a0344e886b0c19cd767412757d1f1ebacd17 Fri Dec 20 14:49:39 2024 -0800
    Cron-driven script to check Andersen Lab's github repo with assemblies of USDA H5N1 SRA data & reformat for my tree build.
• src/hg/utils/otto/mpxv/buildTree.sh
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    5581e1884c54c583fe68844f8271a3baac1617ae Fri Dec 20 15:21:56 2024 -0800
    Accumulated minor updates.
• src/hg/utils/otto/mpxv/getNcbiMpxv.sh
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    5581e1884c54c583fe68844f8271a3baac1617ae Fri Dec 20 15:21:56 2024 -0800
    Accumulated minor updates.
• src/hg/utils/otto/mtb/R00000039_repregions.bed
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    33fffa155ef226b353756253fabf9c79198c44df Fri Dec 20 16:01:29 2024 -0800
    Ranges to mask in M. tuberculosis H37Rv (NC_000962.3). I got the file from Ash O'Farrell who got it from https://github.com/iqbal-lab-org/cryptic_tb_callable_mask/blob/master/R00000039_repregions.bed .
• src/hg/utils/otto/mtb/buildTree.sh
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    61654162481479361c996500c8dcdae120caae95 Fri Dec 20 16:06:08 2024 -0800
    March 2024 build: start with Lily Karim's tree and Ash O'Farrell's metadata, add GenBank sequences, combine metadata.
• src/hg/utils/otto/mtb/combineMetadata.py
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    61654162481479361c996500c8dcdae120caae95 Fri Dec 20 16:06:08 2024 -0800
    March 2024 build: start with Lily Karim's tree and Ash O'Farrell's metadata, add GenBank sequences, combine metadata.
• src/hg/utils/otto/mtb/getNcbiMtb.sh
  • lines changed 81, context: html, text, full: html, text
    61654162481479361c996500c8dcdae120caae95 Fri Dec 20 16:06:08 2024 -0800
    March 2024 build: start with Lily Karim's tree and Ash O'Farrell's metadata, add GenBank sequences, combine metadata.
• src/hg/utils/otto/mtb/transformAshMetadata.py
  • lines changed 149, context: html, text, full: html, text
    61654162481479361c996500c8dcdae120caae95 Fri Dec 20 16:06:08 2024 -0800
    March 2024 build: start with Lily Karim's tree and Ash O'Farrell's metadata, add GenBank sequences, combine metadata.
• src/hg/utils/otto/rsv/buildTree.sh
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    2d6373e8e8e6c30f0ffe140bed6e7d1c21082f46 Fri Dec 20 15:19:55 2024 -0800
    Tweak filtering params, add masking for RSV-A, annotate RSV Genotype Consensus Consortium lineages instead of Ramaekers set.
• src/hg/utils/otto/rsv/exclude.ids
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    9bbe6deba02704509cb2d7314cb13e83a34b4884 Fri Dec 20 15:18:38 2024 -0800
    Exclude sequences that caused weird branch and/or lineage assignment trouble.
• src/hg/utils/otto/rsv/goya.A.clade-mutations.tsv
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    f0c8671e69275687c87a03ab7e28be2694b79dbb Fri Dec 20 15:17:51 2024 -0800
    Tweak lineage mutations to accommodate tree instability.
• src/hg/utils/otto/rsv/mask.A.bb
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    932c14f1ebdceab4db69a750b8f2246f016c88a6 Fri Dec 20 15:16:25 2024 -0800
    Mask RSV-A (NC_038235.1) pos 5508 because it's noisy and interferes with consortium lineage A.3.
• src/hg/utils/otto/rsv/mask.A.bed
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    2d6373e8e8e6c30f0ffe140bed6e7d1c21082f46 Fri Dec 20 15:19:55 2024 -0800
    Tweak filtering params, add masking for RSV-A, annotate RSV Genotype Consensus Consortium lineages instead of Ramaekers set.
• src/hg/utils/otto/rsv/mask.A.vcf
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    932c14f1ebdceab4db69a750b8f2246f016c88a6 Fri Dec 20 15:16:25 2024 -0800
    Mask RSV-A (NC_038235.1) pos 5508 because it's noisy and interferes with consortium lineage A.3.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    b03342c05eb5d5c23ee2a503ee5ce77e874e725c Fri Dec 20 15:39:24 2024 -0800
    (finally) mask G26530A reversion in BA.1 because it kept splitting BA.1.18. Unmask 21770 in BA.2.86 (alignment boundary change / nextclade / subst of interest).
