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Migrate oncoprintjs #4252

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wants to merge 322 commits into from
Closed

Migrate oncoprintjs #4252

wants to merge 322 commits into from

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onursumer
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Checks

  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

@onursumer onursumer force-pushed the migrate-oncoprintjs branch 6 times, most recently from b86687d to 2e4843e Compare May 17, 2022 21:41
Abeshouse, Adam A./Sloan Kettering Institute added 23 commits May 18, 2022 13:40
@onursumer
delete legacy code
aa64ba0
@onursumer
First pass at dragging. A lot of technical debt and optimization left
87c8121
@onursumer
fixing bugs
d63adb4
@onursumer
cleaning up dragging and adding test data
d3f6a06
@onursumer
first commit, adding hongxins toolbar
0665eca
@onursumer
display toolbar (bad layout still)
6c47c34
@onursumer
some performance and other tweaks
7e85a30
@onursumer
new folder for production code
22fb757
@onursumer
change from npm module exports to closure return pattern
397481a
@onursumer
merging changes from trying it in production
2f342e9
@onursumer
update test page for new situation
e95602f
@onursumer
adding mrna to genetic alteration rule, and starting thinking about f…
b83ebf2 
…ast zooming
@onursumer
fast zooming via svg viewboxes
e8ea217
@onursumer
RPPA triangle and proper zoom scaling
1511c85
@onursumer
Cluttered commit...CSS, track groups, GA ruleset impl
b113d1e 
Cleaned up CSS, by changing class names a bit and prepending 'oncoprint-'

Implemented track groups, complete with rendering and dragging

Implemented more of genetic alteration ruleset
@onursumer
clean up a lot, move stuff into another file
8d9700b
@onursumer
taking out useless clipping...browser clips fine apparently. Also add…
3f7a5f4 
…ed useful document fragment rendering
@onursumer
speeding up dragging a bit
52510f7
@onursumer
default genetic alteration config and sorting
8d9e09e
@onursumer
small fix for using default genetic alteration params
689d4bc
@onursumer
legend table instead of svg
16dbff7
@onursumer
small bug fix
18e3434
@onursumer
html for label area instead of svg
cb57de7
adamabeshouse and others added 22 commits May 18, 2022 13:40
@adamabeshouse @onursumer
Merge pull request cBioPortal#118 from cBioPortal/track-group-header
1448ee4 
Track group headers
@adamabeshouse @onursumer
Merge pull request cBioPortal#119 from cBioPortal/allow-sorting-clust…
105aebc 
…ered

Improvements to track sort direction dynamics
@adamabeshouse @onursumer
Merge pull request cBioPortal#120 from cBioPortal/dropdown-issues
8d3d449 
Fix overflow:hidden issues with track group headers, and improve dropdown UIs
@adamabeshouse @onursumer
Merge pull request cBioPortal#121 from cBioPortal/headers-class
c278fdc 
Add classes to track header options elements
@onursumer
Fix error with mouse events caused by column label canvas
f446d8b 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
@adamabeshouse @onursumer
Merge pull request cBioPortal#123 from cBioPortal/custom-na-shapes
4d41a88 
Allow passing in custom na shapes for rule sets
@adamabeshouse @onursumer
Merge pull request cBioPortal#124 from cBioPortal/gaps
803d5c9 
Implement ability to insert column gaps between items of a track that are distinguished in sorting
@adamabeshouse @onursumer
Merge pull request cBioPortal#125 from cBioPortal/fix-zoom-to-fit
af25b1f 
Fix off-by-one error in horz zoom to fit, and rename args to make this error clearer
@onursumer
Fix bug with gap offset calculation due to faulty computation of numb…
4b8ee4c 
…er of for loop steps

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
@adamabeshouse @onursumer
Merge pull request cBioPortal#126 from cBioPortal/on-remove
08fbe87 
Add callback specifically for remove track option in track menu
@adamabeshouse @onursumer
Merge pull request #122 from cBioPortal/number-input
702f5c6 
Performance improvements
@adamabeshouse @onursumer
Merge pull request cBioPortal#127 from cBioPortal/custom-max-height
6610870 
Allow setting max height in initialization
@adamabeshouse @onursumer
Merge pull request cBioPortal#128 from cBioPortal/performance
856fffc 
Performance
@adamabeshouse @onursumer
Merge pull request cBioPortal#129 from cBioPortal/fix-ztf
58d4eb4 
Fix horz zoom to fit calculation
@adamabeshouse @onursumer
Merge pull request cBioPortal#130 from cBioPortal/minimap-placement
93fd60a 
Make minimap appear at top instead of bottom
@adamabeshouse @onursumer
Merge pull request cBioPortal#131 from cBioPortal/inf-fix
ffc870b 
Implement infinite loop in a different way thats hopefully compatible with IE11
@adamabeshouse @onursumer
Merge pull request cBioPortal#132 from cBioPortal/no-prepend
e2ea919 
Dont use prepend, which is not supported in IE11
@adamabeshouse @onursumer
Merge pull request cBioPortal#133 from cBioPortal/dependabot/npm_and_…
31d2c8b 
…yarn/acorn-5.7.4

Bump acorn from 5.7.3 to 5.7.4
@adamabeshouse @onursumer
Merge pull request #134 from cBioPortal/dependabot/npm_and_yarn/jquer…
c76de53 
…y-3.5.0

Bump jquery from 3.4.1 to 3.5.0
@adamabeshouse @onursumer
Merge pull request cBioPortal#136 from cBioPortal/dependabot/npm_and_…
aca7ea3 
…yarn/lodash-4.17.19

Bump lodash from 4.17.15 to 4.17.19
@adamabeshouse @onursumer
Merge pull request cBioPortal#135 from cBioPortal/fix-bug
a5d0a9c 
Fix heatmap bug
@adamabeshouse @onursumer
Merge pull request cBioPortal#137 from cBioPortal/dependabot/npm_and_…
32785b2 
…yarn/elliptic-6.5.3

Bump elliptic from 6.5.1 to 6.5.3
@onursumer onursumer force-pushed the migrate-oncoprintjs branch from 2e4843e to 958a668 Compare May 18, 2022 17:41
onursumer added 3 commits May 18, 2022 17:13
@onursumer
configure build with rollup, fix TS errors
2065dad 
Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>
@onursumer
fix svg files
5c443e9 
Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>
@onursumer
fix tests
e67e2e3 
Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>
@onursumer onursumer force-pushed the migrate-oncoprintjs branch from 958a668 to e67e2e3 Compare May 18, 2022 22:59
@onursumer onursumer mentioned this pull request May 19, 2022
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This PR imports oncoprintjs from an incorrect fork, closing.

Superseded by #4266

@onursumer onursumer closed this May 19, 2022
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4 participants
@onursumer @pambot @inodb @adamabeshouse