Release v2.4

changelog.md

@@ -0,0 +1,14 @@
+# Changelog
+
+## Release 2.4 [unreleased]
+Brief summary of what's in this release:
+
+
+### Breaking changes
+
+Breaking changes include any database updates needed, if we need to edit any files on system (like .env or certs, etc). Things that are outside of the code itself that need changed for the system to work.
+
+
+### Non-breaking changes
+
+Just a place to keep track of things that have changed in the code that we may want to pay special attention to when smoke testing, etc.

package.json

@@ -1,6 +1,6 @@
 {
   "name": "pegasus-web",
-  "version": "2.3.1",
+  "version": "2.4.0",
   "private": true,
   "homepage": "/",
   "dependencies": {

src/components/ConceptSelect/ConceptSelect.js

@@ -124,7 +124,8 @@ class ConceptSelect extends Component {
         if (this.props.smallFormat) {
             customStyles["menu"] = styles => ({
                 ...styles,
-                width: '460px'
+                width: '460px',
+                zIndex: '100'
             })
         }
 

src/components/DataViz/DataTypeSelector.js

@@ -228,6 +228,7 @@ class DataTypeSelector extends Component {
                                 inputValue={this.getInputValue()}
                                 onFocus={() => this.setState({ tissueInputValue: '' })}
                                 className='select d-table-cell w-100 ps-2'
+                                classNamePrefix="select"
                                 isDisabled={this.state.isDatasetSummaryLoading ? true : false}
                             />
                         </Col>
@@ -238,6 +239,7 @@ class DataTypeSelector extends Component {
                                 options={this.state.dataTypeOptions}
                                 onChange={this.handleInputChange.bind(this)}
                                 className='select d-table-cell w-100 ps-2'
+                                classNamePrefix="select"
                                 styles={{ menu: provided => ({ ...provided, zIndex: 999 }) }}
                                 isDisabled={this.state.isDatasetSummaryLoading ? true : false}
                             />

src/components/Explorer/SamplesByDataTypeTable.js

@@ -117,7 +117,13 @@ class SamplesByDataTypeTable extends Component {
                 name: 'dmrCount',
                 sortable: false,
                 hideable: false
-            },
+            }, 
+            {
+                title: 'ALL',
+                name: 'totalCount',
+                sortable: false,
+                hideable: false
+            }   
         ]
     };
 
@@ -129,16 +135,18 @@ class SamplesByDataTypeTable extends Component {
             { columnName: 'ckdCount', align: 'center' },
             { columnName: 'akiCount', align: 'center' },
             { columnName: 'dmrCount', align: 'center' },
+            { columnName: 'totalCount', align: 'center' },
         ]
     }
 
     getDefaultColumnWidths() {
         return [
-            { columnName: 'dataType', width: 320 },
-            { columnName: 'hrtCount', width: 208 },
-            { columnName: 'ckdCount', width: 89 },
-            { columnName: 'akiCount', width: 89 },
-            { columnName: 'dmrCount', width: 89 },
+            { columnName: 'dataType', width: 295 },
+            { columnName: 'hrtCount', width: 190 },
+            { columnName: 'ckdCount', width: 85 },
+            { columnName: 'akiCount', width: 85 },
+            { columnName: 'dmrCount', width: 85 },
+            { columnName: 'totalCount', width: 85 },
         ]
     }
 

src/components/Home/AvailableDatasetsTable.js

@@ -32,7 +32,10 @@ class AvailableDatasetsTable extends Component {
     handleDataTypeValueClick(row, tissueType) {
         let linkType = row.linkInformation.linkType;
         let linkValue = row.linkInformation.linkValue.replace('&', '%26');
-        let mapping = `/repository/?size=n_20_n&filters[0][field]=${linkType}&filters[0][values][0]=${linkValue}&filters[0][type]=any&filters[1][field]=tissue_type&filters[1][values][0]=${tissueType}&filters[1][type]=any`
+        let mapping = `/repository/?size=n_20_n&filters[0][field]=${linkType}&filters[0][values][0]=${linkValue}&filters[0][type]=any`
+        if(tissueType){
+            mapping += `&filters[1][field]=tissue_type&filters[1][values][0]=${tissueType}&filters[1][type]=any`
+        }
         if(linkType && linkValue){
             return encodeURI(mapping).replace('%2526', '%26');
         } else {
@@ -59,6 +62,7 @@ class AvailableDatasetsTable extends Component {
             { columnName: 'hrtCount', width: 'auto', align: 'center'},
             { columnName: 'ckdCount', width: 'auto', align: 'center'},
             { columnName: 'dmrCount', width: 'auto', align: 'center'},
+            { columnName: 'totalCount', width: 'auto', align: 'center'}
         ]
     }
 
