+ >
{Children.map(tabs, (child, i) => (
(onTabClick ? onTabClick(i) : () => {})}
- active={i === activeIndex}
sibling={i}
- theme={theme}
- tabStyle={tabStyle}
side
- >
+ tabStyle={tabStyle}
+ theme={theme}
+ >
{child}
))}
@@ -145,41 +134,43 @@ const Tabs = ({
width: 1,
...(contentStyle || {}),
}}
- >
+ >
{children}
) : (
-
+
{Children.map(tabs, (child, i) => (
(onTabClick ? onTabClick(i) : () => {})}
- active={i === activeIndex}
- sibling={i}
- theme={theme}
- tabStyle={tabStyle}
- side={false}
- >
+ active={i === activeIndex}
+ className="test-tab"
+ onClick={() => (onTabClick ? onTabClick(i) : () => {})}
+ sibling={i}
+ side={false}
+ tabStyle={tabStyle}
+ theme={theme}
+ >
{child}
))}
{tabToolbar && {tabToolbar} }
-
+
{children}
- );
+ ));
Tabs.propTypes = {
- children: PropTypes.node,
activeIndex: PropTypes.oneOfType([PropTypes.string, PropTypes.number]),
+ children: PropTypes.node,
style: PropTypes.object,
tabs: PropTypes.node,
};
-/*----------------------------------------------------------------------------*/
-
export default withTheme(Tabs);
diff --git a/src/packages/@ncigdc/uikit/Tooltip/index.js b/src/packages/@ncigdc/uikit/Tooltip/index.js
index 165f208e0..164331518 100644
--- a/src/packages/@ncigdc/uikit/Tooltip/index.js
+++ b/src/packages/@ncigdc/uikit/Tooltip/index.js
@@ -1,8 +1,4 @@
-// @flow
-
-import GlobalTooltip from './GlobalTooltip';
-import Tooltip from './Tooltip';
-import tooltipReducer, { setTooltip } from './dux';
-import withTooltip from './withTooltip';
-
-export { GlobalTooltip, Tooltip, tooltipReducer, setTooltip, withTooltip };
+export { default as GlobalTooltip } from './GlobalTooltip';
+export { default as Tooltip } from './Tooltip';
+export { default as tooltipReducer, setTooltip } from './dux';
+export { default as withTooltip, TooltipInjector } from './withTooltip';
diff --git a/src/packages/@ncigdc/uikit/Tooltip/withTooltip.js b/src/packages/@ncigdc/uikit/Tooltip/withTooltip.js
index be042f488..d8850d2ce 100644
--- a/src/packages/@ncigdc/uikit/Tooltip/withTooltip.js
+++ b/src/packages/@ncigdc/uikit/Tooltip/withTooltip.js
@@ -2,16 +2,18 @@
import React from 'react';
import {
compose,
- withState,
lifecycle,
- withHandlers,
mapProps,
+ setDisplayName,
+ withHandlers,
+ withState,
} from 'recompose';
import { connect } from 'react-redux';
-import { setTooltip } from '@ncigdc/uikit/Tooltip';
import { omit } from 'lodash';
+import { setTooltip } from './dux';
const enhance = compose(
+ setDisplayName('TooltipEnhancer'),
connect(),
withState('tooltipState', 'setTooltipState', false),
withHandlers({
@@ -27,11 +29,20 @@ const enhance = compose(
}
},
}),
- mapProps(props =>
- omit(props, ['tooltipState', 'setTooltipState', 'dispatch']),
- ),
+ mapProps(props => omit(props, [
+ 'tooltipState',
+ 'setTooltipState',
+ 'dispatch',
+ ]),),
);
const withTooltip = Wrapped => enhance(props =>
+const UnstyledButton = ({ children, style, ...props }) => (
+
{children}
);
+
+export default UnstyledButton;
diff --git a/src/packages/@ncigdc/utils/ageDisplay.js b/src/packages/@ncigdc/utils/ageDisplay.js
index ed01df8c3..f696e815d 100644
--- a/src/packages/@ncigdc/utils/ageDisplay.js
+++ b/src/packages/@ncigdc/utils/ageDisplay.js
@@ -3,19 +3,17 @@
import _ from 'lodash';
export const DAYS_IN_YEAR = 365.25;
-export const getLowerAgeYears = (days: number) =>
- Math.ceil(days / DAYS_IN_YEAR);
-export const getUpperAgeYears = (days: number) =>
- Math.ceil((days + 1 - DAYS_IN_YEAR) / DAYS_IN_YEAR);
+export const getLowerAgeYears = (days: number) => Math.ceil(days / DAYS_IN_YEAR);
