@gen3/core 0.12.55 → 0.12.57

package/dist/cjs/index.js

@@ -424,7 +424,7 @@ const useIsUserLoggedIn = ()=>{
     React.useEffect(()=>{
         if (status === 'uninitialized' || renew) {
             // TODO: need to determine what other states require dispatch
-            coreDispatch(fetchUserState());
+            void coreDispatch(fetchUserState());
         }
     }, [
         status,
@@ -725,12 +725,14 @@ const { useGetExternalLoginsQuery, useLazyGetExternalLoginsQuery, useLazyIsExter
                 if (response.status === 200) {
                     try {
                         return await response.json();
+                    // oxlint-disable-next-line no-unused-vars
                     } catch (error) {
                         throw new ResolveDRSError('Failed to parse response as JSON');
                     }
                 } else {
                     throw new ResolveDRSError(RESOLVE_DRS_ERROR);
                 }
+            // oxlint-disable-next-line no-unused-vars
             } catch (error) {
                 throw new ResolveDRSError(RESOLVE_DRS_ERROR);
             }
@@ -745,6 +747,7 @@ const { useGetExternalLoginsQuery, useLazyGetExternalLoginsQuery, useLazyIsExter
                 throw new ResolveDRSError(RESOLVE_DRS_ERROR);
             }
         }, {});
+    // oxlint-disable-next-line no-unused-vars
     } catch (error) {
         throw new ResolveDRSError(RESOLVE_DRS_ERROR);
     }
@@ -1450,7 +1453,7 @@ const useGetFederatedLoginStatus = ({ selectedFiles })=>{
         };
         // Only run if there's data to act on
         if (!wstIsLoading && wtsResults) {
-            fetchData();
+            void fetchData();
         }
     }, [
         selectedFiles,
@@ -2591,7 +2594,7 @@ const getCurrentCohortId = (state)=>state.currentCohortId;
                         [index]: {
                             mode: state.entities[currentCohortId]?.filters[index]?.mode ?? 'and',
                             root: {
-                                ...state.entities[currentCohortId]?.filters[index]?.root ?? {},
+                                ...state.entities[currentCohortId]?.filters[index]?.root,
                                 [field]: filter
                             }
                         }
@@ -2730,9 +2733,7 @@ const getCurrentCohortId = (state)=>state.currentCohortId;
                 changes: {
                     counts: {
                         ...cohort.counts,
-                        ...{
-                            [index]: counts
-                        }
+                        [index]: counts
                     }
                 }
             });
@@ -3199,7 +3200,7 @@ const rootReducer = toolkit.combineReducers({
             throw new Error(response.statusText);
         }
         let jsonData = await response.json();
-        if (parameters?.rootPath && parameters.rootPath) {
+        if (parameters?.rootPath) {
             // if rootPath is provided, extract the data from the rootPath
             jsonData = jsonpathPlus.JSONPath({
                 json: jsonData,
@@ -3245,7 +3246,7 @@ const downloadJSONDataFromGuppy = async ({ parameters, onAbort = ()=>null, signa
             } : {}
         });
         let jsonData = await response.json();
-        if (parameters?.rootPath && parameters.rootPath) {
+        if (parameters?.rootPath) {
             // if rootPath is provided, extract the data from the rootPath
             jsonData = jsonpathPlus.JSONPath({
                 json: jsonData,
@@ -3572,7 +3573,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 }
             }),
             getRawDataAndTotalCounts: builder.query({
-                query: ({ type, fields, filters, sort, offset = 0, size = 20, accessibility = Accessibility.ALL, format = undefined, indexPrefix = '', filterName = 'filter' })=>{
+                query: ({ type, fields, filters, sort, offset = 0, size = 20, accessibility = Accessibility.ALL, format, indexPrefix = '', filterName = 'filter' })=>{
                     const gqlFilter = convertFilterSetToGqlFilter(filters);
                     const params = [
                         ...sort ? [
@@ -3636,7 +3637,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 },
                 // return . separated fields as proper values
                 transformResponse: (response, _meta, args)=>{
