Merge pull request #58 from gf-dcc/patch/filter-cleanup

Patch/filter cleanup
gf-dcc · Nov 28, 2023 · 080b6fd · 080b6fd
2 parents 8a2b615 + 614b2b6
commit 080b6fd
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Showing 7 changed files with 13 additions and 70 deletions.
diff --git a/components/ExploreSummary.tsx b/components/ExploreSummary.tsx
@@ -21,10 +21,6 @@ export const ExploreSummary: React.FunctionComponent<IExploreSummaryProps> = (
         props.getGroupsByPropertyFiltered[AttributeNames.AtlasName]
     ).length;
 
-    const organCount = _.keys(
-        props.getGroupsByPropertyFiltered[AttributeNames.TissueorOrganofOrigin]
-    ).length;
-
     const cancerTypeCount = _.keys(
         props.getGroupsByPropertyFiltered[AttributeNames.PrimaryDiagnosis]
     ).length;
@@ -43,7 +39,6 @@ export const ExploreSummary: React.FunctionComponent<IExploreSummaryProps> = (
                 </div>
 
                 <div>{pluralize('Team', atlasCount, true)}</div>
-                <div>{pluralize('Organ', organCount, true)}</div>
                 <div>{pluralize('Cancer Type', cancerTypeCount, true)}</div>
                 <div>{pluralize('Case', props.filteredCaseCount, true)}</div>
                 <div>

diff --git a/components/FileTable.tsx b/components/FileTable.tsx
@@ -389,22 +389,11 @@ export default class FileTable extends React.Component<IFileTableProps> {
                 wrap: true,
                 sortable: true,
             },
-            {
-                name: 'Organ',
-                selector: (file: Entity) => {
-                    return _.uniq(
-                        file.diagnosis.map((d) => d.TissueorOrganofOrigin)
-                    ).join(', ');
-                },
-                cell: truncatedTableCell,
-                wrap: true,
-                sortable: true,
-            },
             {
                 name: 'Diagnosis',
                 selector: (file: Entity) => {
                     return _.uniq(
-                        file.diagnosis.map((d) => d.TissueorOrganofOrigin)
+                        file.diagnosis.map((d) => d.PrimaryDiagnosis) // this should probably be repurposed to "Breast Cancer Risk Group" & "Ovarian Cancer Risk Group" unless we get more cancer patients
                     ).join(', ');
                 },
                 cell: truncatedTableCell,
@@ -630,7 +619,7 @@ export default class FileTable extends React.Component<IFileTableProps> {
         };
 
         const listSelectors: any = {
-            HTANParentDataFileID: {
+            ParentDataFileID: {
                 pluralName: 'Files',
             },
         };

diff --git a/components/filter/FilterControls.tsx b/components/filter/FilterControls.tsx
@@ -65,7 +65,6 @@ const FilterControls: React.FunctionComponent<IFilterControlsProps> = observer(
 
         const selectOptions = [
             AttributeNames.AtlasName,
-            AttributeNames.TissueorOrganofOrigin,
             AttributeNames.PrimaryDiagnosis,
             AttributeNames.assayName,
             AttributeNames.Level,
@@ -125,34 +124,6 @@ const FilterControls: React.FunctionComponent<IFilterControlsProps> = observer(
                     </div>
                 </div>
 
-                <div>
-                    <div style={{ width: 120 }}>
-                        <FilterPanel
-                            placeholder={
-                                AttributeMap[
-                                    AttributeNames.TissueorOrganofOrigin
-                                ].displayName
-                            }
-                        >
-                            <FilterPropertyColumnShell
-                                title={
-                                    AttributeMap[
-                                        AttributeNames.TissueorOrganofOrigin
-                                    ].displayName
-                                }
-                            >
-                                <FilterCheckList
-                                    setFilter={props.setFilter}
-                                    filters={props.selectedFiltersByGroupName}
-                                    options={options(
-                                        AttributeNames.TissueorOrganofOrigin
-                                    )}
-                                />
-                            </FilterPropertyColumnShell>
-                        </FilterPanel>
-                    </div>
-                </div>
-
                 <div>
                     <div style={{ width: 164 }}>
                         <FilterPanel
@@ -201,7 +172,7 @@ const FilterControls: React.FunctionComponent<IFilterControlsProps> = observer(
                             <div className={'filter-checkbox-list-container'}>
                                 <FilterPropertyColumnShell
                                     title={
-                                        AttributeMap[AttributeNames.Gender]
+                                        AttributeMap[AttributeNames.Sex]
                                             .displayName
                                     }
                                 >
@@ -210,7 +181,7 @@ const FilterControls: React.FunctionComponent<IFilterControlsProps> = observer(
                                         filters={
                                             props.selectedFiltersByGroupName
                                         }
-                                        options={options(AttributeNames.Gender)}
+                                        options={options(AttributeNames.Sex)}
                                     />
                                 </FilterPropertyColumnShell>
                                 <FilterPropertyColumnShell

