@gen3/core 0.10.67 → 0.10.69

package/LICENSE

@@ -0,0 +1,201 @@
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package/dist/cjs/index.js

@@ -12,9 +12,11 @@ var useSWR = require('swr');
 var jsonpathPlus = require('jsonpath-plus');
 var flat = require('flat');
 var Papa = require('papaparse');
+var reduxPersist = require('redux-persist');
+var createWebStorage = require('redux-persist/lib/storage/createWebStorage');
+var react$1 = require('redux-persist/integration/react');
 var Queue = require('queue');
 var uuid = require('uuid');
-var reduxPersist = require('redux-persist');
 var reactCookie = require('react-cookie');
 
 function _interopNamespaceDefault(e) {
@@ -54,12 +56,12 @@ const GEN3_WTS_API = process.env.NEXT_PUBLIC_GEN3_WTS_API || `${GEN3_API}/wts`;
 const GEN3_DATA_LIBRARY_API = process.env.NEXT_PUBLIC_GEN3_DATA_LIBRARY_API || `${GEN3_API}/library/lists`;
 const GEN3_CROSSWALK_API = process.env.NEXT_PUBLIC_GEN3_CROSSWALK_API || `${GEN3_API}/mds`;
 const GEN3_SOWER_API = process.env.NEXT_PUBLIC_GEN3_SOWER_API || `${GEN3_API}/jobs`;
-exports.Accessibility = void 0;
-(function(Accessibility) {
+var Accessibility = /*#__PURE__*/ function(Accessibility) {
     Accessibility["ACCESSIBLE"] = "accessible";
     Accessibility["UNACCESSIBLE"] = "unaccessible";
     Accessibility["ALL"] = "all";
-})(exports.Accessibility || (exports.Accessibility = {}));
+    return Accessibility;
+}({});
 const FILE_DELIMITERS = {
     tsv: '\t',
     csv: ','
@@ -637,14 +639,18 @@ const slice$2 = toolkit.createSlice({
 const drsHostnamesReducer = slice$2.reducer;
 const { setDRSHostnames } = slice$2.actions;
 
-exports.Modals = void 0;
-(function(Modals) {
+/**
+ * Defines the modals slice of the Redux store.
+ * This slice is used to control the display of standard Gen3 modals.
+ * and can be extended to add custom modals by representing them as strings.
+ */ var Modals = /*#__PURE__*/ function(Modals) {
     Modals["FirstTimeModal"] = "FirstTimeModal";
     Modals["SessionExpireModal"] = "SessionExpireModal";
     Modals["NoAccessModal"] = "NoAccessModal";
     Modals["CreateCredentialsAPIKeyModal"] = "CreateCredentialsAPIKeyModal";
     Modals["GeneralErrorModal"] = "GeneralErrorModal";
-})(exports.Modals || (exports.Modals = {}));
+    return Modals;
+}({});
 const initialState$2 = {
     currentModal: null
 };
@@ -1372,8 +1378,9 @@ toolkit.createSelector([
     (_, rootObjectId)=>rootObjectId
 ], (dataLibrary, rootObjectId)=>dataLibrary[rootObjectId] || []);
 
