File Changes for kent
switch to commits view, user indexv314_preview to v314_preview2 (2015-03-16 to 2015-03-23) v314
- src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
- lines changed 143, context: html, text, full: html, text
Utility to change access attributes of files matching a query seems to work.
- src/hg/cirm/cdw/cdwChangeAccess/makefile
- lines changed 4, context: html, text, full: html, text
Utility to change access attributes of files matching a query seems to work.
- src/hg/cirm/cdw/cdwCreateGroup/cdwCreateGroup.c
- lines changed 46, context: html, text, full: html, text
Making utility to add a group.
- src/hg/cirm/cdw/cdwCreateGroup/makefile
- lines changed 4, context: html, text, full: html, text
Making utility to add a group.
- src/hg/cirm/cdw/cdwFreen/cdwFreen.c
- lines changed 29, context: html, text, full: html, text
Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
- lines changed 86, context: html, text, full: html, text
Exploring a little how to merge different meta.txt files.
- lines changed 81, context: html, text, full: html, text
Making it just print out list of all fields.
- lines changed 8, context: html, text, full: html, text
cdwFreen prints out table description.
- src/hg/cirm/cdw/cdwFreen/makefile
- src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
- lines changed 110, context: html, text, full: html, text
Utility to add group associations to files seems to work.
- lines changed 19, context: html, text, full: html, text
Simplifying command line so you just need the boolean part of the where clause.
- src/hg/cirm/cdw/cdwGroupFile/makefile
- lines changed 4, context: html, text, full: html, text
Utility to add group associations to files seems to work.
- src/hg/cirm/cdw/cdwGroupUser/cdwGroupUser.c
- lines changed 83, context: html, text, full: html, text
Utility to add users to a group seems to work.
- lines changed 3, context: html, text, full: html, text
Saving a couple of lines of code by using a library routine.
- src/hg/cirm/cdw/cdwGroupUser/makefile
- lines changed 4, context: html, text, full: html, text
Utility to add users to a group seems to work.
- src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
- lines changed 7, context: html, text, full: html, text
Making program not worry about a few new types.
- src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
- lines changed 1, context: html, text, full: html, text
Avoiding crash on null assembly for vcf.
- src/hg/cirm/cdw/cdwMakeWigSpotQa/cdwMakeWigSpotQa.c
- lines changed 124, context: html, text, full: html, text
Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
- src/hg/cirm/cdw/cdwMakeWigSpotQa/makefile
- lines changed 4, context: html, text, full: html, text
Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
- src/hg/cirm/cdw/cdwQuery/cdwQuery.c
- lines changed 14, context: html, text, full: html, text
Making it output a header line when out=tab. Rearranged sort so * is still alphabetical, but when fields are explicitly listed the listed order is kept. Things are only alphabetically ordered within a wildcard expansion of the field list.
- lines changed 2, context: html, text, full: html, text
Saving a line of code by using a newr library routine.
- src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
- lines changed 28, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- lines changed 21, context: html, text, full: html, text
Having it revalidate when metadata pointed to by metaId changes. Adding command line option to not revalidate. Removing unused 'believe' command line option.
- src/hg/cirm/cdw/cdwTextForIndex/cdwTextForIndex.c
- lines changed 121, context: html, text, full: html, text
Utility that creates full text index for cdwFileTags seems to work.
- lines changed 6, context: html, text, full: html, text
Making numerical ID rather than accession be used to in search results.
- src/hg/cirm/cdw/cdwTextForIndex/makefile
- lines changed 4, context: html, text, full: html, text
Utility that creates full text index for cdwFileTags seems to work.
- src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
- lines changed 4, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
- lines changed 2, context: html, text, full: html, text
Adding chrom back in track table and bumping version.
- lines changed 94, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- lines changed 4, context: html, text, full: html, text
Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
- lines changed 76, context: html, text, full: html, text
Restricting files and tracks and tags browsing to files you have access to.
- lines changed 66, context: html, text, full: html, text
Restricting oneTag page to only showing info from accessible files. Changing home page total size reports to use GB, TB, PB rather than full number with many commas. Fixed bug when clicking on links on an item that was abbreviated to fit in a table.
- lines changed 86, context: html, text, full: html, text
Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
- lines changed 114, context: html, text, full: html, text
Putting suggest onto the filters controls where appropriate. Tinkering with test page a little.
