Change Log

All notable changes to this project will be documented in this file.

Unreleased

2.83.0

Features:

allow hiercluster to work with numeric dictionary term data

Fixes:

Removed cloneDeep import to fix bundling issue
detect and set the gdc version first before caching

2.82.1

Fixes:

Removed cloneDeep import to fix bundling issue

2.82.0

Features:

Added example of the .mclassOverride argument in the Additional Track Features cards

2.81.6

Fixes:

report genome name on samtools-fasta error

2.81.5

General:

Phenotree parser accepts a new 'unit' column for numeric terms.

Fixes:

create src/helper.ts with joinUrl()
prototype cnv filter prompt to change cnvMaxLength
handle genes that has no expression data for any sample in the gene exp clustering tool
Add a footnote to the bottom of survival plot p-value table to explaine that pvalues are still computed with all survival data when Survival Time Cut-Off is set

2.81.4-0

Fixes:

if a small number of radios, show in a single line by default
do not allow <3 genes in the termdb/cluster request and instruct the user to do a page refresh to clear the error

2.81.3

Fixes:

use string concat to preserve the apiHost.geneExp path that was being stripped by url.resolve()

2.81.2

Fixes:

use url.resolve() for GDC gene_selection route URL

2.81.1

Fixes:

matrix cnv: when cnv has quantification, cell tooltip should show it in addition to gain/loss

2.81.0

Features:

Instead of the code updated date, the header displays the release version a link to the appropriate github release page.

2.80.0

Features:

inclusion of univariate results in a multivariable regression analysis is now a user-controllable option that is enabled in all datasets

2.79.7

Fixes:

wait for the genelookup request to return before detecting when to display genesearch errors

2.79.6

Fixes:

fix geneSearchBox errors: 1. type a valid gene name and enter, see "Gene not found". 2. type a valid gene name and enter, see previous gene typed. 3. type a valid gene name and enter, gene hits still showing.
BAM Slicing Download and Sequence Reads: Disable Submit button when 1. case/file is loading, 2. Under Variants tab, variant not selected, 3. Under Gene or position tab, no valid result from search box.

2.79.5

Fixes:

pass unfrozen filter to launch mds3 tk from Disco

2.79.4

Fixes:

reset highlighted top/left dendrogram to black when data changed

2.79.3

Fixes:

fix the workspace directory detection/loop when publishing packages

2.79.2

Fixes:

fix the order of workspace entries, which affects order of publishing

2.79.1

Fixes:

fix CI-related scripts to include shared workspace versioning and packing

2.79.0

Features:

Survival plot: add a control "Survival Time Cut-Off" to filter out all the survival data with Time-to-Event longer than Survival Time Cut-Off

Fixes:

section 508 issues in singleCellPlot controls: aria-label should be on element with roles
wip fix to limit cnv track to under 200px for lots of cnv segments
support new GDC /status api return in stale cache check
survival plot: use pre-defined order in db for overlay and divideby
scatter plot: use pre-defined order in db for divideby

2.78.0

Features:

compute both univariate and multivariate analyses by default in multivariate regression analysis for Neuro-Oncology datasets
Support GDC scrna gene exp API (only in qa-int) for GDC scRNA-seq plot

Fixes:

address section 508 issues for GDC Sequence Read and BAM slicing download apps
initialize optional matrix tw props in TwBase constructor

2.77.1

Fixes:

genome browser plot now saves mds3 subtracks in state and recover from session

2.77.0

Features:

May change the shape of lollipop skewers when the track is filtered or a subtrack.

2.76.2

Fixes:

Address section 508 issues in OncoMatrix and Gene Expression Clustering tools
fetch genomes supporting specific datasets from a specified host
allow q.mode=continuous for q.type=custom-bin to fix numeric edit UI toggling

2.76.1

Fixes:

At mass summary plot header, when there's only one subtype tab, do not show the toggle

2.76.0

Features:

Support scRNAseq analysis tool in GFF

Fixes:

improve text color contrast in PP SSM lollipop view

2.75.0

Features:

wsiviewer - load files and metadata from db
Add brain imaging as individual chart type, use a sample table to select samples to plot on template.
Able to open an app card on an example with new example URL parameter.
Integration tests for the sample view plot in the mass app.
Prototype for about tab in mass ui. Intended to build out per dataset.
display WSI metadata

Fixes:

Disable sample view download data button when an invalid sample id is entered.
revert opacity=0 on hidden legend items so they are always shown
matrix groups should be sorted based on order defined in divideby term
allow empty categorical term.values
shouldn't show multiple testing correction when association test skipped due to limited sample size
fix sample view WSI checkbox issue
create a custom term with just one group the custom term has equal number of samples in each group
At gdc bam slicing ui, replace outdated sample_type with new terms

2.74.2

Fixes:

Mass app removes invalid plots from the state on init.

2.74.1

Fixes:

always show Processing data... when a divideby term is selected for oncoMatrix and hierCluster
Removed the host from the whole slide imaging card for testing

2.74.0

Features:

WSIViewer launchable from runproteinpaint() as a mass plot.
Example for the WSIViewer available from the app drawer.
hierCluster: click left dendrogram to highlight selected cluster, and show options to list items (add link to GDC gene page for genes) and perform ORA

Fixes:

At GDC lollipop subtrack, disable survival term when building the filter
fix file-based session recovery of regression plot
matrix divideby breaks when using gene exp

2.73.0

Features:

From custom variable -> gene expression, submit one gene will launch violin plot overlayed by the custom variable, submit two genes will launch scatter plot colored by the custom variable.
In the gene set edit UI: If available in the dataset, more controls are available to edit gene lists for top variably expressed genes.