-exports.WorkspaceStatus = void 0;
-(function(WorkspaceStatus) {
+/**
+ * Workspace Pod status
+ */ var WorkspaceStatus = /*#__PURE__*/ function(WorkspaceStatus) {
     WorkspaceStatus["Launching"] = "Launching";
     WorkspaceStatus["Running"] = "Running";
     WorkspaceStatus["Terminating"] = "Terminating";
@@ -1381,28 +1388,53 @@ exports.WorkspaceStatus = void 0;
     WorkspaceStatus["NotFound"] = "Not Found";
     WorkspaceStatus["Errored"] = "Errored";
     WorkspaceStatus["StatusError"] = "Status Error";
-})(exports.WorkspaceStatus || (exports.WorkspaceStatus = {}));
-exports.PodConditionType = void 0;
-(function(PodConditionType) {
+    return WorkspaceStatus;
+}({});
+/**
+ * requested state of pod, either by user or workspace monitor
+ */ var RequestedWorkspaceStatus = /*#__PURE__*/ function(RequestedWorkspaceStatus) {
+    RequestedWorkspaceStatus["Launch"] = "Launch";
+    RequestedWorkspaceStatus["Terminate"] = "Terminate";
+    RequestedWorkspaceStatus["Unset"] = "Unset";
+    return RequestedWorkspaceStatus;
+}({});
+var PodConditionType = /*#__PURE__*/ function(PodConditionType) {
     PodConditionType["PodScheduled"] = "PodScheduled";
     PodConditionType["Initialized"] = "Initialized";
     PodConditionType["ContainersReady"] = "ContainersReady";
     PodConditionType["PodReadyToStartContainers"] = "PodReadyToStartContainers";
     PodConditionType["ProxyConnected"] = "ProxyConnected";
     PodConditionType["Ready"] = "Ready";
-})(exports.PodConditionType || (exports.PodConditionType = {}));
-exports.PodStatus = void 0;
-(function(PodStatus) {
+    return PodConditionType;
+}({});
+var PodStatus = /*#__PURE__*/ function(PodStatus) {
     PodStatus["True"] = "True";
     PodStatus["False"] = "False";
     PodStatus["Unknown"] = "Unknown";
-})(exports.PodStatus || (exports.PodStatus = {}));
+    return PodStatus;
+}({});
+
+// Using the built-in Date object
+const getCurrentTimestamp = ()=>{
+    return Date.now(); // Returns milliseconds since Unix epoch
+};
+// Compare two timestamps and get difference in milliseconds
+const getTimeDifferenceMs = (startTime, endTime = Date.now())=>{
+    return endTime - startTime;
+};
+// Check if time difference is greater than specified minutes
+const isTimeGreaterThan = (startTime, minutes)=>{
+    const diffMs = getTimeDifferenceMs(startTime);
+    const diffMinutes = diffMs / (1000 * 60);
+    return diffMinutes > minutes;
+};
 
 const NO_WORKSPACE_ID = 'none';
 const initialState = {
     id: NO_WORKSPACE_ID,
-    status: exports.WorkspaceStatus.NotFound,
-    requestedStatus: 'NotSet'
+    status: WorkspaceStatus.NotFound,
+    requestedStatus: RequestedWorkspaceStatus.Unset,
+    requestedStatusTimestamp: getCurrentTimestamp()
 };
 const slice = toolkit.createSlice({
     name: 'ActiveWorkspace',
@@ -1430,7 +1462,8 @@ const slice = toolkit.createSlice({
         setRequestedWorkspaceStatus: (state, action)=>{
             return {
                 ...state,
-                requestedStatus: action.payload
+                requestedStatus: action.payload,
+                requestedStatusTimestamp: getCurrentTimestamp()
             };
         },
         setActiveWorkspace: (_state, action)=>{
@@ -1445,6 +1478,7 @@ const { setActiveWorkspaceId, clearActiveWorkspaceId, setActiveWorkspaceStatus,
 const selectActiveWorkspaceId = (state)=>state.activeWorkspace.id;
 const selectActiveWorkspaceStatus = (state)=>state.activeWorkspace.status;
 const selectRequestedWorkspaceStatus = (state)=>state.activeWorkspace.requestedStatus;
+const selectRequestedWorkspaceStatusTimestamp = (state)=>state.activeWorkspace.requestedStatusTimestamp;
 