- lines changed 91, context: html, text, full: html, text
Speeding up code that generates suggestions a bunch by making it use cdwFileTags rather than making a tagStorm.
- lines changed 16, context: html, text, full: html, text
Fixing browse files when there are accessible files, which I just had broken fixing browser files when there are no accessible files.
- lines changed 10, context: html, text, full: html, text
Trying new watermark code on test page. Seems to work.
- lines changed 30, context: html, text, full: html, text
Checking out some of the available graphics in the test page and bumping versino number.
- lines changed 135, context: html, text, full: html, text
Swapping out list of graphic images in test for a pie experiment, and then integrating pie chart into main page.
- lines changed 73, context: html, text, full: html, text
Implementing trix search. Polishing pie charts on home page.
- lines changed 14, context: html, text, full: html, text
Making URL an actual link in doLabs page.
- src/hg/cirm/cdw/cdwWebBrowse/makefile
- lines changed 3, context: html, text, full: html, text
Fixing it so touching .html file remakes .c as well as .h
- lines changed 1, context: html, text, full: html, text
Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
- src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h
- lines changed 46, context: html, text, full: html, text
Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
- lines changed 53, context: html, text, full: html, text
Second pass at tag descriptions.
- src/hg/cirm/cdw/inc/cdw.h
- lines changed 208, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- src/hg/cirm/cdw/inc/cdwLib.h
- lines changed 3, context: html, text, full: html, text
Making utility to add a group.
- lines changed 22, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- lines changed 17, context: html, text, full: html, text
Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
- lines changed 6, context: html, text, full: html, text
Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
- lines changed 3, context: html, text, full: html, text
Adding cdwAccessibleFileList function to get list of all accessible files for a users.
- lines changed 3, context: html, text, full: html, text
Refactoring to expose cdwUserTagStormFromList function, which will help keep us from generating some expensive data structures twice.
- lines changed 5, context: html, text, full: html, text
Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
- src/hg/cirm/cdw/lib/cdw.as
- lines changed 26, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- src/hg/cirm/cdw/lib/cdw.c
- lines changed 470, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- src/hg/cirm/cdw/lib/cdw.sql
- lines changed 31, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- src/hg/cirm/cdw/lib/cdwLib.c
- lines changed 8, context: html, text, full: html, text
Making utility to add a group.
- lines changed 61, context: html, text, full: html, text
Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
- lines changed 85, context: html, text, full: html, text
Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
- lines changed 17, context: html, text, full: html, text
Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
- lines changed 36, context: html, text, full: html, text
Adding cdwAccessibleFileList function to get list of all accessible files for a users.
- lines changed 19, context: html, text, full: html, text
Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
- src/hg/cirm/cdw/lib/cdwTagStorm.c
- lines changed 45, context: html, text, full: html, text
Adding info from cdwVcfFile to storm. Calculating amount of vcf that is explained by common snps by looking up common_snp in cdwEnrich.
- lines changed 46, context: html, text, full: html, text
Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
- lines changed 21, context: html, text, full: html, text
Refactoring to expose cdwUserTagStormFromList function, which will help keep us from generating some expensive data structures twice.
- lines changed 19, context: html, text, full: html, text
Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
- lines changed 4, context: html, text, full: html, text
Fixing a bug where was crashing if you weren't logged in.
- src/hg/cirm/cdw/lib/cdwValid.c
- lines changed 1, context: html, text, full: html, text
Correcting age_unit to be singular the way t_unit is.
- lines changed 8, context: html, text, full: html, text
Making use of periods more consistent in descriptions.
- src/hg/cirm/cdw/makefile
- lines changed 5, context: html, text, full: html, text
Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
- src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c
- lines changed 1, context: html, text, full: html, text
Doing little bit of resource freeing, but not to matter in the absense of a vcfRecordFree. This utility currently leaks memory. On the 1000 genomes data was up to using 400 Gig on chr1 before I killed it.
- lines changed 19, context: html, text, full: html, text
Commenting out some statistics gathering that I feared was making things too slow. Making it free up memory from time to time.
- src/hg/hgLogin/hgLogin.c
- lines changed 5, context: html, text, full: html, text
Moving cartSaveSession() to inside of a form so that it actually does save the session ID.