Fixes:

fix the error that when hiercluster is using divideBy, the tw will not show in Cases menu for gdc"
from matrix term group edit menu, term group name submit button will close the term group edit menu.
fix the error: from matrix term group edit menu, delete group name and submit still show the old name.
Assign alive/dead labels to GDC survival exit codes
add missing return in switch statement that breaks dual-term select ui
when a term has no computable values, do not calculate descriptive stats that breaks
Fix wsi request type issue

2.72.0

Features:

support up to 1000 genes in GDC Gene Expression Clustering tool
Add Whole Slide Images Viewer to the project

2.71.0

Features:

In addition to launching the sample view, the user may also see a simplified list and/or create a group from selected samples from the facet table.
Allow to divide hierCluster by a term
Allow to launch geneExpression hierCluster from custom variable

Fixes:

Proper pass case filter to GenesTable gdc query so ssm case count can correspond to filter

2.70.4

Fixes:

Facet table renders for all datasets.
oncomatrix and gene expression hiercluster genes menu: at editing a group, move the group selector from secondary menu to primary menu

2.70.3

Fixes:

prototype to allow GDC dictionary terms to work for barchart and query data without any genomic filter

2.70.2

Fixes:

on validating container, gdc logic will skip case caching and stale cache check
improve getData() to handle missing bin config for gene exp term for better performance

2.70.1

Fixes:

pp and gdc filter are passed to getDefaultBin request for gene exp terms etc. bins are always computed against cohort to be precise
violin data request at gene exp termsetting ui observes filter0

2.70.0

Features:

prototype periodic check if gdc case-id-cache is stale and re-cache

Fixes:

Allow to add survival term to GDC gene expression clustering map

2.69.0

General:

bug fix: when clicking labels on violin plot breaks on master

Features:

matrix and hiercluster: allow to recompute term shown in continuous mode as zscore

Fixes:

pass filter0 in barchart request to work for gdc data

2.68.0

Features:

New Data Matrix and Gene Expression cards on the homepage
Enable edit option for geneVariant terms in oncoMatrix
New continuous variables scatter plot example available from the scatter plot card on the homepage.
New GDC sample disco plot example available from the disco card on the homepage.
implemented the "snp" term type for summarizing and analyzing sample genotypes for a given SNP
allow the drag/drop of rows from non-clustered row groups
Added Facet plot to the UI
New gene expression example available from the scatter plot card on the homepage.
In the gene set edit UI, user is able to choose returning all genes or compare against a predefined or custom gene set.
Handle custom matrix geneset input option
In GDC gene exp clustering, when screening user-defined gene sets, use a close-to-zero min_median_log2_uqfpkm parameter to keep more genes expressed at low level

Fixes:

hierCluster group Add_Rows ui can only add compatible terms
filter0 is passed to violin request and improve to enable type checking
gene expression hierCluster group Add_Rows ui can only add gene expression terms
pass filter0 at sampleScatter to enable gdc gene exp plot, remove duplicating backend call for gene exp data
allow GDC gene exp scatter plot to show case name

2.67.1

Fixes:

improve oncomatrix non-ci test to include gene expression and survival, and CNV-only cohort

DevOps:

Trigger browser notiffications of dev events such as rebundling status

2.67.0

Features:

Support inputing custom CNV segments in mds3 tk, improve cnv rendering
Support overall survival data from gdc
New Publications button in the ProteinPaint header. Results are searchable in the omnisearch.
support drag-and-drop groupsetting for geneVariant term
support geneVariant term in regression analysis

Fixes:

provide null values to brush range if there is no selection on brushing
hiercluster refactored not to pretend geneVariant term type
Centralize filter rehydration
hiercluster: set missing term type based on data type

2.66.0

Features:

Added use case to open the single cell gene expression violin of a sample

Fixes:

At oncomatrix, allow gene expression term to pull data on all cases
matrix: hover/click menu over geneexp/metabolite rows should indicate term type, and do not show undefined for missing data
singlecell native gene exp data is loaded from rds file; no longer grep
Speed up top variably expressed genes query from gdc api, directly submit case filter and do not first retrieve list of cases
fix definitions for termsbyid route

2.65.0

Features:

Single cell plots support now color by gene if geneExpression data it is provided

Fixes:

Handle json payload for requests that contain authentication token

2.64.0

Features:

Allow switching to other color scheme for hierCluster

Fixes:

getFilterName() treats geneExp and metabolite same as float terms
use Mds3 ttype, to catch potential typescript errors, early in termdb/config route handler functions

2.63.6

Fixes:

create minified msigdb and associate to hg38-test for CI
set appropriate response headers for all responses

2.63.5

Fixes:

bug fix to pass terms[] when filtering by metaboliteIntensity
use diagnosis specific age cutoff for the CHC burden calculation
mds3 tk assigns vocabApi.app.opts.genome in adhoc manner for gene search to work in stateless filter UI
fix the detection of hierCluster term group when handling a gene expression cell click

2.63.4

Fixes:

fix the generation of Function constructor arguments for dataset configured data getters and mappers

2.63.3

Fixes:

make the matrix react to divide-by term edits from the label click

2.63.3-2

Features:

Matrix plot survival term improvements: mouseover time-to-event and exit code info, color coding

2.63.3-1

Fixes:

Replace "patients" with "samples" in barchart plots

2.63.3-0

Fixes:

Fix termsetting scale for density plots

2.63.2

Fixes:

bug fix to only apply niceNumLabels() when numeric tvs is not unbounded
bug fix to allow for interactions with molecular variables in regression analysis
test run on all genome tabix files on server launch to detect old index file issue early
add missing jsonwebtoken import

DevOps:

use esbuild in client unit and integration tests

2.63.1

Fixes:

Fix setHostUrl function.

2.63.0

Features:

Allow to add survival terms to oncoMatrix

Fixes:

show a border on select dropdown elements, within sja scope

DevOps:

replace client dev scripts and html to use esbuild-bundled code

2.62.0

Features:

geneVariant term now supports grouping variants into predefined groups

2.61.2

Fixes:

Limit the css reset to not conflict with embedder styles, by using scoped normalize css rules

2.61.1

Fixes:

handle prebuilt matrix plots to work with the advanced sorter UI
scope PP-specific css resets and styles to the root holder, such as the previously unscoped h2 style

2.61.0

Features:

Adding sorting samples options for hierCluster

2.60.0

Features:

Data for the hic whole genome view is cached for faster load. Additional UI improvements in the hic app.