 /**
  * Creates a base class core API for guppy API calls.
@@ -1818,7 +1852,7 @@ const useGetStatus = ()=>{
                 }
             }),
             getRawDataAndTotalCounts: builder.query({
-                query: ({ type, fields, filters, sort, offset = 0, size = 20, accessibility = exports.Accessibility.ALL, format = undefined })=>{
+                query: ({ type, fields, filters, sort, offset = 0, size = 20, accessibility = Accessibility.ALL, format = undefined })=>{
                     const gqlFilter = convertFilterSetToGqlFilter(filters);
                     const params = [
                         ...sort ? [
@@ -1875,7 +1909,7 @@ const useGetStatus = ()=>{
                 }
             }),
             getAggs: builder.query({
-                query: ({ type, fields, filters, accessibility = exports.Accessibility.ALL })=>{
+                query: ({ type, fields, filters, accessibility = Accessibility.ALL })=>{
                     const queryStart = isFilterEmpty(filters) ? `
               query getAggs {
               _aggregation {
@@ -1900,7 +1934,7 @@ const useGetStatus = ()=>{
                 }
             }),
             getSubAggs: builder.query({
-                query: ({ type, mainField, termsFields = undefined, missingFields = undefined, numericAggAsText = false, gqlFilter = undefined, accessibility = exports.Accessibility.ALL })=>{
+                query: ({ type, mainField, termsFields = undefined, missingFields = undefined, numericAggAsText = false, gqlFilter = undefined, accessibility = Accessibility.ALL })=>{
                     const nestedAggFields = {
                         termsFields: termsFields,
                         missingFields: missingFields
@@ -1925,7 +1959,7 @@ const useGetStatus = ()=>{
                 }
             }),
             getCounts: builder.query({
-                query: ({ type, filters, accessibility = exports.Accessibility.ALL })=>{
+                query: ({ type, filters, accessibility = Accessibility.ALL })=>{
                     const gqlFilters = convertFilterSetToGqlFilter(filters);
                     const queryLine = `query totalCounts ${gqlFilters ? '($filter: JSON)' : ''}{`;
                     const typeAggsLine = `${type} ${gqlFilters ? '(filter: $filter, ' : '('} accessibility: ${accessibility}) {`;
@@ -1949,7 +1983,7 @@ const useGetStatus = ()=>{
                 }
             }),
             getFieldCountSummary: builder.query({
-                query: ({ type, field, filters, accessibility = exports.Accessibility.ALL })=>{
+                query: ({ type, field, filters, accessibility = Accessibility.ALL })=>{
                     const gqlFilters = convertFilterSetToGqlFilter(filters);
                     const query = `query summary ($filter: JSON) {
         _aggregation {
@@ -2265,9 +2299,46 @@ const rootReducer = toolkit.combineReducers({
     [userAuthApiReducerPath]: userAuthApiReducer
 });
 
+/* eslint @typescript-eslint/no-unused-vars: 0 */ // Credit to: https://github.com/vercel/next.js/discussions/15687
+const createNoopStorage = ()=>{
+    return {
+        getItem (_key) {
+            return Promise.resolve(null);
+        },
+        setItem (_key, value) {
+            return Promise.resolve(value);
+        },
+        removeItem (_key) {
+            return Promise.resolve();
+        }
+    };
+};
+const storage = typeof window !== 'undefined' ? createWebStorage('local') : createNoopStorage();
+typeof window !== 'undefined' ? createWebStorage('session') : createNoopStorage();
+
+const persistConfig = {
+    key: 'root',
+    version: 1,
+    storage,
+    whitelist: [
+        'cohorts',
+        'activeWorkspace'
+    ]
+};
 const coreStore = toolkit.configureStore({
-    reducer: rootReducer,
-    middleware: (getDefaultMiddleware)=>getDefaultMiddleware().concat(gen3ServicesReducerMiddleware, guppyAPISliceMiddleware, userAuthApiMiddleware)
+    reducer: reduxPersist.persistReducer(persistConfig, rootReducer),
+    middleware: (getDefaultMiddleware)=>getDefaultMiddleware({
+            serializableCheck: {
+                ignoredActions: [
+                    reduxPersist.FLUSH,
+                    reduxPersist.REHYDRATE,
+                    reduxPersist.PAUSE,
+                    reduxPersist.PERSIST,
+                    reduxPersist.PURGE,
+                    reduxPersist.REGISTER
+                ]
+            }
+        }).concat(gen3ServicesReducerMiddleware, guppyAPISliceMiddleware, userAuthApiMiddleware)
 });
 query.setupListeners(coreStore.dispatch);
 
@@ -2376,7 +2447,7 @@ const fetchFencePresignedURL = async ({ guid, method = 'GET', onAbort = ()=>null
             }
             throw new HTTPError(response.status, errorMessage, errorData);
         }
-        return await response.json();
+        return (await response.json())['url'];
     } catch (error) {
         if (error instanceof Error) {
             if (error.name === 'AbortError') {
@@ -2387,10 +2458,14 @@ const fetchFencePresignedURL = async ({ guid, method = 'GET', onAbort = ()=>null
     }
 };
 