-                    const containsDots = args?.fields?.filter((f)=>f.includes('.'));
+                    const containsDots = args.fields?.filter((f)=>f.includes('.'));
                     // check if dot seperated in arry and not object
                     if (containsDots && containsDots.length > 0 && response.data) {
                         const containsDotsUniqueBase = containsDots.reduce((acc, field)=>{
@@ -3699,7 +3700,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 transformResponse: (response, _meta, args)=>{
                     const buckets = processHistogramResponse(response?.data?.[`${args?.indexPrefix ?? ''}_aggregation`][args.type] ?? {});
                     // check for totals
-                    const count = response?.data?.[`${args?.indexPrefix ?? ''}_aggregation`][args.type]?._totalCount ?? null;
+                    const count = response.data?.[`${args?.indexPrefix ?? ''}_aggregation`][args.type]?._totalCount ?? null;
                     return {
                         _totalCount: [
                             {
@@ -3715,7 +3716,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 ]
             }),
             getStatsAggregations: builder.query({
-                query: ({ type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId = undefined, indexPrefix = '', filterName = 'filter' })=>{
+                query: ({ type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId, indexPrefix = '', filterName = 'filter' })=>{
                     return buildGetStatsAggregationQuery(type, fields, filters, accessibility, filterSelf, queryId, indexPrefix, filterName);
                 },
                 transformResponse: (response, _meta, args)=>{
@@ -3726,14 +3727,14 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 ]
             }),
             getSubAggs: builder.query({
-                query: ({ type, mainField, termsFields = undefined, missingFields = undefined, numericAggAsText = false, filters = undefined, accessibility = Accessibility.ALL, indexPrefix = '', filterName = 'filter' })=>{
+                query: ({ type, mainField, termsFields, missingFields, numericAggAsText, filters, accessibility = Accessibility.ALL, indexPrefix = '', filterName = 'filter' })=>{
                     const nestedAggFields = {
                         termsFields: termsFields,
                         missingFields: missingFields
                     };
-                    const query = `query getSubAggs ( ${filters ?? `$${filterName}: JSON,`} $nestedAggFields: JSON) {
+                    const query = `query getSubAggs ( ${filters && `$${filterName}: JSON,`} $nestedAggFields: JSON) {
     ${indexPrefix}_aggregation {
-      ${type} ( ${filters ?? `filter: $${filterName}, filterSelf: false,`} nestedAggFields: $nestedAggFields, accessibility: ${accessibility}) {
+      ${type} ( ${filters && `filter: $${filterName}, filterSelf: false,`} nestedAggFields: $nestedAggFields, accessibility: ${accessibility}) {
       _totalCounts
         ${nestedHistogramQueryStrForEachField(mainField, numericAggAsText)}
       }`;
@@ -3755,7 +3756,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 ]
             }),
             getCounts: builder.query({
-                query: ({ type, filters, accessibility = Accessibility.ALL, queryId = undefined, indexPrefix = '', filterName = 'filter' })=>{
+                query: ({ type, filters, accessibility = Accessibility.ALL, queryId, indexPrefix = '', filterName = 'filter' })=>{
                     const gqlFilters = convertFilterSetToGqlFilter(filters);
                     const queryLine = `query totalCounts${queryId ? `${indexPrefix}_${queryId}` : ''} ${gqlFilters ? `($${filterName}: JSON)` : ''}{`;
                     const typeAggsLine = `${type} ${gqlFilters ? `(filter: $${filterName}, ` : '('} accessibility: ${accessibility}) {`;
@@ -3808,9 +3809,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                     return {
                         query: query,
                         variables: {
-                            ...gqlFilters && {
-                                [filterName]: gqlFilters
-                            }
+                            [filterName]: gqlFilters
                         }
                     };
                 }
@@ -3843,7 +3842,7 @@ const explorerTags = guppyApi.enhanceEndpoints({
                 }