+export const getUpperAgeYears = (days: number) => Math.ceil((days + 1 - DAYS_IN_YEAR) / DAYS_IN_YEAR);
export default (
ageInDays: number,
yearsOnly: boolean = false,
defaultValue: string = '--',
): string => {
- const DAYS_IN_YEAR = 365.25;
- const leapThenPair = (years: number, days: number): number[] =>
- days === 365 ? [years + 1, 0] : [years, days];
+ const leapThenPair = (years: number, days: number): number[] => (
+ days === 365 ? [years + 1, 0] : [years, days]
+ );
const timeString = (
num: number,
singular: string,
diff --git a/src/packages/@ncigdc/utils/constants.js b/src/packages/@ncigdc/utils/constants.js
index bc335e6e0..ebcab40fb 100644
--- a/src/packages/@ncigdc/utils/constants.js
+++ b/src/packages/@ncigdc/utils/constants.js
@@ -48,18 +48,72 @@ export const LOCAL_STORAGE_API_OVERRIDE = API_OVERRIDE_KEYS.some(
k => localStorage[k]
);
+const DATA_CATEGORIES_COMMON = {
+ SEQ: {
+ full: 'Sequencing Reads',
+ abbr: 'Seq',
+ },
+ EXP: {
+ full: 'Transcriptome Profiling',
+ abbr: 'Exp',
+ },
+ SNV: {
+ full: 'Simple Nucleotide Variation',
+ abbr: 'SNV',
+ },
+ CNV: {
+ full: 'Copy Number Variation',
+ abbr: 'CNV',
+ },
+ METH: {
+ full: 'DNA Methylation',
+ abbr: 'Meth',
+ },
+};
+
export const DATA_CATEGORIES = {
- SEQ: { full: 'Sequencing Reads', abbr: 'Seq' },
- EXP: { full: 'Transcriptome Profiling', abbr: 'Exp' },
- SNV: { full: 'Simple Nucleotide Variation', abbr: 'SNV' },
- CNV: { full: 'Copy Number Variation', abbr: 'CNV' },
- METH: { full: 'DNA Methylation', abbr: 'Meth' },
- CLINICAL: { full: 'Clinical', abbr: 'Clinical' },
- BIOSPECIMEN: { full: 'Biospecimen', abbr: 'Bio' },
+ ...DATA_CATEGORIES_COMMON,
+ CLINICAL: {
+ full: 'Clinical',
+ abbr: 'Clinical',
+ },
+ BIOSPECIMEN: {
+ full: 'Biospecimen',
+ abbr: 'Bio',
+ },
+};
+
+export const DATA_CATEGORIES_FOR_PROJECTS_TABLE = {
+ ...DATA_CATEGORIES_COMMON,
+ CLINICAL_METADATA: {
+ full: '',
+ abbr: 'Clinical',
+ tooltip: 'Clinical Metadata',
+ },
+ CLINICAL_SUPPLEMENT: {
+ full: 'Clinical',
+ dataCategory: 'Clinical',
+ abbr: 'Clinical Supplement',
+ tooltip: 'Clinical Supplement',
+ },
+ BIOSPECIMEN_METADATA: {
+ full: '',
+ abbr: 'Bio',
+ tooltip: 'Biospecimen Metadata',
+ },
+ BIOSPECIMEN_SUPPLEMENT: {
+ full: 'Biospecimen',
+ dataCategory: 'Bio',
+ abbr: 'Bio Supplement',
+ tooltip: 'Biospecimen Supplement',
+ },
};
export const DATA_TYPES = {
- GEQ: { full: 'Gene Expression Quantification', abbr: 'GEQ' },
+ GEQ: {
+ full: 'Gene Expression Quantification',
+ abbr: 'GEQ',
+ },
};
export const EXPERIMENTAL_STRATEGIES = [
@@ -115,7 +169,11 @@ export const MUTATION_SUBTYPE_MAP = {
'small insertion': 'Insertion',
};
-export const DNA_CHANGE_MARKERS = ['del', 'ins', '>'];
+export const DNA_CHANGE_MARKERS = [
+ 'del',
+ 'ins',
+ '>',
+];
export const HUMAN_BODY_SITES_MAP = {
'accessory sinuses': 'Head and Neck',
@@ -287,20 +345,41 @@ export const IMPACT_SHORT_FORMS = {
export const FAKE_USER =
localStorage.REACT_APP_ALLOW_FAKE_USER || process.env.REACT_APP_ALLOW_FAKE_USER
- ? {
+ ? {
username: 'DEV_USER',
projects: {
phs_ids: {
- phs000178: ['_member_', 'read', 'delete'],
+ phs000178: [
+ '_member_',
+ 'read',
+ 'delete',
+ ],
},
gdc_ids: {
- 'TCGA-LIHC': ['read', 'delete', 'create', 'update', 'read_report'],
- 'CGCI-BLGSP': ['create', 'update', 'release', 'read_report'],
- 'TCGA-DEV3': ['read', 'create', 'update', 'release', 'delete'],
+ 'TCGA-LIHC': [
+ 'read',
+ 'delete',
+ 'create',
+ 'update',
+ 'read_report',
+ ],
+ 'CGCI-BLGSP': [
+ 'create',