+const persistor = reduxPersist.persistStore(coreStore);
 const CoreProvider = ({ children })=>{
     return /*#__PURE__*/ React.createElement(reactRedux.Provider, {
         store: coreStore
-    }, children);
+    }, /*#__PURE__*/ React.createElement(react$1.PersistGate, {
+        loading: null,
+        persistor: persistor
+    }, children));
 };
 
 /**
@@ -2495,6 +2570,11 @@ const HasEnoughData = (data, keys, limit)=>{
                         url: `metadata?${params}`
                     })
             }),
+            getMetadataById: builder.query({
+                query: (params)=>({
+                        url: `${GEN3_MDS_API}/metadata/${params}`
+                    })
+            }),
             // TODO: Move this to own slice
             getCrosswalkData: builder.query({
                 queryFn: async (arg, _queryApi, _extraOptions, fetchWithBQ)=>{
@@ -2550,7 +2630,7 @@ const HasEnoughData = (data, keys, limit)=>{
             })
         })
 });
-const { useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery } = metadataApi;
+const { useGetAggMDSQuery, useGetMDSQuery, useGetTagsQuery, useGetDataQuery, useGetMetadataByIdQuery, useGetCrosswalkDataQuery, useLazyGetCrosswalkDataQuery, useGetIndexAggMDSQuery } = metadataApi;
 
 // using a random uuid v4 as the namespace
 const GEN3_APP_NAMESPACE = '7bfaa818-c69c-457e-8d87-413cf60c25f0';
@@ -2581,7 +2661,7 @@ const getGen3AppId = (name, version)=>{
     // });
     const Gen3AppWrapper = (props)=>{
         React.useEffect(()=>{
-            document.title = `GEN3 - ${name}`;
+            document.title = `${name}`;
         });
         return /*#__PURE__*/ React.createElement(App, props);
     };
@@ -2815,7 +2895,7 @@ const WorkspaceWithTags = gen3Api.enhanceEndpoints({
     ]
 });
 const EmptyWorkspaceStatusResponse = {
-    status: exports.WorkspaceStatus.NotFound,
+    status: WorkspaceStatus.NotFound,
     conditions: [],
     containerStates: [],
     idleTimeLimit: 0,
@@ -2874,9 +2954,9 @@ const workspacesApi = WorkspaceWithTags.injectEndpoints({
                     if (workspaceStatus.error) {
                         return workspaceStatus;
                     }
-                    // TODO: try to find out IF this is code is required
+                    // TODO: Find out IF this is code is required
                     const workspaceStatusData = workspaceStatus.data;
-                    if (workspaceStatusData.status === exports.WorkspaceStatus.Running && (currentWorkspaceStatus === 'Not Found' || currentWorkspaceStatus === 'Launching')) {
+                    if (workspaceStatusData.status === WorkspaceStatus.Running && (currentWorkspaceStatus === 'Not Found' || currentWorkspaceStatus === 'Launching')) {
                         const proxyStatus = await fetchWithBQ(`${GEN3_WORKSPACE_API}/proxy/`);
                         let statusError = undefined;
                         if (isFetchParseError(proxyStatus.error)) {
@@ -2889,11 +2969,11 @@ const workspacesApi = WorkspaceWithTags.injectEndpoints({
                             return {
                                 data: {
                                     ...workspaceStatusData,
-                                    status: exports.WorkspaceStatus.Launching,
+                                    status: WorkspaceStatus.Launching,
                                     conditions: [
                                         {
                                             type: 'ProxyConnected',
-                                            status: exports.PodStatus.False
+                                            status: PodStatus.False
                                         }
                                     ]
                                 }
@@ -2940,10 +3020,12 @@ const workspaceStatusSelector = workspacesApi.endpoints.getWorkspaceStatus.selec
 const selectWorkspaceStatusFromService = toolkit.createSelector(workspaceStatusSelector, (status)=>status.data ?? {
         ...EmptyWorkspaceStatusResponse
     });
-const selectWorkspaceStatus = toolkit.createSelector(workspaceStatusSelector, (status)=>status?.data?.status ?? exports.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);
 