Fixes:

fixed rendering of barchart and violin when terms have uncomputable categories
Fixed issues with the resolution in the hic detail view.

2.59.0

Features:

GDC bam app can visualize truncated bam slice when streaming is terminated due to hitting max size
Supported geneExpression filtering

Fixes:

Mds3 backend reuse gene search helper to be able to find a gene by isoform access in addition to symbol

2.58.1

Fixes:

import findParent in the groups component and create tests

2.58.0

General:

Update custom mutation data instruction.

Features:

Significant improvements to the whole genome hic app including: faster load, ability to launch the chromosome pair and detail view from runproteinpaint(), rendering fixes, additional min cutoff input, and change to reactive app.
support dataset-specific healthcheck information
In mds3 tk, add Point up/down option when in skewer mode

Fixes:

Filter mutations checkbox is not shown for if there is no CGC
Bcf url argument for mds3 tracks fixed.
No empty gdc filter elements will be created when mapping pp filter to GDC format
show the incomplete caching message in the gene expression app
COSMIC mds3 track bug fix, number of variants will go down in subtrack with sample filtering

2.57.0

Features:

enable 'lollipop' plot btn through tsne sample clicking for geneVariant terms

Fixes:

GDC sequence reads viz no longer limits slicing range; the only limit is slice file size
GDC bam slicing ui show actual number of available bam files which can be lower than 1000, fix scrollbar appearance
Updated protein domain color is applied to all instances of this domain, not just first one
replace 'view' with 'Sample view' on tsne sample label clicking

2.56.0

Features:

Disco plot: added hambuger menu
Disco plot: added option to render CNVs as heatmap and barchart
Disco plot: added option to set percentile for CNV rendering

2.55.1

Fixes:

prevent showing a blank CNV legend in the lolllipop app

2.55.0

Features:

oncoMatrix: after hiding a category from divideBy term, add an option to divideBy button to bring it back

Fixes:

numeric setdefaultq() will default to term's own default bin type rather than always hardcoding to regular-bin
Pass request header containing session when querying arriba file which is controlled
improve GDC cohortMAF ui to add case link and make scrollbar more apparent

2.54.0

Features:

Click on protein domain legend to show menu options to toggle visibility and change color.

Fixes:

email log bug fix

2.53.0

Features:

Both mutation and sv/fusion data can be submitted in one ui to create custom mds3 tk
New BCF card on the home page. See proteinpaint.stjude.org/?appcard=BCF.

Fixes:

fix npm start
address mds3 mclass legend error by not setting uninitiated flag to true

2.52.0

Features:

enable downloading data for oncoMatrix

2.51.2

Fixes:

fix position errors after oncoMatrix/hierCluster zooming in/out caused by outdated imgBox
when parsing phenotree, enforce uncomputable categories are numbers also

2.51.1

Fixes:

Oncomatrix do not allow to hide all the alteration groups

2.51.0

Features:

Support survival term as outcome variable in regression analysis

2.50.0

Features:

include auth test status in server healthcheck
Hide synonymous mutations by default for GDC oncoMatrix
Improve the matrix sorting options to easily toggle sorting by cnv and/or consequence

Fixes:

fix the error from genomic alterations rendering when there are no mutations or CNV data
In GDC query, do not supply empty "case_filters{content[]}" that will slow down API. lollipop and oncomatrix are now faster when there's no cohort
at GDC bam slicing UI, the table listing available cases and bam files can be filtered by assay types
Add to GDC oncoMatrix mutation/cnv buttons all available mutation/cnv classes in GDC instead of all available mutation/cnv classes in the current matrix

2.49.0

Features:

Display hints about persisted matrix gene set and option to unhide CNV and mutations when there is no matrix data to render
Stream data into and out of R using the run_R.js module
Reenable the option to create a single sample cohort from a lollipop sample table/menu

Fixes:

refactor to move all gdc plot launchers into a separate folder

2.48.1

Fixes:

GDC bam slicing download app now calls gdc api directly from client without going through pp backend
Group similar mutation class colors together when sorting matrix samples and if CNVs are displayed
Add Single style for GDC oncoMatrix

2.48.0

Features:

enable selecting individual mclasses upon clicking GDC oncomatrix mutation/cnv button

Fixes:

Fix the timeout issues when using ky http client
change the defination of trancating/protein-changing mutation, change oncomatrix mclasses sorting order
Fix to unhide a survival series by clicking its corresponding legend entry
Do not persist highlighted dendrogram branch selection when the hier. cluster data changes due to changes to cohort, clustering method, etc.
Disable the geneset submit button when there there is less than a minNumGenes option (3 for hier cluster, 1 for matrix)

2.47.1

Fixes:

Include gfClient to the pp deps image
remove main menu renderer from disco plot

2.47.0

Features:

Add Mutation and CNV control buttons for GDC. Hide CNV by default for GDC.