             }),
             customRange: builder.query({
-                query: ({ filters, field, ranges, rangeBaseName, index, indexPrefix, accessibility = Accessibility.ALL, isNested = true, asTextHistogram = false })=>{
+                query: ({ filters, field, ranges, rangeBaseName, index, indexPrefix, accessibility, isNested = true, asTextHistogram = false })=>{
                     // remove field from FilterSet
                     const queryData = buildRangeQuery(field, ranges, filters, rangeBaseName, index, indexPrefix, isNested, asTextHistogram);
                     const gqlFilters = Object.entries(queryData.filters).reduce((acc, [key, filter])=>{
@@ -3913,7 +3912,7 @@ const useGetIndexFields = (index, indexPrefix = '')=>{
     });
     return data ?? [];
 };
-const buildGetAggregationQuery = (type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId = undefined, indexPrefix = '', filterName = 'filter')=>{
+const buildGetAggregationQuery = (type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId, indexPrefix = '', filterName = 'filter')=>{
     const queryStart = isFilterEmpty(filters) ? `query getAggs${queryId ? `_${queryId}` : ''} {
               ${indexPrefix}_aggregation {
               ${type} (accessibility: ${accessibility}) {` : `query getAggs ($${filterName}: JSON) {
@@ -3932,7 +3931,7 @@ const buildGetAggregationQuery = (type, fields, filters, accessibility = Accessi
     };
     return queryBody;
 };
-const buildGetStatsAggregationQuery = (type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId = undefined, indexPrefix = '', filterName = 'filter')=>{
+const buildGetStatsAggregationQuery = (type, fields, filters, accessibility = Accessibility.ALL, filterSelf = false, queryId, indexPrefix = '', filterName = 'filter')=>{
     const queryStart = isFilterEmpty(filters) ? `
               query getStatsAggs${queryId ? `_${queryId}` : ''} {
               ${indexPrefix}_aggregation {
@@ -4206,7 +4205,7 @@ class CohortStorage {
         try {
             const db = await this.getDb();
             const tx = db.transaction(this.storeName, 'readwrite');
-            tx.objectStore(this.storeName).put(cohort);
+            await tx.objectStore(this.storeName).put(cohort);
             await tx.done;
             return {
                 status: 200,
@@ -4380,7 +4379,7 @@ class CohortStorage {
                 ...existing,
                 modifiedDatetime: timestamp
             };
-            store.put(updated);
+            await store.put(updated);
             await tx.done;
             return {
                 status: 200,
@@ -4415,7 +4414,7 @@ class CohortStorage {
                     message: 'cohort not found'
                 };
             }
-            store.delete(id);
+            await store.delete(id);
             await tx.done;
             return {
                 status: 200,
@@ -4437,7 +4436,7 @@ class CohortStorage {
             const db = await this.getDb();
             const tx = db.transaction(this.storeName, 'readwrite');
             const store = tx.objectStore(this.storeName);
-            store.clear();
+            await store.clear();
             await tx.done;
             return {
                 status: 200,
@@ -4579,7 +4578,7 @@ const selectCurrentCohortName = (state)=>cohortSelectors.selectById(state, getCu
     if (!cohort) {
         console.error('No Cohort Defined');
     }
-    return cohort?.filters?.[index] ?? EmptyFilterSet;
+    return cohort.filters?.[index] ?? EmptyFilterSet;
 };
 
 const isFileItem = (item)=>{
@@ -4852,8 +4851,8 @@ const extractIndexFromDataLibraryCohort = (query)=>{
             const md5Sum = dataObject[dataFieldMapping?.dataObjectMd5sumField ?? 'md5sum'] ?? 'N/A';
             const url = dataObject[dataFieldMapping?.dataObjectUrlField ?? 'url'] ?? 'N/A';
             let fileType = 'GA4GH_DRS';
-            if (dataFieldMapping?.dataObjectFileTypeValue) fileType = dataFieldMapping.dataObjectFileTypeValue;
-            if (dataFieldMapping?.dataObjectFileTypeField) fileType = dataObject[dataFieldMapping?.dataObjectFileTypeField];
+            if (dataFieldMapping.dataObjectFileTypeValue) fileType = dataFieldMapping.dataObjectFileTypeValue;
+            if (dataFieldMapping.dataObjectFileTypeField) fileType = dataObject[dataFieldMapping.dataObjectFileTypeField];
             return {
                 ...dataAcc,