diff --git a/data/export_syn_data.clj b/data/export_syn_data.clj
@@ -153,6 +153,7 @@
            {:ParticipantID (:ParticipantID x)
             :Race (or (:Race x) "NA")
             :Ethnicity (or (:Ethnicity x) "NA")
+            :Sex (or (:Sex x) "NA")
             :atlas_id (:inAtlas x)}}) data))
 
 (defn transform-diagnosis [data]
@@ -245,7 +246,7 @@
 
   (def placeholder_P
     {:NA_Participant {:Component "Demographics" :ParticipantID "NA_Participant"
-                      :Race "NA" :Ethnicity "NA" :atlas_id "" :atlas_name ""}})
+                      :Race "NA" :Ethnicity "NA" :Sex "NA" :atlas_id "" :atlas_name ""}})
 
   (def clinical-demographics (conj (transform-demographics clinical-participants) placeholder_P))
 

diff --git a/lib/helpers.ts b/lib/helpers.ts
@@ -37,8 +37,7 @@ export interface BaseSerializableEntity {
     BiospecimenID: string;
     DataFileID: DataFileID; // this is used as the stable UID
     ParentBiospecimenID: string;
-    HTANParentDataFileID: string;
-    TissueorOrganofOrigin: string;
+    ParentDataFileID: string;
     PrimaryDiagnosis: string;
     AgeatDiagnosis: number;
     fileFormat: string;
@@ -48,8 +47,7 @@ export interface BaseSerializableEntity {
     AssayType?: string;
     Race: string;
     Ethnicity: string;
-    CountryofResidence: string;
-    Gender: string;
+    Sex: string;
 
     // Derived or attached in frontend
     atlas_id: string;

diff --git a/lib/types.ts b/lib/types.ts
@@ -18,12 +18,10 @@ export type ExploreSelectedFilter = {
 
 export enum AttributeNames {
     // Synapse attribute names
-    TissueorOrganofOrigin = 'TissueorOrganofOrigin',
     PrimaryDiagnosis = 'PrimaryDiagnosis',
-    Gender = 'Gender',
+    Sex = 'Sex',
     Race = 'Race',
     Ethnicity = 'Ethnicity',
-    CountryofResidence = 'CountryofResidence',
     Component = 'Component',
     Biospecimen = 'Biospecimen',
     AtlasName = 'AtlasName',
@@ -53,11 +51,7 @@ function getCaseValues(propName: keyof Entity) {
 }
 
 export const AttributeMap: { [attr in AttributeNames]: IAttributeInfo } = {
-    [AttributeNames.TissueorOrganofOrigin]: {
-        getValues: getCaseValues('TissueorOrganofOrigin'),
-        displayName: 'Organ',
-        caseFilter: true,
-    },
+
     [AttributeNames.PrimaryDiagnosis]: {
         getValues: getCaseValues('PrimaryDiagnosis'),
         displayName: 'Disease Type',
@@ -73,14 +67,9 @@ export const AttributeMap: { [attr in AttributeNames]: IAttributeInfo } = {
         displayName: 'Ethnicity',
         caseFilter: true,
     },
-    [AttributeNames.CountryofResidence]: {
-        getValues: getCaseValues('CountryofResidence'),
-        displayName: 'Country of Residence',
-        caseFilter: true,
-    },
-    [AttributeNames.Gender]: {
-        getValues: getCaseValues('Gender'),
-        displayName: 'Gender',
+    [AttributeNames.Sex]: {
+        getValues: getCaseValues('Sex'),
+        displayName: 'Sex',
         caseFilter: true,
     },
     [AttributeNames.Component]: {

diff --git a/public/processed_syn_data.json.gz b/public/processed_syn_data.json.gz