Fixes:

Fix custom jwt processing by replacing the remaining webpack_require in auth code
Do not force the sample table to be positioned relative to screen bottom after a sunburst click

2.46.4

Fixes:

updated mclass definitions and rank for protein_altering_variant
mds3 tk temporarily disables sample selection button in single sample table, to avoid creating single-case cohort in GDC
deprecated term "sample_type" is dropped from GDC dictionary

2.46.3

Fixes:

preliminary fix for mds3 tk using custom bcf file to pull mutated smples

2.46.2

Fixes:

Dataset configuration should have limited access to server code

2.46.1

Fixes:

when a term has only 2 categories, then only a single category needs to be tested in the association test
Return early on server validation instead of proceeding with startup

2.46.0

Features:

Migrate the CJS server workspace into an ESM package

Fixes:

Fix disco plot width issue
Restore drag to resize on legacy ds gene exp panel

2.45.0

Features:

Add test-data-ids to enable mds3 e2e testing

2.44.0

2.43.2

Fixes:

GDC BAM slicing will be terminated if slice file size exceeds a limit (user is informed)

2.43.1

Fixes:

switching GDC mds3 track from gene to genomic mode it can properly display ssm now

2.43.0

Features:

enable geneVariant legend group filter for hierCluster
combine all dts (except for dt=4) into mutations/consequences legend group for dt without assay availability

Fixes:

allow to use a simplified filterObj on mds3 tk that will be hydrated on launch

2.42.2

Fixes:

mds3 tk sample summary table will scroll if too tall

2.42.1

Fixes:

Replace require syntax with import to prevent bundling errors in client package bundlers

2.42.0

Features:

upgrade node from v16 to v20

Fixes:

Show user error message for an invalid genome provided in a URL. Error message contains the list of available genomes from that server.

2.41.1

Fixes:

when downloading GDC bam slice (no caching), do not limit request region max size;
Reload page while streaming/downloading gdc bam slice to client will not crash server
GDC bam slice ui requires hitting Enter to search and no longer auto search to avoid showing duplicate ssm table
support ?massnative=genome,dslabel url parameter shorthand

2.41.0

Features:

adding geneset edit ui from Gene Expression chart button

Fixes:

Bug fix to show correct category total size by passing a missing filter0
profilegenevalue track reports subtrack file error in a legible way
Bug fix for disco plot launched from sunburst shows aachange in sandbox header rather than undefined

2.40.8

Fixes:

BAM track bug fix to handle reads with no sequence and not to break.
BAM track bug fix to not to break by hide/show toggling at track menu
In GDC BAM slicing, before creating new cache file, find out old enough ones to delete to free up storage
Bug fix to convert "case." to "cases." in case_filters[] for GDC mds3 sunburst clicking to load sample table
Bug fix for GDC mds3 category total sample count to respond/shrink with cohort change
Prevent double-clicking on a sunburst ring so that same sample table will not appear duplicated

2.40.7

Fixes:

Fix the detection of sorting-related updates in the matrix app, as distinct from the hier cluster
Pass the cohort filter to the lollipop track from the matrix gene label click
Pass the cohort filter to the lollipop track from the matrix and disco plot label click

2.40.6

Fixes:

Refactor and improve backend GDC BAM slicing logic
BAM track in variant-typing mode, read group header clicking is disabled due to known issue with GFF
GDC BAM slicing will reject if range>=50kb to be safe
reliably detect stale async results using a rx component api method
Cancel stale fetch requests to unblock current geneset, matrix, and hierCluster requests that are being throttled by the browser's concurrent request limit
Do not re-render the matrix controls as part of displaying a no data message when svg dimensions and layout have not been computed yet
Do not assign a non-auth related error as a token verification message, which caused the matrix to not rerender even with subsequent valid data
Do not display a mouseover over a hidden matrix or hier cluster svg
an unrendered matrix or hierCluster should not react to window resize

2.40.5

Fixes:

do not redispatch a plot_splice from the oncomatrix and gene expression launchers

2.40.4

Fixes:

Hide the undo/redo buttons until a more thorough fix is implemented for the oncomatrix and gene expression

2.40.3

Fixes:

Matrix must skip data processing steps after detecting stale action, to avoid confusing rerenders

2.40.2

Fixes:

Fix OncoMatrix and hierCluster brushing and list samples issue
refresh the case count when there is no matching oncomatrix data
pass opts.hierCluster in the launcher to handle create cohort
hide the svg on error or matching data
darken table2col row titles to meet Section 508 contrast requirements
do not show the option to replace a gene expression/hierCluster term

2.40.1

Fixes:

Return a defined adjusted state for the GDC matrix and gene expression tools, so that the undo/redo component can react
Increase the contrast of the table header text in the BAM files and variants list
Fix the geneFilter handling in the gdc tool launchers

2.40.0

Features:

Hi-C whole genome view supports different matrix types (e.g. observed, expected, etc.). Users can select different matrix types from dropdown.
The Hi-C whole genome view now calculates the cutoff on load and with user changes. Previously, the default was 5000.

Fixes:

GDC bam slicing UI can still pull BAM files when experimental_strategy=Methylation Array filtering is used
support navigation-by-keyboard of bam UI elements
fix the display of no data error message and hiding of previously rendered heatmap in the hier cluster app
For hierCluster, set left dendrogram position based on max gene label length, ignore variable labels.
ignore the computed twlst of the hierCluster term group when tracking recoverable state
Do not modify the hierCluster term group lst with server data, to avoid unnecessary state tracking and to prevent unwanted geneset edits
Use the geneset edit UI when there is no initial computed geneset for hierCluster

2.39.6

Fixes:

Do not show the "Edit" option when clicking a gene row label in matrix
detect and handle race conditions in the matrix and hiercluster server data requests

2.39.5

Fixes:

Use graphql query to replace /analysis/top_mutated_genes_by_project in GDC OncoMatrix
Ensure that an embedder loading overlay gets triggered using the app callbacks.preDispatch option

2.39.4

Fixes:

GDC bam slicing UI bug fix to forget previous coordinate input box search result
Always trigger the closing of an embedder's loading overlay, even when there are no chart state changes
Block track menu will not allow to hide a GDC bam tk, and no longer shows delete button for custom tracks

2.39.3

Fixes:

Supply the missing api reference when launching a gdc matrix
Option to override the matrix default of not rendering samples that are not annotated for any dictionary term, for more intuitive behavior in gene-centric use-cases
Matrix should update when the filter0 changes while the geneset edit UI is displayed
Ensure that the zoom controls has valid dimensions on update, in case it was initially rendered in an invisible div

DevOps:

Detect unreleased notes in the CHANGELOG, in addition to the release.txt

2.39.2

Fixes:

Detect empty hits before trying to render bam variants
Reenable the handling of genome-level termdbs in the migrated server route
Display an initial geneset edit UI when the GDC default matrix genes is empty
Exclude embedder state in the standalone recover tracked state, for the matrix and hier cluster undo/redo

2.39.1

Fixes:

Disable the term group menu for hierCluster gene expression term group, and remove the 'edit' and 'sort' options for other hier cluster term groups
Fix the navigation of matrix and gene expression controls by keyboard

2.39.0

Features:

GDC cohort-MAF tool: allow to customize output file columns
Clicking matrix cell to show similar info table as hovering over the matrix cell.
Mds3 track uses simpler radio buttons to toggle between view modes such as lollipop and occurrence

Fixes:

Gene exp clustering will display an alert msg to inform user that a map is not doable when there is just one gene
display total number of mutations on disco plot
Fix oncomatrix error: adding dictionary term from row group menu
Numeric termsetting edit UI allows a term to be default with custom bin config and will not switch to regular binning

2.38.1

Fixes:

for hierCluster, nodejs always transform to zscore; use scaleLinear for improved heatmap rendering
Fix the handling of multi-valued samples and group overlaps
GDC gene exp clustering bug fix on querying data for dictionary variables and leads to speeding up

2.38.0

Features:

Always show a menu after brushing matrix: Zoom in, List samples, and Add to a group/create cohort.

Fixes:

Add clang missing dependency
Fixed issues showing variable definition with termsetting instance, especially in chart edit menu.
GDC OncoMatrix: use a more human-readable case ID as label instead of the UUID
Fix the samplelst filter editor and auto-update of the pill label

2.37.0

Features:

custom colors can now be assigned to custom groups

Fixes:

Show a message about loading top gene in GDC hierCluster app

2.36.0

Features:

show # of samples and add link for samples for dendrogram list sample menu option

Fixes:

do not re-parse the already parsed result from cachedFetch
Detect failure on GDC data caching and abort launch
fix hierCluster gene dendrogram misaligned upon panning

2.35.1

Fixes:

fix the toFixed error that randomly occurs when zoom on matrix.

2.35.0

Features:

Click dendrogram to highlight sub-branches, zoom in and select cases underneath

Fixes:

topVariablyExpressedGenes is changed from a GDC-specific route to general purpose route. Awaiting further work for non-gdc dataset

2.34.1

Fixes:

GDC BAM slicing UI will reject non-BAM files.
GDC BAM slicing UI now works with submitter or UUID of samples and aliquots, in addition to cases
GDC BAM slicing UI shares a common route to retrieve ssm by case, reducing code duplication

2.34.0

Features:

Disco plot UI now allows users to upload tab delimited data

Fixes:

Use a urlTemplates.gene.defaultText option to make a gene external link more intuitive
Allow ssm url to be supplied from both snvindel query and termdb, so termdb-less clinvar is able to link to ClinVar portal
Hardcoded normalization methods replaced with values encoded in Hi-C files.
Disco plot now detects and reports data issues from user submitted data.
Gdc bam slice download handles case with no ssm; bam table changes to radio to force single-selection; table.js bug fix to use unique input name
Fix the processing of hierCluster overrides

2.33.1

Fixes:

Use a urlTemplates.gene.defaultText option to make a gene external link more intuitive

2.33.0

Features:

GDC BAM slicing UI supports new "download mode", will directly download BAM slice to client, including unmapped reads.
Click matrix cell to launch gene summary and case summary page, click row label to launch gene summary page, click case id to launch case summary

2.32.1

Fixes:

Bug fix to allow mds3 track variant download to work again

2.32.0

Features:

In mds3 track, new option allows to show/hide variant labels
Support optional postRender and error callbacks from the embedded wrapper code

Fixes:

Bug fix that creating mds3 subtrack with long filter name breaks

2.31.0

Features:

highlight the row and column of the matrix cell when hovering over it, allow the users to select color for the highlighter
profile plots now have filters to the left and the new data model is plotted
Use the GDC gene expression API to request top variably expressed genes

Fixes:

In genetic association analysis, principal component covariates now use actual term names from db, rather than hardcoded adhoc name

2.30.5

Fixes:

After creating mds3 subtrack via filtering, term name may be printed with value if short enough
Mutation AAchange showing in scatterplot and matrix are now based on canonical isoform
Darken selected colors for gencode and sandbox title, to address Section 508 contrast issues

2.30.4

Fixes:

skip the GDC aliquot caching when validating the server configuration, data, and startup

2.30.3

Fixes:

GDC maf ui indicates total size of selected files
Bin default age ranges by 30 and 60 years for GDC age_at_diagnosis

2.30.2

Fixes:

In mass sampleview, expanding tree branch everytime no longer triggers rerendering of disco/ssgq plots
Disco: file name of downloaded svg preserves context including sample name and gene.
Disco: by default it now prioritize CGC genes in hg38.
Various scatterplot fixes: tooltip dot scale, divideBy bug
Fix the session recovery within an embedder portal

2.30.1

Fixes:

use a more specific class selector for detecting pill divs in the data download app

2.30.0

Features:

Support clicking matrix legends and matrix legend group names to use as filters.

Fixes:

Revert prev change that cause hic genome view to misalign

2.29.6

Fixes:

Restore yellow highlight line when moving cursor over a genome browser block

2.29.5

Fixes:

In GDC disco and bam slicing UI, detect when total number of SSM exceeds view limit and indicate such

2.29.4

Fixes:

Supply the svg element as argument to the disco plot download handler
in termsetting constructor option, getBodyParams() replaces getCurrentGeneNames() as a general and flexible solution

DevOps:

fix the tp dir setup and package.json deps update for the integration test CI

2.29.3

Fixes:

Bug fix to revert termdb/category route usage.
search term with space character for genomic-equipped dataset should not break by gene search msg

2.29.2

Fixes:

Use a jwt bearer auth to propagate basic session state to multiple PP server processes, beyond the server process that processed the /dslogin request
Bug fix.