                 [fileId]: {
@@ -4949,7 +4948,7 @@ class LocalStorageService {
             const db = await this.getDb();
             const tx = db.transaction(STORE_NAME, 'readwrite');
             const id = toolkit.nanoid(); // Create an id for the list
-            tx.objectStore(STORE_NAME).put({
+            await tx.objectStore(STORE_NAME).put({
                 id,
                 version: 0,
                 items: list?.items ?? {},
@@ -4969,6 +4968,7 @@ class LocalStorageService {
                 status: 200,
                 message: 'list added'
             };
+        // oxlint-disable-next-line no-unused-vars
         } catch (_error) {
             return {
                 isError: true,
@@ -4991,15 +4991,13 @@ class LocalStorageService {
             const version = listData.version ? listData.version + 1 : 0;
             const updated = {
                 ...listData,
-                ...{
-                    name,
-                    items
-                },
-                version: version,
+                name,
+                items,
+                version,
                 updated_time: timestamp,
                 created_time: listData.created_time
             };
-            store.put(updated);
+            await store.put(updated);
             await tx.done;
             return {
                 status: 200,
@@ -5026,7 +5024,7 @@ class LocalStorageService {
             if (!item) {
                 throw new Error(`List ${id} does not exist`);
             }
-            store.delete(id);
+            await store.delete(id);
             await tx.done;
             return {
                 status: 200,
@@ -5045,7 +5043,7 @@ class LocalStorageService {
         try {
             const db = await this.getDb();
             const tx = db.transaction(STORE_NAME, 'readwrite');
-            tx.objectStore(STORE_NAME).clear();
+            await tx.objectStore(STORE_NAME).clear();
             await tx.done;
             return {
                 status: 200,
@@ -5079,7 +5077,7 @@ class LocalStorageService {
             const db = await this.getDb();
             const tx = db.transaction(STORE_NAME, 'readwrite');
             for (const [id, list] of Object.entries(allLists)){
-                tx.objectStore(STORE_NAME).put({
+                await tx.objectStore(STORE_NAME).put({
                     id,
                     ...list
                 });
@@ -5109,7 +5107,7 @@ class LocalStorageService {
         try {
             const db = await this.getDb();
             const tx = db.transaction(STORE_NAME, 'readwrite');
-            tx.objectStore(STORE_NAME).put({
+            await tx.objectStore(STORE_NAME).put({
                 id: id,
                 ...data
             });
@@ -5152,7 +5150,7 @@ class LocalStorageService {
                 const db = await this.getDb();
                 const tx = db.transaction(STORE_NAME, 'readwrite');
                 for (const [id, list] of Object.entries(allLists)){
-                    tx.objectStore(STORE_NAME).put({
+                    await tx.objectStore(STORE_NAME).put({
                         id,
                         ...list
                     });
@@ -5174,7 +5172,7 @@ class LocalStorageService {
     }
 }
 
-const fetchFromDataLibraryAPI = async (url, method = HttpMethod.GET, body = undefined)=>{
+const fetchFromDataLibraryAPI = async (url, method = HttpMethod.GET, body)=>{
     try {
         return {
             data: await fetchJSONDataFromURL(url, true, method, body)
@@ -5215,7 +5213,7 @@ class APIStorageService {
         this.pendingRequests = new Map();
         this.apiBaseUrl = apiBaseUrl;
     }
-    async dedupedRequest(url, method = HttpMethod.GET, body = undefined) {
+    async dedupedRequest(url, method = HttpMethod.GET, body) {
         // Create a unique key for this request
         const requestKey = `${method}:${url}:${body ? JSON.stringify(body) : ''}`;
         // If this exact request is already in progress, return the pending promise
@@ -5978,12 +5976,10 @@ const { useGraphQLQuery } = graphQLAPI;
                 query: ({ type, filter, accessibility, fields, sort })=>{
                     const queryBody = {
                         filter: convertFilterSetToGqlFilter(filter),
-                        ...{
-                            type,
-                            accessibility,
