0) {
+ _.forEach(child.bars, function (grandChild) {
+ grandChild.baseColor = grandChild.baseColor || child.baseColor || child.color;
+ sections.push(grandChild);
+ });
+ } else {
+ sections.push(child);
+ }
+ });
+
+ if (sections.length === 0) {
+ return [_.extend({}, node, { 'color': node.color || '#5da5da', 'baseColor': node.baseColor || node.color })];
+ }
+
+ return sections;
+ }
+
renderBarSection(d, i, all){
var { hoverTerm, hoverParentTerm, selectedTerm, selectedParentTerm, onBarPartClick,
onBarPartMouseEnter, onBarPartMouseOver, onBarPartMouseLeave,
@@ -173,17 +233,15 @@ class Bar extends React.PureComponent {
return (
);
}
render(){
const { canBeHighlighted, showBarCount, node: d } = this.props;
- const hasSubSections = Array.isArray(d.bars);
- const barSections = (hasSubSections ?
- // If needed, remove sort + reverse to keep order of heaviest->lightest aggs regardless of color
- barplot_color_cycler.sortObjectsByColorPalette(d.bars).reverse() : [_.extend({}, d, { color : '#5da5da' })]
- );
+ const barSections = this.getRenderableSections();
let className = "chart-bar";
const topLabel = showBarCount ?
{ d.count } : null;
@@ -195,7 +253,7 @@ class Bar extends React.PureComponent {
className={className}
data-term={d.term}
data-count={d.count}
- data-field={Array.isArray(d.bars) && d.bars.length > 0 ? d.bars[0].field : null}
+ data-field={d.field || (Array.isArray(d.bars) && d.bars.length > 0 ? d.bars[0].field : null)}
key={"bar-" + d.term}
style={this.barStyle()}
ref={this.barElemRef}>
@@ -371,32 +429,49 @@ export class PopoverViewContainer extends React.PureComponent {
constructor(props){
super(props);
this.getCoordsCallback = this.getCoordsCallback.bind(this);
+ this.heightToTop = this.heightToTop.bind(this);
+ this.getRootNode = this.getRootNode.bind(this);
+ }
+
+ getRootNode(node){
+ let current = node;
+ while (current && current.parent){
+ current = current.parent;
+ }
+ return current || node;
+ }
+
+ heightToTop(node){
+ if (!node) return 0;
+ const parent = node.parent;
+ if (!parent || !Array.isArray(parent.bars)) {
+ return (node.attr && typeof node.attr.height === 'number') ? node.attr.height : 0;
+ }
+ let heightWithinParent = 0;
+ let found = false;
+ _.forEach(parent.bars, function(sibling){
+ if (found) return;
+ heightWithinParent += (sibling.attr && typeof sibling.attr.height === 'number') ? sibling.attr.height : 0;
+ if (sibling === node) {
+ found = true;
+ }
+ });
+
+ return this.heightToTop(parent) - ((parent.attr && parent.attr.height) || 0) + heightWithinParent;
}
getCoordsCallback(node, containerPosition, boundsHeight){
var bottomOffset = (this.props && this.props.styleOptions && this.props.styleOptions.offset && this.props.styleOptions.offset.bottom) || 0;
var leftOffset = (this.props && this.props.styleOptions && this.props.styleOptions.offset && this.props.styleOptions.offset.left) || 0;
- var barYPos = node.attr.height;
-
- if (node.parent){
- var done = false;
- barYPos = _.reduce(
- node.parent.bars,//.slice(0).reverse(),
- //_.sortBy(node.parent.bars, 'term').reverse(),
- function(m, siblingNode){
- if (done) return m;
- if (siblingNode.term === node.term){
- done = true;
- }
- return m + siblingNode.attr.height;
- },
- 0
- );
- }
+ var rootNode = this.getRootNode(node);
+ const rootAttrs = (rootNode && rootNode.attr) || {};
+ const rootX = typeof rootAttrs.x === 'number' ? rootAttrs.x : 0;
+ const rootWidth = typeof rootAttrs.width === 'number' ? rootAttrs.width : 0;
+ var barYPos = this.heightToTop(node);
return {
- 'x' : containerPosition.left + leftOffset + (node.parent || node).attr.x + ((node.parent || node).attr.width / 2),
+ 'x' : containerPosition.left + leftOffset + rootX + (rootWidth / 2),
'y' : containerPosition.top + boundsHeight - bottomOffset - barYPos,
};
}