2.29.1

Fixes:

Minor bug fixes.

2.29.0

2.28.0

Features:

Added radar plots to the profile

2.27.2

Correctly parse a null URL parameter value

2.27.1

Features:

Disco plot UI with an example on the app drawer. Users can provide SNV, SV, and CNV data to create a disco plot.
We can support now reading hic files for versions 7, 8 and 9
Support different auth methods for the same dataset, by server route and app embedder.
New button in geneset edit UI allowing to load top variably expressed genes in hierarchical clustering, for eligible datasets
Support clicking matrix legends to use as filters.

2.27.0

Features:

Prototyped single sample viewer
Default bin configs for GDC numeric variables are determined on the fly and no longer hardcoded
For matrix plot, when hovering over gene label, show the percentage of mutation (#mutated samples / #tested sample)
Click the divide-by term at the top left corner of matrix plot to edit, replace, or delete
Display average admix coefficient for filter-vs-population comparison in genome browser
Prototyped a server route for cumulative burden estimates
Prototyped support for disco plot to show adhoc data

Fixes:

Fix for sorting the custom bin labels on numeric terms in violin plot
Gracefully handle a Hi-C file with no frag resolutions
Display Age at diagnosis in years instead of days for GDC
Fix the GDC Days to birth axis issue
Fix the issues results from term conversion between continous and discrete mode
Indicate the original value unit in termsetting UI if the term value is converted; safety check on bin size to avoid crashes
Add a safety check for the first bin stop and last bin start in numeric discrete termsetting, make the ui actually usable
Bug fix for the broken single variant panel from mds3 tk, by requiring tooltipPrintValue() to return [{k,v}]
Mds3 variant2samples.get() returns an object to wrap the optional bin labels
Allow a sample to be missing files for disco and singleSampleGenomeQuantification data types and do not break server
Display matrix cell tooltip as two column table, and group events of same dt under same heading
Bug fix to not to print text when average admix value is missing; improve population item UI in genomebrowser controls
Improve INFO field UI in genome browser group selection
Option to disable switching GDC SSM lollipop track to genomic mode, due to issues with api query

DevOps:

Support more release note section titles and their corresponding commit keywords
Avoid unnecessarily running unit test CI, for pull requests with unaffected workspaces and on automated push
Improve the release text detection and generator, to minimize potential conflicts when merging

2.26.1

Fix

add a latest tag to the docker build

2.26.0

Features:

For hg38-based datasets, Disco plot may prioritize gene labels by Cancer Gene Census genes.
Numeric termsetting edit UI shows density curve at mode=continuous.
Update gene filter to restrict filtering for multiple alteration groups.
Unify click behavior for survival and cuminc legend items.
Mds3 numeric axis (e.g. occurrence) y scale can be edited.
PrOFILE polar and barchart bug fixes and improvements.
Implemented at-risk count filter in mass cuminc plot
GDC "Age at diagnosis" value by day is shown as "X years, Y days" in mds3 sample table.
Prototype a hierarchical cluster plot using the matrix plot
New Info fields from gnomAD added to clinvar datasets for mds3 track
CancerHotspot hg19 data added for mds3 track
Display sample and catergory numbers in each subgroup when hovering over term label in matrix plot

Fixes:

Ignore hidden values when conducting association tests for mass barchart.
Do not force a matrix barplot min scale to 0;
Fix the missing tooltip when mousing over second+ continuous matrix barplot rows
For matrix plot, when the "Group Samples By" variable has a predefined order, use that order for subgroups.
Fix the sessionid handling to allow more OncoMatrix data to be shown for a signed-in user.
For SSM from GDC API, use consequence from canonical transcript designated by GDC.
GDC SSM range query by graphql appropriately accounts for sample filtering from a subtrack.
In GDC bam slicing block display, clicking on a transcript from native gene tk will disable the "View in protein" option.
Improve the hierarchical clustering R script to include the scaling step.
Add CNV information to label tooltips in disco plot.
Fixed legend labels for continuous term and uncomputable categories in violin plot

2.25.0

Features:

Display pairlst data, if available, for a fusion event on matrix cell mouseover
Launch lollipop from a geneVariant row label of matrix
User-controllable filter for at-risk counts in cumulative incidence plot
Default binning improved for GDC numeric dictionary variables with stats{} from graphql query

Fixes:

Bug fix to change cutoff grade for condition term
Fix the matrix sample sorting by name, to use the display sampleName instead of sample ID
Fix the matrux sample group sorting by group name, to use predefined or group name as applicable
In lollipop tk, upon creating a subtk with a filtering criteria, sunburst generated from subtk will show correct total sample count for sunburst wedges by accounting for subtk filtering criteria. this fix works for both GDC and local TK
Scatterplot bug fix to improve behavior upon filtering by gene mutation
When filtering results in 0 eligible sample, big file query will not happen.

2.24.1

Devops:

Fix the npm publish CI to use the list of changed workspace dirs as argument
Fix the empty change detection in the version jump script

2.24.0

Features

Profile plots have now filters and a download button
Make disco plot rings width configurable
Added to scatter plot scale dot option. Added also test for it.
Support a reset button option for the rx recover component

Fixes:

Selecting hundreds of samples from GDC lollipop no longer hangs or crashes (using a cached mapping to case uuid)
Fix the numeric edit menu when violin plot data is requested for a GDC variable, which needs currentGeneNames
Bug fix to show reduced sample summaries when creating sub-track from GDC lollipop (mds3) track
Correctly handle special uncomputable numeric term values in a matrix row bar plot, when mode='continuous'
GDC OncoMatrix has switched to use case uuid but not case submitter id to align data, while still displaying submitter ids on UI; the latter is not unique between projects.

