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Development #452

Merged
merged 143 commits into from
Jul 18, 2023
Merged

Development #452

merged 143 commits into from
Jul 18, 2023

Commits on Jan 28, 2022

  1. Update README.md

    @jli0980
    jli0980 authored Jan 28, 2022
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  2. Merge pull request #373 from web4bio/beginning 

    Update README.md
    Adit Anand authored Jan 28, 2022
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Commits on Feb 4, 2022

  1. Update README.md

    @prvshenoy01
    prvshenoy01 authored Feb 4, 2022
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Commits on Feb 7, 2022

  1. Update README.md

    @ericr491
    ericr491 authored Feb 7, 2022
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  2. Merge pull request #376 from web4bio/prvshenoy01-patch-1 

    Update README.md
    Adit Anand authored Feb 7, 2022
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  3. Merge pull request #377 from web4bio/ericr491-patch-1 

    Update README.md
    Adit Anand authored Feb 7, 2022
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Commits on Feb 18, 2022

  1. Updated README with Spring 2022 notebooklink

    Adit Anand committed Feb 18, 2022
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Commits on Feb 23, 2022

  1. Merge pull request #379 from web4bio/AditUpdateReadMe 

    Updated README with Spring 2022 notebook link
    Adit Anand authored Feb 23, 2022
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Commits on Apr 29, 2022

  1. Merge branch 'release'

    @rmoffitt
    rmoffitt committed Apr 29, 2022
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  2. Bump minimist from 1.2.5 to 1.2.6 in /archive/eric/imaging 

    Bumps [minimist](https://github.com/substack/minimist) from 1.2.5 to 1.2.6.
- [Release notes](https://github.com/substack/minimist/releases)
- [Commits](https://github.com/substack/minimist/compare/1.2.5...1.2.6)

---
updated-dependencies:
- dependency-name: minimist
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Apr 29, 2022
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  3. Bump url-parse from 1.4.7 to 1.5.10 in /archive/eric/imaging 

    Bumps [url-parse](https://github.com/unshiftio/url-parse) from 1.4.7 to 1.5.10.
- [Release notes](https://github.com/unshiftio/url-parse/releases)
- [Commits](unshiftio/url-parse@1.4.7...1.5.10)

---
updated-dependencies:
- dependency-name: url-parse
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Apr 29, 2022
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  4. Bump async from 2.6.3 to 2.6.4 in /archive/eric/imaging 

    Bumps [async](https://github.com/caolan/async) from 2.6.3 to 2.6.4.
- [Release notes](https://github.com/caolan/async/releases)
- [Changelog](https://github.com/caolan/async/blob/v2.6.4/CHANGELOG.md)
- [Commits](caolan/async@v2.6.3...v2.6.4)

---
updated-dependencies:
- dependency-name: async
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Apr 29, 2022
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  5. Cleaned up alumni

    @rmoffitt
    rmoffitt committed Apr 29, 2022
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  6. Merge pull request #403 from web4bio/cleanup-readme 

    Cleaned up alumni
    @rmoffitt
    rmoffitt authored Apr 29, 2022
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  7. Create dependabot.yml 

    Hopefully?
    @ericr491
    ericr491 authored Apr 29, 2022
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Commits on Jul 1, 2022

  1. Modularize by: 

    - Defining function: computeGeneMutationFrequencies
    @enemeth19
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  2. Modularize by: 

        - Defining function: computeClinicalFeatureFrequencies
    @enemeth19
    enemeth19 committed Jul 1, 2022
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  3. Update variable name to match parameter

    @enemeth19
    enemeth19 committed Jul 1, 2022
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Commits on Jul 4, 2022

  1. Update conf.json

    @ericr491
    ericr491 authored Jul 4, 2022
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  2. Update README.md

    @enemeth19
    enemeth19 authored Jul 4, 2022
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  3. Merge pull request #412 from web4bio/eric 

    Update conf.json
    Adit Anand authored Jul 4, 2022
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  4. Merge pull request #413 from web4bio/enemeth19-patch-1 

    Update README.md
    Adit Anand authored Jul 4, 2022
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  5. Merge pull request #402 from web4bio/dependabot/npm_and_yarn/archive/… 

    …eric/imaging/url-parse-1.5.10

Bump url-parse from 1.4.7 to 1.5.10 in /archive/eric/imaging
    Adit Anand authored Jul 4, 2022
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  6. Merge pull request #401 from web4bio/dependabot/npm_and_yarn/archive/… 

