Commits for chmalee
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v476_preview to v476_preview2 (2024-12-16 to 2025-01-06) v476
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38f09bba769d92e139b92d4bc5dde05c132a3a23 Tue Oct 17 11:46:58 2023 -0700
- Add a ctags option to js directory
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/cgilib/cartJson.c - lines changed 9, context: html, text, full: html, text
- src/hg/hgCustom/hgCustom.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgMyData/hgMyData.c - lines changed 140, context: html, text, full: html, text
- src/hg/hgMyData/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 79, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 124, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 23, context: html, text, full: html, text
- src/hg/lib/customTrack.c - lines changed 43, context: html, text, full: html, text
dbc7d6bb2237141fdbea01fff6c265ade6738c57 Fri Oct 6 13:03:41 2023 -0700
- Start on trackHubWizard module
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 15, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 22, context: html, text, full: html, text
- src/hg/hgHubConnect/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 151, context: html, text, full: html, text
- src/hg/hgMyData/hgMyData.c - lines changed 39, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 5, context: html, text, full: html, text
- src/hg/htdocs/style/hgHubConnect.css - lines changed 13, context: html, text, full: html, text
- src/hg/js/external/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/js/external/tus.min.js - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/js/hgMyData.js - lines changed 399, 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/hooklib.c - lines changed 44, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/hooklib.h - lines changed 22, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/makefile - lines changed 25, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 151, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 122, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/testPostFinishHook.txt - lines changed 96, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/testPreCreateHook.txt - lines changed 44, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/tests/README - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 16, context: html, text, full: html, text
- src/hg/lib/customTrack.c - lines changed 37, 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/hgHubConnect/hgHubConnect.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 107, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 17, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 160, 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
- src/hg/hgHubConnect/hooks/hooklib.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 5, 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
- src/hg/hgHubConnect/hooks/hooklib.c - lines changed 29, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/hooklib.h - lines changed 11, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 12, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 14, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 3, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 151, 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
1827d67ca6a757fe0ea3613763635bcf323404a9 Tue Mar 12 09:22:23 2024 -0700
- Adding unminified tus source
- src/hg/js/external/tus.js - lines changed 4973, 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
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 3, context: html, text, full: html, text
a2707301aa6d5239200eed6442e9e265091bde78 Mon Apr 8 16:35:53 2024 -0700
- Add some more file extensions to allowed extension list
7fcc1e23a0d728ecbd075342576d1b989829eecb Tue Apr 9 11:21:10 2024 -0700
- Make progress meter work with tus uploads, fix typo in error checks and abort functions
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
- src/hg/hgHubConnect/hooks/hooklib.h - lines changed 2, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 11, 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/hgHubConnect.c - lines changed 20, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 13, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/hooklib.c - lines changed 18, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/hooklib.h - lines changed 10, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 23, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 74, 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.c - lines changed 13, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 56, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 16, context: html, text, full: html, text
- src/hg/lib/hubSpace.as - lines changed 13, context: html, text, full: html, text
- src/hg/lib/hubSpace.c - lines changed 291, context: html, text, full: html, text
- src/hg/lib/hubSpace.sql - lines changed 26, 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/cartJson.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 17, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 8, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 16, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 55, context: html, text, full: html, text
- src/hg/lib/hubSpace.sql - lines changed 3, 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
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 12, 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
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 27, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 58, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 59, context: html, text, full: html, text
04410cb2d7a71910ca1e0cfbfb1e66662f798467 Thu Sep 26 10:59:47 2024 -0700
- Do not leave lastModified undefined
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 1, 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
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 15, context: html, text, full: html, text
979ae40501044410b8375bdb5840dcdfcb70c712 Wed Oct 2 12:26:27 2024 -0700
- Working hub deletion
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 24, context: html, text, full: html, text
- src/hg/htdocs/style/jquery-ui.css - lines changed 17, 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/hgHubConnect/hgHubConnect.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 1, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 16, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 18, context: html, text, full: html, text
- src/hg/htdocs/style/hgHubConnect.css - lines changed 13, context: html, text, full: html, text
- src/hg/htdocs/style/hgMyData.css - lines changed 31, context: html, text, full: html, text
- src/hg/htdocs/style/jquery-ui.css - lines changed 8, context: html, text, full: html, text
- src/hg/htdocs/style/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 297, context: html, text, full: html, text
b2cd11b937042bae6919758a5fa695a1d6c86426 Wed Oct 16 10:39:19 2024 -0700
- Rebuild hook scripts automatically
- src/hg/hgHubConnect/hooks/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/makefile - lines changed 2, 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
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 20, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/testPostFinishHook.txt - lines changed 25, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 52, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 127, context: html, text, full: html, text
- src/hg/lib/hubSpace.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/userdata.c - lines changed 105, context: html, text, full: html, text
2dfd61094ec3e548f25f56e83379f85ec22cfab5 Thu Oct 31 16:48:26 2024 -0700
- Start using Uppy instead of my own UI
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 6, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 20, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 277, 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
- src/hg/lib/hubSpace.sql - 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
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 18, 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
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/hgHubConnect/hooks/post-finish.c - lines changed 16, context: html, text, full: html, text
- src/hg/lib/hubSpace.sql - lines changed 8, 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/post-finish.c - lines changed 15, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/testPostFinishHook.txt - lines changed 52, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 2, 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
524d04aa83224bad2d1dcda060506694c858db0f Thu Nov 14 16:22:50 2024 -0800
- Style the batch change selectors better, add a batch change hub name input
- src/hg/js/hgMyData.js - lines changed 104, 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
- src/hg/js/hgMyData.js - lines changed 429, 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
- src/hg/hgHubConnect/trackHubWizard.c - 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/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/post-finish.c - lines changed 206, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-finish.c - lines changed 206, 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
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 16, 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
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/HGStyle.css - lines changed 5, 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
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 10, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 6, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 199, 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/hgHubConnect/hgHubConnect.c - lines changed 39, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 8, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 9, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-finish.c - lines changed 9, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 29, context: html, text, full: html, text
- src/hg/inc/hubSpaceKeys.h - lines changed 69, context: html, text, full: html, text
- src/hg/lib/hubSpaceKeys.as - lines changed 6, context: html, text, full: html, text
- src/hg/lib/hubSpaceKeys.c - lines changed 136, context: html, text, full: html, text
- src/hg/lib/hubSpaceKeys.sql - lines changed 13, 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/hgCustom/hgCustom.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/hgHubConnect.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-finish.c - lines changed 21, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 82, context: html, text, full: html, text
- src/hg/hgMyData/hgMyData.c - lines changed 104, context: html, text, full: html, text
- src/hg/hgMyData/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 9, context: html, text, full: html, text
- src/hg/htdocs/style/hgMyData.css - lines changed 25, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 308, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 22, context: html, text, full: html, text
- src/hg/lib/userdata.c - lines changed 118, context: html, text, full: html, text
7a4be41f979526de9de6d06aa816df9591246ddb Mon Dec 16 16:57:14 2024 -0800
- Woops fix missing braces left out during rebase somehow
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/hubSpaceQuotas.h - lines changed 85, context: html, text, full: html, text
- src/hg/lib/hubSpaceQuotas.as - lines changed 6, context: html, text, full: html, text
- src/hg/lib/hubSpaceQuotas.c - lines changed 193, context: html, text, full: html, text
- src/hg/lib/hubSpaceQuotas.sql - lines changed 12, 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/hgMyData.css - lines changed 8, context: html, text, full: html, text
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