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    8c617473dc72f3a1875453a4c238d5c3b7a7cd10 Fri Dec 20 15:49:06 2024 -0800
    Use .pb.gz instead of .pb; install hgPhyloPlace files in /gbdb not cgi-bin.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
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    d48d0f53ee67f93d7193241cd226c8aa039cde42 Fri Dec 20 15:37:20 2024 -0800
    Uniquify to guard against occasional duplicates.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    65c23c156f13dfd1d7acf81390842bc021989cfe Fri Dec 20 15:37:51 2024 -0800
    cleanup typo fix
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
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    3c3aea0b7973d9497b04647d7c8ed4ebb0f64f5c Fri Dec 20 15:40:01 2024 -0800
    Tweak to run one more command in parallel.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedMaple.sh
  • lines changed 337, context: html, text, full: html, text
    3d604489e76b3d834ebed86f8e9b610f2c9c20d8 Fri Dec 20 15:57:02 2024 -0800
    Call makeNewMaskedMaple.sh instead of makeNewMaskedVcf.sh (no more new*fa to clean up at end); use .pb.gz instead of .pb; install hgPhyloPlace files in /gbdb instead of cgi-bin. Make omicron-only subtree; not sure if we'll keep that though, it's still quite large at half the tree.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    a1a0265a5423d4b6433b85e920974f1c5b4c8790 Fri Dec 20 15:57:36 2024 -0800
    Add 24F - 24I.
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
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    e6d4c01b643aaaf0aea8d0cbc7fbd1ca7cb76232 Fri Dec 20 15:42:16 2024 -0800
    Use /dev/shm as TMPDIR; new compute nodes don't set it and don't have /data/tmp.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    3d604489e76b3d834ebed86f8e9b610f2c9c20d8 Fri Dec 20 15:57:02 2024 -0800
    Call makeNewMaskedMaple.sh instead of makeNewMaskedVcf.sh (no more new*fa to clean up at end); use .pb.gz instead of .pb; install hgPhyloPlace files in /gbdb instead of cgi-bin. Make omicron-only subtree; not sure if we'll keep that though, it's still quite large at half the tree.
• src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/utils/vcfToBed/vcfToBed.c
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    f952b14fca3833e9d8fef0ae8a086ad15485b552 Wed Jan 1 02:11:38 2025 -0800
    fix various errors for utils compiled on Rocky 9 hgwdev-new.
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
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    b51de84be3c8b388916f05772c42979170331ea0 Tue Dec 31 21:11:42 2024 -0800
    fix compiler warning in hgVisiGene on hgwdev-new with Rocky 9.
• src/htslib/hts.c
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    cde73cd256f16555d283a8e7539e946e63151ede Mon Dec 30 22:47:21 2024 -0800
    fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new.
• src/htslib/sam.c
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    cde73cd256f16555d283a8e7539e946e63151ede Mon Dec 30 22:47:21 2024 -0800
    fixing compiler warnings for htslib compiling Rocky 9 hgwdev-new.
• src/inc/common.h
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    ad6fd12391f2b2c8ef95a161a5c90351da65256e Wed Jan 1 05:10:29 2025 -0800
    add pragma for the last compile issue not fixed yet.
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    59c5d74bd333b5e2a11b22f1bb29f512a6eb9c7a Thu Jan 2 17:37:11 2025 -0800
    ifdef the code for the ArraySize macro so the older compiler will see what it usually sees and the new one sees what it wants - TO BE FIXED - eventually refs #34990
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    fc1c3661b9fb623c6d87e635a4825ebc24947b26 Thu Jan 2 18:26:27 2025 -0800
    the new compiler needs the pragma, mistake to comment it out refs #34990
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    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
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    1d02fe3264e9f1d78757a31540e33c17d05691d8 Sat Jan 4 22:56:49 2025 -0800
    added an explanatory note about using 0 not NULL to ArraySize macro.
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    72de391e0d76b4a71f9d4663af78dabbe08fdabd Sat Jan 4 23:00:06 2025 -0800
    added another explanatory note about using 0 not NULL to ArraySize macro.
• src/inc/common.mk
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    59a24235a4ba60e2f5767d05faefa89bb4ecf2db Wed Jan 1 05:12:19 2025 -0800
    fixes for common.mk to work with hgwdev and hgwdev-new. handles static compiling as much as possible.
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    927af5b0b1e586bc82412794462ac4816c793a59 Sun Jan 5 02:55:53 2025 -0800
    minor optimization to use static curl with old hgwdev.
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    5590f261bd5aabebc972325525462e1dd08de39d Sun Jan 5 09:29:37 2025 -0800
    added commented out HALDIR for Rocky9 testing
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    328190a152da44ce967a29932ca5c822416a8670 Sun Jan 5 09:35:25 2025 -0800
    opps, check in comment out path to a test HALDIR, not the shared one
• src/lib/basicBed.c
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    ab198fbbb00ac11d304283667e18fff758d3f07e Sun Jan 5 01:41:49 2025 -0800
    fix compiler warning on home rocky 8 server.