    …eric/imaging/async-2.6.4

Bump async from 2.6.3 to 2.6.4 in /archive/eric/imaging
    Adit Anand authored Jul 4, 2022
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  7. Bump eventsource from 1.0.7 to 1.1.2 in /archive/eric/imaging 

    Bumps [eventsource](https://github.com/EventSource/eventsource) from 1.0.7 to 1.1.2.
- [Release notes](https://github.com/EventSource/eventsource/releases)
- [Changelog](https://github.com/EventSource/eventsource/blob/master/HISTORY.md)
- [Commits](EventSource/eventsource@v1.0.7...v1.1.2)

---
updated-dependencies:
- dependency-name: eventsource
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
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  8. Merge pull request #400 from web4bio/dependabot/npm_and_yarn/archive/… 

    …eric/imaging/minimist-1.2.6

Bump minimist from 1.2.5 to 1.2.6 in /archive/eric/imaging
    Adit Anand authored Jul 4, 2022
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  9. Merge pull request #414 from web4bio/dependabot/npm_and_yarn/archive/… 

    …eric/imaging/eventsource-1.1.2

Bump eventsource from 1.0.7 to 1.1.2 in /archive/eric/imaging
    @enemeth19
    enemeth19 authored Jul 4, 2022
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  10. Update dependabot.yml

    @ericr491
    ericr491 authored Jul 4, 2022
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Commits on Jul 5, 2022

  1. Merge pull request #411 from web4bio/config-bot 

    Create dependabot.yml
    Adit Anand authored Jul 5, 2022
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Commits on Jul 30, 2022

  1. Tidy code

    @enemeth19
    enemeth19 committed Jul 30, 2022
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  2. Selectively exclude 'cohort' from clinical dropdwn

    @enemeth19
    enemeth19 committed Jul 30, 2022
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  3. Merge pull request #405 from web4bio/master 

    Update development branch
    @amaraim22
    amaraim22 authored Jul 30, 2022
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  4. Update URLs for gene and pathway lists

    @enemeth19
    enemeth19 committed Jul 30, 2022
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  5. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …mutationBugs
    @enemeth19
    enemeth19 committed Jul 30, 2022
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  6. Merge pull request #419 from web4bio/mutationBugs 

    Housekeeping
    Adit Anand authored Jul 30, 2022
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Commits on Jul 31, 2022

  1. Merge pull request #421 from web4bio/release 

    Update development and remove release branch
    @enemeth19
    enemeth19 authored Jul 31, 2022
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  2. Merge branch 'release' of https://github.com/web4bio/webgen into erika

    @enemeth19
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  3. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …erika
    @enemeth19
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  4. Modularize buildDataExplorePlots function by: 

    - Defining helper functions:
  - setChartDimensions
  - setLegendLocation
    @enemeth19
    enemeth19 committed Jul 31, 2022
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Commits on Aug 1, 2022

  1. Correct wrong for loop indexing

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  2. Rename variables to be more informative

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  3. Remove redundant code

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  4. Remove redundant code

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  5. Update title and header

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  6. Remove unnecessary helper function

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  7. Remove unnecessary helper function

    @enemeth19
    enemeth19 committed Aug 1, 2022
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  8. Apply usage of global variable: selectedTumorTypes

    @enemeth19
    enemeth19 committed Aug 1, 2022
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Commits on Aug 5, 2022

  1. Modularize buildDataExplorePlots()

    @enemeth19
    enemeth19 committed Aug 5, 2022
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  2. Remove unecessary function calls 

    - Prevent gene 1 select box's onclick  from being triggered on page load
    @enemeth19
    enemeth19 committed Aug 5, 2022
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  3. Prevent re-rendering of all pie charts each time 

    - Only render a pie chart when it is selected by user
- Only delete a pie chart when it is deselected by user
    @enemeth19
    enemeth19 committed Aug 5, 2022
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  4. Prevent errors on window resize

    @enemeth19
    enemeth19 committed Aug 5, 2022
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  5. Add test for presence of element before removal

    @enemeth19
    enemeth19 committed Aug 5, 2022
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Commits on Aug 6, 2022

  1. Add back histograms for continuous data

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  2. Add histogram axis labels and remove underscores

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  3. Update isSelected property of clinicalType array... 