-                            fields,
-                            sort
-                        }
+                        type,
+                        accessibility,
+                        fields,
+                        sort
                     };
                     return {
                         url: `${GEN3_GUPPY_API}/download`,
@@ -6158,6 +6154,11 @@ const HasEnoughData = (data, keys, limit)=>{
                         url: `${GEN3_MDS_API}/metadata/${params}`
                     })
             }),
+            getMetadataByUrl: builder.query({
+                query: (url)=>({
+                        url: url
+                    })
+            }),
             // TODO: Move this to own slice
             getCrosswalkData: builder.query({
                 queryFn: async (arg, _queryApi, _extraOptions, fetchWithBQ)=>{
@@ -6213,7 +6214,7 @@ const HasEnoughData = (data, keys, limit)=>{
             })
         })
 });
-const { useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetMetadataByIdQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery } = metadataApi;
+const { useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetMetadataByIdQuery, useGetMetadataByUrlQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery } = metadataApi;
 
 const queryMultipleMDSRecords = async (guids, useAggMDS = false, signal)=>{
     const result = {};
@@ -6488,7 +6489,7 @@ const listifyMethodsFromMapping = (actions)=>{
 const userHasDataUpload = (userAuthMapping = {})=>{
     const actionIsFileUpload = (x)=>x.method === 'file_upload';
     const resource = userAuthMapping['/data_file'];
-    return resource !== undefined && resource.some(actionIsFileUpload);
+    return resource !== resource && resource.some(actionIsFileUpload);
 };
 const userHasMethodForServiceOnResource = (method, service, resourcePath, userAuthMapping = {})=>{
     const actions = userAuthMapping[resourcePath];
@@ -6571,8 +6572,9 @@ const SubmissionGraphqlQuery = `query transactionList {
                     };
                     const projects = projectsResponse?.data.data.project;
                     const projectIds = projects.map((p)=>p.project_id);
+                    const slicedProjectIds = projectIds.slice(args.offset, args.offset + args.size);
                     // given the list of projects, get all of them by executing the projectDetailsQuery for each project
-                    const projectDetails = await Promise.all(projectIds.map(async (projectId)=>{
+                    const projectDetails = await Promise.all(slicedProjectIds.map(async (projectId)=>{
                         const result = await fetchWithBQ({
                             url: `${GEN3_SUBMISSION_API}/graphql`,
                             method: 'POST',
@@ -6794,7 +6796,7 @@ const workspaceStatusSelector = workspacesApi.endpoints.getWorkspaceStatus.selec
 const selectWorkspaceStatusFromService = toolkit.createSelector(workspaceStatusSelector, (status)=>status.data ?? {
         ...EmptyWorkspaceStatusResponse
     });
-const selectWorkspaceStatus = toolkit.createSelector(workspaceStatusSelector, (status)=>status?.data?.status ?? WorkspaceStatus.NotFound);
+const selectWorkspaceStatus = toolkit.createSelector(workspaceStatusSelector, (status)=>status.data?.status ?? WorkspaceStatus.NotFound);
 const paymodelStatusSelector = workspacesApi.endpoints.getWorkspacePayModels.select();
 const selectPaymodelStatus = toolkit.createSelector(paymodelStatusSelector, (status)=>status);
 
@@ -6906,7 +6908,7 @@ const pValueSlice = graphQLAPI.injectEndpoints({
                             variables: data
                         }
                     }),
-                transformResponse: (response)=>response?.data?.analysis.pvalue
+                transformResponse: (response)=>response.data?.analysis.pvalue
             })
         })
 });
@@ -7335,6 +7337,7 @@ exports.useGetLoginProvidersQuery = useGetLoginProvidersQuery;
 exports.useGetMDSQuery = useGetMDSQuery;
 exports.useGetManifestServiceStatusQuery = useGetManifestServiceStatusQuery;
 exports.useGetMetadataByIdQuery = useGetMetadataByIdQuery;
+exports.useGetMetadataByUrlQuery = useGetMetadataByUrlQuery;
 exports.useGetMetadataFromManifestQuery = useGetMetadataFromManifestQuery;
 exports.useGetMetadataManifestQuery = useGetMetadataManifestQuery;
 exports.useGetObjectIdsQuery = useGetObjectIdsQuery;