diff --git a/src/encoded/static/components/viz/ChartDetailCursor/ChartDetailCursor.js b/src/encoded/static/components/viz/ChartDetailCursor/ChartDetailCursor.js
index 387f4ee27..6c5b2c874 100644
--- a/src/encoded/static/components/viz/ChartDetailCursor/ChartDetailCursor.js
+++ b/src/encoded/static/components/viz/ChartDetailCursor/ChartDetailCursor.js
@@ -148,7 +148,9 @@ class Body extends React.PureComponent {
if (Array.isArray(path) && path.length === 0){
return null;
}
- const leafNode = path[path.length - 1];
+
+ // see workaround in Crumbs component why we do this for length 3
+ const leafNode = path[path.length === 3 ? 1 : path.length - 1];
const leafNodeFieldTitle = Schemas.Field.toName(leafNode.field, schemas);
return (
@@ -198,10 +200,18 @@ const Crumbs = React.memo(function Crumbs({ path, schemas, primaryCount }){
if (isEmpty) return null;
//var maxSkewOffset = (this.props.path.length - 2) * offsetPerCrumb;
+ //workaround: if path has three elemennts, swap the second and the third to fix the order (clone the path first)
+ const clonedPath = path.slice();
+ if (path.length === 3) {
+ const temp = clonedPath[1];
+ clonedPath[1] = clonedPath[2];
+ clonedPath[2] = temp;
+ }
+
return (
{
- path.slice(0,-1).map(function(n, i){
+ clonedPath.slice(0,-1).map(function(n, i){
return (
.label-container {
position: relative;
diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py
index 10a62add1..7457b2273 100644
--- a/src/encoded/types/file.py
+++ b/src/encoded/types/file.py
@@ -306,6 +306,8 @@ class CalcPropConstants:
SAMPLE_SUMMARY_TISSUES = "tissues"
SAMPLE_SUMMARY_TISSUE_SUBTYPES = "tissue_subtypes"
SAMPLE_SUMMARY_TISSUE_DETAILS = "tissue_details"
+ SAMPLE_SUMMARY_TISSUE_PROTOCOL_IDS = "tissue_protocol_ids"
+ SAMPLE_SUMMARY_TISSUE_SHORT_NAMES = "tissue_short_names"
SAMPLE_SUMMARY_SAMPLE_NAMES = "sample_names"
SAMPLE_SUMMARY_SAMPLE_DESCRIPTIONS = "sample_descriptions"
SAMPLE_SUMMARY_ANALYTES = "analytes"
@@ -349,6 +351,20 @@ class CalcPropConstants:
"type": "string",
},
},
+ SAMPLE_SUMMARY_TISSUE_PROTOCOL_IDS: {
+ "title": "Tissue Protocol ID",
+ "type": "array",
+ "items": {
+ "type": "string",
+ },
+ },
+ SAMPLE_SUMMARY_TISSUE_SHORT_NAMES: {
+ "title": "Tissue Short Name",
+ "type": "array",
+ "items": {
+ "type": "string",
+ },
+ },
SAMPLE_SUMMARY_SAMPLE_NAMES: {
"title": "Sample ID",
"type": "array",
@@ -1232,6 +1248,8 @@ def _get_sample_summary_fields(
file_utils.get_tissues(file_properties, request_handler),
tissue_utils.get_location,
),
+ constants.SAMPLE_SUMMARY_TISSUE_PROTOCOL_IDS: file_utils.get_tissue_protocol_id(file_properties, request_handler),
+ constants.SAMPLE_SUMMARY_TISSUE_SHORT_NAMES: file_utils.get_tissue_short_name(file_properties, request_handler),
constants.SAMPLE_SUMMARY_SAMPLE_NAMES: get_property_values_from_identifiers(
request_handler,
file_utils.get_samples(file_properties, request_handler),
@@ -1261,6 +1279,7 @@ def _get_sample_summary_fields(
analyte_utils.get_molecule,
),
}
+
return {key: value for key, value in to_include.items() if value}
def _get_analysis_summary(
diff --git a/src/encoded/types/tissue.py b/src/encoded/types/tissue.py
index a99e7c740..bd491e532 100644
--- a/src/encoded/types/tissue.py
+++ b/src/encoded/types/tissue.py
@@ -85,6 +85,18 @@ def tissue_type(self, request: Request):
request_handler = RequestHandler(request=request)
tissue_type = tissue_utils.get_tissue_type(self.properties, request_handler=request_handler)
return tissue_type or None
+
+ @calculated_property(
+ schema={
+ "title": "Protocol ID",
+ "description": "Protocol ID associated with tissue",
+ "type": "string"
+ }
+ )
+ def protocol_id(self, request: Request) -> Optional[str]:
+ """Get protocol ID associated with tissue."""
+ protocol_id = tissue_utils.get_protocol_id(self.properties)
+ return protocol_id or None
@link_related_validator