    ...on removal of data explore plot)
    @enemeth19
    enemeth19 committed Aug 6, 2022
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  4. Update for loop indexing and spacing

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  5. Make var names more informative; Adjust spacing

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  6. Remove duplicate function call

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  7. Update histogram hover label; Remove title

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  8. Fix error on double click of histogram 

    - Also:
    - Bind plotly onclick event ONLY to pie charts
    - Bind plotly ondoubleclick event ONLY to histograms
    @enemeth19
    enemeth19 committed Aug 6, 2022
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  9. Correct typo

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  10. Rename vars & remove unecessary call to firebrowse

    @enemeth19
    enemeth19 committed Aug 6, 2022
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  11. Comment out rangeslider on histograms 

    - To simplify UX
    @enemeth19
    enemeth19 committed Aug 6, 2022
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  12. Change background color of histogram hover label

    @enemeth19
    enemeth19 committed Aug 6, 2022
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Commits on Aug 7, 2022

  1. Replace rangeselector w/ horizontal dragmode 

    (for histogram selections)
    @enemeth19
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  2. Correct pageCount: 

    Previously, it was causing a duplicate copy of the clinical data to...
...be returned
    @enemeth19
    enemeth19 committed Aug 7, 2022
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  3. Add back functionality that got lost: 

    (I think it got lost in commit b939e25)

Previously, we were retrieving clinical data for patients that...
...did not have mrnaSeq data, which was not useful.

Now, we only retrieve clinical data for patients that...
...do have mrnaSeq data.
    @enemeth19
    enemeth19 committed Aug 7, 2022
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  4. Remove unecessary clinical data fetch

    @enemeth19
    enemeth19 committed Aug 7, 2022
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Commits on Aug 8, 2022

  1. Merge pull request #425 from web4bio/erika 

    Project maintenance
    @amaraim22
    amaraim22 authored Aug 8, 2022
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Commits on Aug 11, 2022

  1. Remove mode bar from Plotly plots 

    - To simplify UX
    @enemeth19
    enemeth19 committed Aug 11, 2022
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  2. Apply font family to plots 

    (to match rest of app)
    @enemeth19
    enemeth19 committed Aug 11, 2022
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  3. Remove unnecessary call to Firebrowse 

    (firebrowse.fetchCounts)
    @enemeth19
    enemeth19 committed Aug 11, 2022
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  4. Update mutationDataForAllGenesSelected if... 

    ...gene was unselected
    @enemeth19
    enemeth19 committed Aug 11, 2022
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Commits on Aug 31, 2022

  1. Merge pull request #426 from web4bio/erika 

    Data explore plot styling & code maintenance
    @amaraim22
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Commits on Sep 7, 2022

  1. Compute frequencies of combined mutations 

    - i.e., number of patients with >1 mutation type
- Display this info as new sectors in pie charts
- Note: This update is not yet fully integrated with rest of app:
    - Issues with label length on hover
    - Click event of these new pie sectors not yet working
    - Small pie sectors suggest perhaps abadoning pie charts..
    ..in favor of another method of selection
    @enemeth19
    enemeth19 committed Sep 7, 2022
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  2. Integrated with smart caching module

    @ericr491
    ericr491 committed Sep 7, 2022
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Commits on Sep 14, 2022

  1. adding a loading icon for querying cohorts

    @amaraim22
    amaraim22 committed Sep 14, 2022
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Commits on Sep 21, 2022

  1. add a loading icon to load tumor types

    @amaraim22
    amaraim22 committed Sep 21, 2022
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  2. add a loading icon to load tumor types

    @amaraim22
    amaraim22 committed Sep 21, 2022
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  3. Merge pull request #429 from web4bio/page-loading-icon 

    Page loading icon to load tumor types selectbox
    Adit Anand authored Sep 21, 2022
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Commits on Sep 23, 2022

  1. Added debugging console.log statements

    Adit R Anand committed Sep 23, 2022
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  2. Merge remote-tracking branch 'origin/development' into erika

    Adit R Anand committed Sep 23, 2022
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Commits on Sep 28, 2022

  1. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …eric-smart-caching
    @ericr491
    ericr491 committed Sep 28, 2022
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Commits on Oct 5, 2022