+ 'update',
+ 'release',
+ 'read_report',
+ ],
+ 'TCGA-DEV3': [
+ 'read',
+ 'create',
+ 'update',
+ 'release',
+ 'delete',
+ ],
},
},
}
- : null;
+ : null;
export const IS_DEV = process.env.NODE_ENV === 'development';
@@ -324,4 +403,11 @@ export const CLINICAL_BLACKLIST = [
export const IS_CDAVE_DEV =
localStorage.REACT_APP_IS_CDAVE_DEV ||
process.env.NODE_ENV === 'development' ||
- false;
\ No newline at end of file
+ false;
+
+export const analysisColors = {
+ Demographic: '#1f77b4',
+ Diagnosis: '#ff7f0e',
+ Treatment: '#2ca02c',
+ Exposure: '#9467bd',
+};
diff --git a/src/packages/@ncigdc/utils/data/types.ts b/src/packages/@ncigdc/utils/data/types.ts
index 6106c9a89..070283dc0 100644
--- a/src/packages/@ncigdc/utils/data/types.ts
+++ b/src/packages/@ncigdc/utils/data/types.ts
@@ -15,13 +15,13 @@ export type TCategory =
| 'Biospecimen';
export type TCategoryAbbr =
- | 'Seq'
- | 'Exp'
- | 'SNV'
- | 'CNV'
- | 'Clinical'
| 'Bio'
- | 'Meth';
+ | 'Clinical'
+ | 'CNV'
+ | 'Exp'
+ | 'Meth'
+ | 'Seq'
+ | 'SNV';
export type TCategoryMap = { [k in TCategoryAbbr]: TCategory };
diff --git a/src/packages/@ncigdc/utils/filters/index.ts b/src/packages/@ncigdc/utils/filters/index.ts
index 44e7954a1..b859384ed 100644
--- a/src/packages/@ncigdc/utils/filters/index.ts
+++ b/src/packages/@ncigdc/utils/filters/index.ts
@@ -19,8 +19,8 @@ import {
function compareTerms(a: IValueFilter, b: IValueFilter): boolean {
return (
- a.content.field === b.content.field &&
- a.op.toLowerCase() === b.op.toLowerCase()
+ a.content && (a.content.field === b.content.field) &&
+ a.op && (a.op.toLowerCase() === b.op.toLowerCase())
);
}
@@ -82,7 +82,6 @@ const replace: TMergeFilters = (x, y) => ({
});
const addIn: TMergeFilters = (x, y) => ({
- op: 'and',
content: y.content
.reduce((acc, curr) => {
const found = acc.find(a => compareTerms(a, curr));
@@ -95,6 +94,7 @@ const addIn: TMergeFilters = (x, y) => ({
].filter(removeNoValueFilter);
}, x.content)
.sort(sortFilters),
+ op: y.op || 'and',
});
const filterNoContent = (f: IGroupFilter) => (f.content.length ? f : null);
diff --git a/src/packages/@ncigdc/utils/withFacetSelection.js b/src/packages/@ncigdc/utils/withFacetSelection.js
index c7f5bc987..5fb4cb11a 100644
--- a/src/packages/@ncigdc/utils/withFacetSelection.js
+++ b/src/packages/@ncigdc/utils/withFacetSelection.js
@@ -2,7 +2,13 @@
/* eslint fp/no-this: 0, max-len: 1 */
import _ from 'lodash';
import { connect } from 'react-redux';
-import { withState, withProps, withHandlers, compose } from 'recompose';
+import {
+ compose,
+ setDisplayName,
+ withHandlers,
+ withProps,
+ withState,
+} from 'recompose';
import { add, remove, reset } from '@ncigdc/dux/customFacets';
import withRouter from '@ncigdc/utils/withRouter';
import { removeFilter } from '@ncigdc/utils/filters/index';
@@ -21,57 +27,63 @@ export default ({
presetFacetFields,
validFacetDocTypes,
validFacetPrefixes,
-}: TProps) =>
- compose(
- connect((state, props) => ({
- userSelectedFacets: state.customFacets[entityType],
- })),
- withState('shouldShowFacetSelection', 'setShouldShowFacetSelection', false),
- withProps(({ userSelectedFacets }) => ({
- facetExclusionTest: facet => {
- const facetFieldNamesToExclude = presetFacetFields.concat(
- userSelectedFacets.map(x => x.field),
- );
- const match = _.some([
- !_.includes(validFacetDocTypes, facet.doc_type),
- _.includes(facetFieldNamesToExclude, facet.field),
- validFacetPrefixes &&
+}: TProps) => compose(
+ setDisplayName('WithFacetSelection'),
+ connect((state, props) => ({