DevOps:

Reuse a published dependencies image for releasing new image versions to improve build times and stability

2.19.2

Fixes

Use import() instead of require() for dynamic import, so that rollup can bundle properly

2.19.1

Enhancements

Display sample counts in matrix sample group labels, mouseovers, and legend.
Option to toggle a matrix sample group visibility by clicking on the corresponding legend item

Fixes

Cohort creation in the matrix plot, where sample atttribute mapping is required.
Allow continuous variables to be added to GDC matrix without breaking. Next will support query of graphql API to retrieve min/max of the variables.
Sort matrix samples by gene variant hits before grouping, then sort again within each group
Reenable selecting samples from lollipop view for cohort creation. On the fly aliquote-to-case.case_id conversion is performed on selected samples, allowing to create GDC cohort; next the conversion will be supported by caching to allow to work with large number of samples.

2.19.0

Fusion event labels in disco plot are prioritized and displayed with a tooltip
Various minor disco plot bug fixes
Improved matrix sample sorting options and labels
Option to truncate matrix labels for columns and rows
Improved readme detection, sorting, and error handling
Started type definitions for termwrapper and termsetting-related code
Prototyped a custom profile barchart

2.18.3

supported a matrix cell click option
added a dtsv case in the bulk.svjson parser
prototyped new chart profileBarplot
handled on the fly cnv call from genebody probe signals
defaulted to truncate matrix samples against gene variant hits even when there are selected dictionary terms
fixed the matrix rezoom-by-outline zooming out instead of zooming in
fixed bugs found in 3d plot opened from the new dynamic scatter

2.18.2

handle optional action.config in mass store.plot_edit()
fix recover to not prematurely replace state
fix LohArc import for rollup

2.18.1

fix the rollup bundling error caused by the dynamic import of Disco.ts

2.18.0

fixed the matrix sample grouping input lag, edit menu error, empty column bug
contextualized the matrix row label mouseover title
removed GDC terms that are IDs or cause server response errors
removed the numeric axis in the matrix row label when switching from continuous to discrete mode
removed an empty matrix term group after its last remaining term gets moved to a different term
supported launching disco plot from a matrix sample label click
improved the geneset edit UI by having group input and fixing bugs
supported a standalone scatter plot button in the charts tab
mds3 gdc convert to case.case_id on the fly for disco plot
improved disco plot tooltip, ring logic, other features and bug fixes
use typescript for genomes, dataset, termsetting code

2.17.0

start using typescript in core code
option to filter by survival data
precompute intermediate cuminc data to improve server response
reactivate the support for selecting samples in the matrix plot
create an improved geneset edit UI that can be used in matrix and other plots
disambiguate variant and testing status matrix data by alteration type and origin
fix the matrix sorting by fusion data
fix the GDC server-side data query for matrix data, using cnv_occurrences
fix the barchart sort order
option to customize the violin plot "thickeness"
experimental: prototype more features in the new disco plot

2.16.0

improve the matrix control layout, labels, and mouseover information
option to display quantitative CNV data using a chromatic scale in the matrix plot
support new flags to disable custom track ui to guard against html injection
support divide-by term and regression curve fitting for sample scatter plot
support downloading multiple charts as one svg image file for survival and sample scatter plots
update the optional origin values for variant data
improve wholegenome numeric data plotting
fix epaint panel positioning
manual info filtering due to bcftools not filtering multi-ALT
fix violin plot bugs related to scales, uncomputable values, pvalue table, and condition terms
detect missing sample vcf file

2.15.0

pin the base node image version for the Docker build
improved gene/variable search result logic and display
more migrated disco plot features
synchronize scatter groups with mass state.groups
prototype sample scatter divide by variable
fixed current and added new integration tests: regression, cuminc, search, matrix
fixed the ordering of condition terms and added integration tests

GDC-related

fix the missing gene isoform error, by allowing empty query result from the gdc genedb

2.14.4

support a matrix sort filter for a multi-valued sample, where a non-targeted filter value may be used for sorting
fix adding a gene term to the matrix plot, by including a unique termwrapper $id
fix failing client-side integration tests

2.14.3

use a null filter0 for the OncoMatrix
use dataset-defined matrix settings in the GDC launcher

2.14.2

fix the expected scope for local workspaces when bumping versions
fix the serverconfig detection in the container app scripts
cap cnv values in the disco plot
use dissimilarity mesaure for computing y-axis of nodes
test fixes

2.14.1

fix the matrix zoom outline in firefox
fix dom canvas scaling in browsers that do not support OffscreenCanvas
fix unit and integration tests

GDC-related

move the CGC filter input to the gene control menu
label the OncoMatrix undo/redo buttons to address Section 508 errors
fix and improve the zoom UI labels to address Section 508 warnings

2.14.0

persisted custom terms in termdb-based charts and apps
matrix zoom/pan/scrolling, canvas rendering
customizable colors for overlays/legends in more charts
improved termdb database schema, ETL scripts, and queries
prototype dendograms and heatmap using rust
reimplement disco plot in proteinpaint
log-scale in violin plot
more unit and integratin tests, inluding fixes and improvements

2.13.0

matrix zoom and pan
feature improvement and bug fixes for sampleScatter

2.12.1

Switch to npmjs registry for npm publishing.

2.11.2

improved docker build and release
sample lists when allowed for violin and sample scatter plots

2.11.2-1

allow listing samples from rendered charts for authorized users
improved gene variant filters

2.11.2-0

added license
simplified file requests

2.11.1

copy the gdc.hg38.js file from sjpp/dataset for the gdc Docker build
configure the gdc.hg38.js dataset to de-prioritize cnv data for matrix sorting

2.11.0

check the user permission using session id when generating GDC BAM search results
option to set a default geneSymbol for mds3 gene search

2.10.1

fix the rollup bundling of client code that breaks GDC bundling

2.10.0

option to select samples from mds3 track
activated more integration and unit tests on CI

2.9.8-2

Bundle all cards.

2.9.8-1

Bundle spliceevent.prep.js, spliceevent.a53ss.js and spliceevent.exonskip.js

2.9.8-0

Set a default cards directory ONLY if it exists.