  1. Merge pull request #430 from web4bio/eric-smart-caching 

    Enabled the use of Smart Caching module
    Adit Anand authored Oct 5, 2022
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Commits on Oct 6, 2022

  1. Created proposed data structure for storing mutation data with update… 

    …d labels
    Adit R Anand committed Oct 6, 2022
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  2. Merge remote-tracking branch 'origin/development' into erika

    Adit R Anand committed Oct 6, 2022
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Commits on Oct 19, 2022

  1. Added labels

    @ericr491
    ericr491 committed Oct 19, 2022
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  2. Fixed clipping

    @ericr491
    ericr491 committed Oct 19, 2022
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  3. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …eric-smart-caching
    @ericr491
    ericr491 committed Oct 19, 2022
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  4. Added functionality to compute multiple mutation counts. Edge case wh… 

    …ere some wild-type patients are overcounted exists.
    Adit Anand committed Oct 19, 2022
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Commits on Oct 26, 2022

  1. Address clipping

    @ericr491
    ericr491 committed Oct 26, 2022
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  2. computeGeneMutationFrequencies() now computes the correct counts for … 

    …each mutation type. Code needs to be cleaned up for redundant lines.
    Adit Anand committed Oct 26, 2022
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Commits on Nov 2, 2022

  1. Reformatting

    @ericr491
    ericr491 committed Nov 2, 2022
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  2. Patients with multiple mutations now have a valid cohort type mapped … 

    …to their JSON element in global mutation data
    Adit Anand committed Nov 2, 2022
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  3. Patients with multiple mutations now have a valid cohort type mapped … 

    …to their JSON element in global mutation data
    Adit Anand committed Nov 2, 2022
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Commits on Nov 5, 2022

  1. Global mutation object does not store duplicate gene information now.

    Adit Anand committed Nov 5, 2022
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  2. Created getter function for global mutation data object.

    Adit Anand committed Nov 5, 2022
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  3. Updated formatting of computeGeneMutationFrequencies() and revised co… 

    …de to handle the edge case of there being no mutation data associated with a gene.
    Adit Anand committed Nov 5, 2022
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  4. Revised JSON property names for global mutation data object

    Adit Anand committed Nov 5, 2022
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Commits on Nov 7, 2022

  1. v1

    @ericr491
    ericr491 committed Nov 7, 2022
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Commits on Nov 9, 2022

  1. Added comments for incorporating new mutation data object after data … 

    …exploration.
    Adit Anand committed Nov 9, 2022
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  2. Merge remote-tracking branch 'origin/eric-smart-caching' into erika

    Adit Anand committed Nov 9, 2022
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Commits on Nov 10, 2022

  1. Made some variable name/scope fixes to smartCache functions. Added de… 

    …bug messages to computeGeneMutationFrequencies() for Eric's convenience
    Adit Anand committed Nov 10, 2022
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Commits on Nov 16, 2022

  1. Implemented setTimeout() function in fetchWrapperMU()

    Adit Anand committed Nov 16, 2022
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Commits on Dec 6, 2022

  1. Reverted caching of mutation data to original data structure format. … 

    …Need to update to reflect 11-30 updates.
    Adit Anand committed Dec 6, 2022
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Commits on Dec 8, 2022

  1. Merge pull request #431 from web4bio/eric-smart-caching 

    Added x and y labels to the HeatMap
    Adit Anand authored Dec 8, 2022
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Commits on Feb 4, 2023

  1. Merge pull request #436 from web4bio/erika 

    computeGeneMutationFrequencies() Functionality and Smart Caching for Mutation Data
    @amaraim22
    amaraim22 authored Feb 4, 2023
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Commits on Feb 8, 2023

  1. Change title of index.html for future generations

    Adit Anand committed Feb 8, 2023
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Commits on Mar 8, 2023

  1. Added barcode caching (works in debugger mode) and changed index.html… 

    … title property
    Adit Anand committed Mar 8, 2023
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  2. debugging

    @amaraim22
    amaraim22 committed Mar 8, 2023
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Commits on Mar 28, 2023

  1. Finished barcode caching functionality. Still need to replace firebro… 

    …wse function call in executeQueriesBAR() with higher-level caching method.
    Adit Anand committed Mar 28, 2023
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Commits on Mar 29, 2023

  1. Merge pull request #447 from web4bio/barcodeCaching 

    Barcode caching
    @amaraim22
    amaraim22 authored Mar 29, 2023
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  2. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …clinical_data_caching
    @amaraim22
    amaraim22 committed Mar 29, 2023
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Commits on Apr 5, 2023