+ userSelectedFacets: state.customFacets[entityType],
+ })),
+ withState('shouldShowFacetSelection', 'setShouldShowFacetSelection', false),
+ withProps(({ userSelectedFacets }) => ({
+ facetExclusionTest: facet => {
+ const facetFieldNamesToExclude = presetFacetFields.concat(
+ userSelectedFacets.map(x => x.field),
+ );
+ const match = _.some([
+ !_.includes(validFacetDocTypes, facet.doc_type),
+ _.includes(facetFieldNamesToExclude, facet.field),
+ validFacetPrefixes &&
!_.includes(validFacetPrefixes.map(p => facet.full.indexOf(p)), 0),
- ]);
- return match;
- },
- })),
- withRouter,
- withHandlers({
- handleSelectFacet: ({
- userSelectedFacets,
- setShouldShowFacetSelection,
- dispatch,
- }) => facet => {
- setShouldShowFacetSelection(false);
- dispatch(add({ entityType, facet }));
- },
- handleResetFacets: ({ dispatch }) => () => {
- dispatch(reset({ entityType }));
- },
- handleRequestRemoveFacet: ({
- userSelectedFacets,
- dispatch,
- push,
- query,
- }) => facet => {
- dispatch(remove({ entityType, field: facet.field }));
- const newFilters = removeFilter(
- facet.full,
- parseFilterParam(query.filters),
- );
+ ]);
+ return match;
+ },
+ })),
+ withRouter,
+ withHandlers({
+ handleSelectFacet: ({
+ dispatch,
+ setShouldShowFacetSelection,
+ userSelectedFacets,
+ }) => facet => {
+ setShouldShowFacetSelection(false);
+ dispatch(add({
+ entityType,
+ facet,
+ }));
+ },
+ handleResetFacets: ({ dispatch }) => () => {
+ dispatch(reset({ entityType }));
+ },
+ handleRequestRemoveFacet: ({
+ dispatch,
+ push,
+ query,
+ userSelectedFacets,
+ }) => facet => {
+ dispatch(remove({
+ entityType,
+ field: facet.field,
+ }));
+ const newFilters = removeFilter(
+ facet.full,
+ parseFilterParam(query.filters),
+ );
- return push({
- query: removeEmptyKeys({
- ...query,
- filters: newFilters && stringifyJSONParam(newFilters),
- }),
- });
- },
- }),
- );
+ return push({
+ query: removeEmptyKeys({
+ ...query,
+ filters: newFilters && stringifyJSONParam(newFilters),
+ }),
+ });
+ },
+ }),
+);
diff --git a/src/packages/@ncigdc/utils/wrapSvg.js b/src/packages/@ncigdc/utils/wrapSvg.js
index 60b28f5f5..5d4f70d74 100644
--- a/src/packages/@ncigdc/utils/wrapSvg.js
+++ b/src/packages/@ncigdc/utils/wrapSvg.js
@@ -67,7 +67,7 @@ function buildForeignObject({
}): { html: string, height: number } {
const foreignObjects = elements.filter(Boolean);
// $FlowIgnore
- const elementsHeight = sum(foreignObjects.map(e => e.offsetHeight || 15));
+ const elementsHeight = sum(foreignObjects.map(e => (e.className === 'p-value' ? 25 : e.offsetHeight || 17)));
return {
height: elementsHeight,
@@ -175,10 +175,10 @@ const wrapSvg = ({
22,
])}"
viewBox="0 0 ${width} ${sum([
- height,
- afterObject.height,
- 22,
-])}"
+ height,
+ afterObject.height,
+ 22,
+ ])}"
style="font-size: 10px"
class="${EXPORT_CLASS} ${svgClass || ''} ${className}"
>
@@ -191,14 +191,14 @@ const wrapSvg = ({
${beforeObject.html}
${rightObject.html}
+ titleHeight,
+ margins.top,
+ beforeObject.height,
+ ])})">
${svg.innerHTML.replace(
- /url\(['"]?https?:\/\/[^#]+(#.+)['"]?\)/g,
- 'url($1)',
- )}
+ /url\(['"]?https?:\/\/[^#]+(#.+)['"]?\)/g,
+ 'url($1)',
+ )}
${afterObject.html}
${legends
diff --git a/tslint.json b/tslint.json
index 5d5e0f0e3..405081b63 100644
--- a/tslint.json
+++ b/tslint.json
@@ -11,7 +11,8 @@
"coverage/lcov-report/*.js",
"__mocks__/*.js",
"data/*.js",
- "public/*.js"
+ "public/*.js",
+ "src/packages/@oncojs/**/*"
]
},
"rules": {
@@ -77,4 +78,4 @@
"allow-snake-case"
]
}
-}
\ No newline at end of file
+}