- lines changed 23, context: html, text, full: html, text
Making it deal with situations like under a VPN where the web address is not qualified with . anything, and effectively there is thus no domain to use for the cookies.
- src/hg/htdocs/images/stem-cell-talk-57210.jpg
- lines changed 0, context: html, text, full: html, text
Adding a stem cell photo.
- src/hg/inc/tablesTables.h
- lines changed 1, context: html, text, full: html, text
Adding 'shortVal' parameter to webTableOutputWrapperType. This is so can use the full value for constructing urls and the like, but display the short value in the table so as to keep it from getting too wide.
- lines changed 2, context: html, text, full: html, text
Adding suggestHash to tables so they can do suggestions.
- src/hg/inc/wikiLink.h
- lines changed 6, context: html, text, full: html, text
A little refactoring so can reuse login system for CIRM.
- src/hg/js/cdwPersona.js
- lines changed 45, context: html, text, full: html, text
No need for persona in cdw it looks like.
- src/hg/js/cdwSuggest.js
- lines changed 85, context: html, text, full: html, text
Exploring some suggest stuff in CIRM data warehouse.
- lines changed 1, context: html, text, full: html, text
Some tinkering, but generally looks like won't be using this module for long. Most of the logic has moved.
- lines changed 86, context: html, text, full: html, text
No longer useing cdwSuggest.js
- src/hg/js/d3pie.min.js
- lines changed 9, context: html, text, full: html, text
Adding a pie chart maker that is pretty nice and depends on D3.
- src/hg/js/jquery.watermark.js
- lines changed 625, context: html, text, full: html, text
Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
Exploring some suggest stuff in CIRM data warehouse.
- lines changed 1, context: html, text, full: html, text
No longer useing cdwSuggest.js
- lines changed 1, context: html, text, full: html, text
Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
- src/hg/lib/cart.c
- lines changed 7, context: html, text, full: html, text
Making it work behind a firewall/VPN where there is effectively no domain.
- src/hg/lib/omiciaUi.c
- lines changed 55, context: html, text, full: html, text
Adding up or down arrow after a column we sort on.
- lines changed 55, context: html, text, full: html, text
Oops, did not mean to add these!
- src/hg/lib/oregannoOther.c
- lines changed 591, context: html, text, full: html, text
Adding up or down arrow after a column we sort on.
- lines changed 591, context: html, text, full: html, text
Oops, did not mean to add these!
- src/hg/lib/tablesTables.c
- lines changed 3, context: html, text, full: html, text
Adding 'shortVal' parameter to webTableOutputWrapperType. This is so can use the full value for constructing urls and the like, but display the short value in the table so as to keep it from getting too wide.
- lines changed 34, context: html, text, full: html, text
Starting to have suggest javascript going on in filter row
- lines changed 49, context: html, text, full: html, text
Adding suggestHash to tables so they can do suggestions.
- lines changed 15, context: html, text, full: html, text
Putting in but then ifdefing out some watermark code that looked nice, but left the word 'filter' printed all over the cart. Will try and fix soon. Wordsmithing one line of instructions a little.
- lines changed 14, context: html, text, full: html, text
Trying another shot at watermarks on the filter row. Seems to work with new library.
- lines changed 14, context: html, text, full: html, text
Adding up or down arrow after a column we sort on.
- lines changed 14, context: html, text, full: html, text
Making it print numerical fields right justified. Tweaking instructiona line a little.
- src/hg/lib/wikiLink.c
- lines changed 31, context: html, text, full: html, text
A little refactoring so can reuse login system for CIRM.
- src/hg/makeDb/schema/dbSnoop/dbSnoop.c
- src/hg/oneShot/freen/freen.c
- lines changed 23, context: html, text, full: html, text
Freen does reality speed check on loading all exons for a chrom into a rangeTree.
- src/inc/obscure.h
- lines changed 3, context: html, text, full: html, text
Adding printWithGreekByte, just a wrapper around sprintWithGreekByte.
- src/lib/obscure.c
- lines changed 8, context: html, text, full: html, text
Adding printWithGreekByte, just a wrapper around sprintWithGreekByte.
- src/tagStorm/tagStormHoist/expected.out
- src/tagStorm/tagStormHoist/test.in
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