  1. Developed proper constructQueries() and executeQueries() functions fo… 

    …r gene expression caching. Function now needs to return properly set-up 2-D array for gene expression data.
    Adit Anand committed Apr 5, 2023
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  2. fetchWrapperGE() now caches gene expression data properly! Need to st… 

    …ress-test and possibly change structure of how data is returned by function.
    Adit Anand committed Apr 5, 2023
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Commits on Apr 19, 2023

  1. initial clinical cache

    @amaraim22
    amaraim22 committed Apr 19, 2023
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  2. finished fetchWrapper, contructQueries, and getCache

    @amaraim22
    amaraim22 committed Apr 19, 2023
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Commits on Apr 26, 2023

  1. Gene caching is now functional

    = committed Apr 26, 2023
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  2. Added better comments to fetchWrapperGE() and remove extraneous comments

    = committed Apr 26, 2023
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  3. Added caching call to getDataFromSelectedPieSectors.js for testing pu… 

    …rposes
    = committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. setting up clinical caching

    @amaraim22
    amaraim22 committed Apr 27, 2023
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  2. Merge pull request #448 from web4bio/gene-expression-caching-testing 

    Gene expression caching complete
    @amaraim22
    amaraim22 authored Apr 27, 2023
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  3. merged PR from GE caching

    @amaraim22
    amaraim22 committed Apr 27, 2023
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Commits on May 3, 2023

  1. error at unsync document

    @amaraim22
    amaraim22 committed May 3, 2023
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Commits on Jul 10, 2023

  1. Added content to fetchWrapperMU()

    @adit-anand
    adit-anand committed Jul 10, 2023
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  2. Updated base URL for _fetchFromFireBrowse() to corsproxy.io

    @adit-anand
    adit-anand committed Jul 10, 2023
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  3. Merge pull request #449 from web4bio/update-fetch-url 

    Update Base URL
    @amaraim22
    amaraim22 authored Jul 10, 2023
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  4. Merge remote-tracking branch 'origin/development' into mutation-caching

    @adit-anand
    adit-anand committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. Mutation formatting code is now in caching main.js file

    @adit-anand
    adit-anand committed Jul 11, 2023
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Commits on Jul 14, 2023

  1. Completed mutation caching functionality and mutation type pie charts… 

    … now get generated
    @adit-anand
    adit-anand committed Jul 14, 2023
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  2. Added documentation to fetchWrapperMU()

    @adit-anand
    adit-anand committed Jul 14, 2023
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  3. Multiple mutation records for the same mutation type are now not trea… 

    …ted as distinct when categorizing a patient's mutation
    @adit-anand
    adit-anand committed Jul 14, 2023
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  4. When mutation labels are created, the variant classifications that co… 

    …mprise them are now sorted alphabetically
    @adit-anand
    adit-anand committed Jul 14, 2023
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  5. Added documentation to caching functions

    @adit-anand
    adit-anand committed Jul 14, 2023
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Commits on Jul 15, 2023

  1. Changed mutation caching interface to filter by barcodes instead of m… 

    …utation type
    @adit-anand
    adit-anand committed Jul 15, 2023
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Commits on Jul 16, 2023

  1. Merge branch 'development' of https://github.com/web4bio/webgen into … 

    …clinical_data_caching
    @amaraim22
    amaraim22 committed Jul 16, 2023
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  2. clinical caching initial stage

    @amaraim22
    amaraim22 committed Jul 16, 2023
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  3. Fixed bug with excess clinical data being fetched

    @adit-anand
    adit-anand committed Jul 16, 2023
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Commits on Jul 17, 2023

  1. Updated parameters for clinical caching add() and saveToDB()

    @adit-anand
    adit-anand committed Jul 17, 2023
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  2. Resolved merge conflicts

    @adit-anand
    adit-anand committed Jul 17, 2023
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  3. Added error handling for Firebrowse calls

    @adit-anand
    adit-anand committed Jul 17, 2023
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  4. Added barcode filtering logic to fetchWrapperCLIN()

    @adit-anand
    adit-anand committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. Merge pull request #450 from web4bio/mutation-caching 

    Mutation caching
    @amaraim22
    amaraim22 authored Jul 18, 2023
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