@@ -132,7 +136,22 @@ class AvailableDatasetsTable extends Component {
               ,
               getCellValue: row => this.handleEmptyCounts(row.dmrCount, row, "DM-R"),
               name: 'dmrCount',
-          }
+          },   
+          {
+              title: 
+                <span>
+                    <span className="table-header data-type-table-header" id="AllHeader">
+                    ALL
+                    </span> 
+                    <UncontrolledTooltip
+                      placement="bottom"
+                      target="AllHeader">
+                        Repository files including KPMP and non-KPMP data
+                    </UncontrolledTooltip>
+                </span>,
+              name: 'totalCount',
+              getCellValue: row => this.handleEmptyCounts(row.totalCount, row, null),
+          }   
       ]
   };
 

src/components/Home/SamplesByDataTypeTable.js

@@ -18,11 +18,11 @@ class SamplesByDataTypeTable extends Component {
     async componentDidMount(){
 
         let spatialSummary = await fetchSummaryData("spatialViewerSummary");
-        spatialSummary = spatialSummary.sort(this.compare)
+        spatialSummary = [...spatialSummary].sort(this.compare)
         spatialSummary = spatialSummary.filter(availableDataVisibilityFilter)
 
         let explorerSummary = await fetchDataTypeSummaryInformation();
-        explorerSummary = explorerSummary.sort(this.compare)
+        explorerSummary = [...explorerSummary].sort(this.compare)
         explorerSummary = explorerSummary.filter(availableDataVisibilityFilter)
 
         // adding lines to separate the sections in the table
@@ -153,6 +153,20 @@ class SamplesByDataTypeTable extends Component {
                     </span>
                 ,
                 name: 'dmrCount',
+            },   
+            {
+                title: 
+                    <span>
+                        <span className="table-header data-type-table-header" id="AllParticipantsHeader">
+                        ALL
+                        </span> 
+                        <UncontrolledTooltip
+                        placement="bottom"
+                        target="AllParticipantsHeader">
+                            All Participants
+                        </UncontrolledTooltip>
+                    </span>,
+                name: 'totalCount'
             }   
         ]
     };
@@ -165,6 +179,7 @@ class SamplesByDataTypeTable extends Component {
             { columnName: 'ckdCount', width: 'auto', align: 'center' },
             { columnName: 'akiCount', width: 'auto', align: 'center' },
             { columnName: 'dmrCount', width: 'auto', align: 'center' },
+            { columnName: 'totalCount', width: 'auto', align: 'center' },
         ]
     }
 

src/helpers/ApolloClient.js

@@ -149,6 +149,7 @@ export const fetchDataTypeSummaryInformation = async (fetchPolicy = 'no-cache')
                     akiCount
                     ckdCount
                     dmrCount
+                    totalCount
                     participantCount
                 }
             }`;
@@ -438,6 +439,7 @@ export const fetchSummaryData = async (dataType) => {
                 akiCount
                 ckdCount
                 dmrCount
+                totalCount
                 participantCount
             }
         }`;
@@ -485,6 +487,7 @@ export const fetchAtlasSummaryRows = async () => {
               ckdCount
               hrtCount
               dmrCount
+              totalCount
               omicsType
               linkInformation {
                 linkType

src/index.scss

@@ -963,4 +963,9 @@ tr.MuiTableRow-root:nth-child(even) {
   @media (min-width: 992px) {
     margin-right: 15px;
   }
+}
+
+.select__menu {
+  top: auto !important;
+  z-index: 100 !important;
 }