2.9.7-0

Bundle shared/vcf.js.

2.9.6-0

Budle dictionary.parse.js.

2.9.5-0

Bundle termdb initbinconfig.

2.9.4-0

Bundle checkReadingFrame and bedj.parseBed to the server module

2.9.3-0

fixed rollup bundle issue

2.9.2-0

Add violin plot integration tests
Bundle lines2R to server module

2.9.0

Improved matrix sorting

GDC-related

OncoMatrix analysis card prototyped

2.8.x

Release testing only for continuous delivery

2.7.3

Fix the duplicate rows in about:filesize in bam track

2.7.2

GDC-related

fit the gdc bam slice request by not using compression

2.7.1

improve tvs and filter UIs, and fix the integration tests

GDC-related

fix the alert visibility when submitting a BAM slice + variant selection

2.7.0

samplelst edit UI
bean plot over violin plot

GDC-related

preliminary support for the GDC filter0 in the matrix plot

2.6.1

fixes to the summary plot toggling
track integration test data including minimal reference data slices

GDC-related

more checks for gdc bam slice download, indexing

2.6.0

support a samplelst term-type
Github Actions for unit tests

GDC-related

launch a separate SSM lollipop track using a term/variable filter
fix the package files list for the GDC build
temporary fix to GDC permission check request

2.5.1

fixes to server tests

GDC-related

fix the handling of optional environment variable for GDC API URL

2.5.0

support for MSigDb genesets
violin and TSNE plot prototypes
auto-column width and more sorting options for the matrix plot
improvements to other MASS UI plots

GDC-related

handle sessionid cookie for the portal.gdc.cancer.gov
oncoprint-like prototype

2.4.0

d3 upgrade to version 7
prototype the sample scatter plot in the MASS UI

GDC-related

Use the portal.gdc.* URL to handle the sessionid cookie, instead of api.gdc.* with X-Auth-Token

2.3.1

GDC-related

fix the cohort filter handling for GDC case search and BAM slice
input border for text and search input within sja_root div

Dev-related

readme.html to easily navigate and view readme's in one place

2.3.0

data download app in the MASS UI
improvements to the cuminc plot
app drawer refactor

GDC-related

more customized mutation colors for Section 508 compliance

Dev-related

Upgrade to Node 16 for development, non-breaking as transpilation still targets Node 12 for deployed builds, until SJ servers are upgraded to have python3
node-canvas 2.9.3, fixes hardcoded requirement for Node 12 fonts
Support Apple Silicon for Docker builds
Support developer containers

2.2.0

option to easily override colors for mutation class and other styles
Improvements to MASS UI plots, including a data downloader app
Updates to the BAM sequence read app

2.1.5

move all React wrapper code to the GDC frontend framework repo

2.1.4

make the React wrapper work in the GDC frontend framework

2.1.3

include utils/install.pp.js in the package

2.1.2

fix the Docker build and npm packing for pp-dist

2.1.1

bug-fix for trailing comma in gencode bigbed
BAM: determine by read width whether to clip arrowhead; clean up re-align logic

GDC-related

alert if token is missing when doing GDC BAM slicing

2.1.0

new regresssion options in MASS UI
BAM track improvements
started the MASS matrix prototype

2.0.0

Breaking Changes

Now uses bigbed dbsnp files
Requires additional columns for termdb database tables: terms.[type, isleaf], subcohort_terms.[child_types, includes_types]

Non-breaking features

MASS UI: supersedes the dictionary tree-based UI as the default termdb portal app

1.10

move targets/ contents under the build/ directory
improve the app drawer and examples
prototype cumulative incidence plots in the termdb app
extract or synthesize data for testing

GDC-related

Use the GDC API to view slices in the BAM track

1.9.1

Synchronize the version update in client and server package.json
Delete unneeded build scripts
Fix the extraction of files from a clean git workspace

1.9.0

Reorganize the code into a monorepo structure using NPM workspaces
Split the build and packing scripts to handle each respective target
TODO: improve SJ server and client builds

GDC-related

Prototype a GDC-specific build script and Dockerfile
TODO: create tiny test data files to test GDc features while building a Docker image

1.8.3

Export the base_zindex from client.js

1.8.2

Selectively import and re-order code in mds3/makeTk to address bundling issues in consumer apps or portal code that use Webpack v3

GDC-related

do not use the test/init.js and pp bundle for automated tests of gdc-related code

1.8.1

Bug fix: use the webpack.config.client.js (renamed) in build/pack.sh

1.8.0

GDC-related

Support passing gene, filters, and ssm_id as props (NOTE: URL parsed information will be deprecated when the gdc portal app switches to passing via props only)
Highlight a lolliplot disc when ssm_id is available
Link to sample aliquot information from a sample details table

Files

CHANGELOG.md

Latest commit

History

CHANGELOG.md

File metadata and controls

Change Log

Unreleased

2.83.0

2.82.1

2.82.0

2.81.6

2.81.5

2.81.4-0

2.81.3

2.81.2

2.81.1

2.81.0

2.80.0

2.79.7

2.79.6

2.79.5

2.79.4

2.79.3

2.79.2

2.79.1

2.79.0

2.78.0

2.77.1

2.77.0

2.76.2

2.76.1

2.76.0

2.75.0

2.74.2

2.74.1

2.74.0

2.73.0

2.72.0

2.71.0

2.70.4

2.70.3

2.70.2

2.70.1

2.70.0

2.69.0

2.68.0

2.67.1

2.67.0

2.66.0

2.65.0

2.64.0

2.63.6

2.63.5

2.63.4

2.63.3

2.63.3-2

2.63.3-1

2.63.3-0

2.63.2

2.63.1

2.63.0

2.62.0

2.61.2

2.61.1

2.61.0

2.60.0

2.59.0

2.58.1

2.58.0

2.57.0

2.56.0

2.55.1

2.55.0

2.54.0

2.53.0

2.52.0

2.51.2

2.51.1

2.51.0