• src/lib/cheapcgi.c
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    902e6b3728a6003f4de94c1a4a2893ac2a713d65 Sat Dec 21 17:06:32 2024 -0800
    fix for compiler warning on hgwdev-new.
• src/lib/common.c
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    642b015b684a57d9e42b0a867ed4dc1e516c7897 Sat Dec 21 23:26:22 2024 -0800
    fixing more warnings on R9.
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    1b32cf0583db4331765a056c45ff4fc98c36b649 Tue Dec 31 22:39:16 2024 -0800
    minor fix in clarity for safecpy in lib.
• src/lib/htmshell.c
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    7545a188d43c6e1ea33f692b0d833ec96a7f76c5 Wed Aug 14 09:21:15 2024 -0700
    refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt
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    2dfd61094ec3e548f25f56e83379f85ec22cfab5 Thu Oct 31 16:48:26 2024 -0700
    Start using Uppy instead of my own UI
  • lines changed 1, context: html, text, full: html, text
    95e2c3a93202ee912624bb730724313faae7c886 Wed Dec 4 16:41:31 2024 -0800
    Use the DataTables select API instead of implementing my own checkboxes Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet Make select/deselect work with child files. Remove some dead code Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail Fix new table rows not animating on add Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom Fix up some comments to be more correct Remove old CGI experiment
• src/lib/https.c
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    ebd67b0a1ea3e1fdf5cd5d1ef7d9e3a618c25169 Thu Dec 19 17:46:25 2024 -0800
    Mac OSX needs O_NONBLOCK instead of SOCK_NONBLOCK no redmine
• src/lib/vcf.c
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    d61df7dc771a130c58e59709121e41b9ec85b4c8 Sat Jan 4 21:53:30 2025 -0800
    Fixes for the many compiler issues with ArraySize called on NULL. Now compiles without any errors, warnings, or pramga.
• src/lib/wormdna.c
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    bc6bf7b8c9b952dd6434acbb09b99f25b46a9ab3 Mon Dec 30 21:07:43 2024 -0800
    Fixing compiler warngins compiling on hgwdev-new with Rocky 9
• src/parasol/inc/paraCommon.h
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    8c4b84f67d26cc242ead927a758e19314ce22d24 Mon Dec 30 21:38:38 2024 -0800
    _REENTRANT is now set in common.h
• src/product/installer/browserSetup.sh
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    4289758601bbabfbe7f19370470fa9a30831fb38 Fri Dec 20 22:18:24 2024 -0800
    Update browserSetup.sh after running it on Rocky 9.5 in vm on hgwdev.
• src/utils/ccCp/ccCp.c
  • lines changed 1, context: html, text, full: html, text
    967b1ecc11ceda965dc043f2bf607b8ffce4ac2d Tue Dec 31 23:39:34 2024 -0800
    minor compilter fix for ccCCp util.
• src/utils/faSplit/faSplit.c
  • lines changed 6, context: html, text, full: html, text
    e323c52d6da91a50d484da6ff11dbbf0c706a29c Tue Dec 31 22:17:30 2024 -0800
    fix faSplit found by Rocky 9 compiler on hgwdev-new
• src/utils/findMotif/findMotif.c
  • lines changed 3, context: html, text, full: html, text
    a67466b94ea03dd7890183553292999d10197f30 Mon Jan 6 12:01:26 2025 -0800
    fix segfault error on missing -motif argument no redmine
• src/utils/fixCr/fixCr.c
  • lines changed 2, context: html, text, full: html, text
    7371ef06216ade7c7e1bc85b99c2043ac4220efa Tue Dec 31 23:42:58 2024 -0800
    minor compilter fix for fixCr.
• src/utils/pslSpliceJunctions/pslSpliceJunctions.c
  • lines changed 2, context: html, text, full: html, text
    22a69e4fe63f977e217b1aabfc0ad41df2990334 Tue Dec 31 23:34:43 2024 -0800
    minor compilter fix for pslSpliceJunctions.
• src/utils/qa/checkHTTPS
  • lines changed 2, context: html, text, full: html, text
    3e2cc3db1410c65a9830e252b96199d6fe4c373d Mon Jan 6 09:30:36 2025 -0800
    Removing the store domains as we no longer support them, no RM.
• src/utils/qa/qaTestScript.py
  • lines changed 2, context: html, text, full: html, text
    c92b0d5c0e7395d0c6c25059a8797dbe7b042714 Sat Dec 21 16:28:28 2024 -0800
    Updating the qaTestScript.py to avoid a multi-region error caused by the alignment tracks on hgwdev, No Redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ea5010f2ce147def6f55f2baba27637328230fc4 Mon Jan 6 13:44:50 2025 -0800
    v476 preview2, refs #34963

• lines changed: 17362
• files changed: 390