-const isWorkspaceActive = (status)=>status === exports.WorkspaceStatus.Running || status === exports.WorkspaceStatus.Launching || status === exports.WorkspaceStatus.Terminating;
-const isWorkspaceRunningOrStopping = (status)=>status === exports.WorkspaceStatus.Running || status === exports.WorkspaceStatus.Terminating;
+const isWorkspaceActive = (status)=>status === WorkspaceStatus.Running || status === WorkspaceStatus.Launching || status === WorkspaceStatus.Terminating;
+const isWorkspaceRunningOrStopping = (status)=>status === WorkspaceStatus.Running || status === WorkspaceStatus.Terminating;
 
 const resourcePathFromProjectID = (projectID)=>{
     const split = projectID.split('-');
@@ -3184,6 +3266,7 @@ const { useGetProjectsQuery, useGetSubmissionGraphQLQuery, useGetProjectsDetails
 });
 const { useGetSowerJobListQuery, useLazyGetSowerJobListQuery, useSubmitSowerJobMutation, useGetSowerJobStatusQuery, useGetSowerOutputQuery, useGetSowerServiceStatusQuery } = loadingStatusApi;
 
+exports.Accessibility = Accessibility;
 exports.CoreProvider = CoreProvider;
 exports.EmptyWorkspaceStatusResponse = EmptyWorkspaceStatusResponse;
 exports.GEN3_API = GEN3_API;
@@ -3201,6 +3284,11 @@ exports.GEN3_SUBMISSION_API = GEN3_SUBMISSION_API;
 exports.GEN3_WORKSPACE_API = GEN3_WORKSPACE_API;
 exports.HTTPError = HTTPError;
 exports.HTTPErrorMessages = HTTPErrorMessages;
+exports.Modals = Modals;
+exports.PodConditionType = PodConditionType;
+exports.PodStatus = PodStatus;
+exports.RequestedWorkspaceStatus = RequestedWorkspaceStatus;
+exports.WorkspaceStatus = WorkspaceStatus;
 exports.clearActiveWorkspaceId = clearActiveWorkspaceId;
 exports.clearCohortFilters = clearCohortFilters;
 exports.clearDataLibrarySelection = clearDataLibrarySelection;
@@ -3227,6 +3315,7 @@ exports.fetchJson = fetchJson;
 exports.fetchUserState = fetchUserState;
 exports.fieldNameToTitle = fieldNameToTitle;
 exports.gen3Api = gen3Api;
+exports.getCurrentTimestamp = getCurrentTimestamp;
 exports.getGen3AppId = getGen3AppId;
 exports.getNumberOfItemsInDatalist = getNumberOfItemsInDatalist;
 exports.getTimestamp = getTimestamp;
@@ -3268,6 +3357,7 @@ exports.isPending = isPending;
 exports.isProgramUrl = isProgramUrl;
 exports.isRootUrl = isRootUrl;
 exports.isString = isString;
+exports.isTimeGreaterThan = isTimeGreaterThan;
 exports.isWorkspaceActive = isWorkspaceActive;
 exports.isWorkspaceRunningOrStopping = isWorkspaceRunningOrStopping;
 exports.listifyMethodsFromMapping = listifyMethodsFromMapping;
@@ -3296,7 +3386,9 @@ exports.selectGen3AppMetadataByName = selectGen3AppMetadataByName;
 exports.selectHeadersWithCSRFToken = selectHeadersWithCSRFToken;
 exports.selectIndexFilters = selectIndexFilters;
 exports.selectIndexedFilterByName = selectIndexedFilterByName;
+exports.selectPaymodelStatus = selectPaymodelStatus;
 exports.selectRequestedWorkspaceStatus = selectRequestedWorkspaceStatus;
+exports.selectRequestedWorkspaceStatusTimestamp = selectRequestedWorkspaceStatusTimestamp;
 exports.selectUser = selectUser;
 exports.selectUserAuthStatus = selectUserAuthStatus;
 exports.selectUserData = selectUserData;
@@ -3352,6 +3444,7 @@ exports.useGetIndexFields = useGetIndexFields;
 exports.useGetJWKKeysQuery = useGetJWKKeysQuery;
 exports.useGetLoginProvidersQuery = useGetLoginProvidersQuery;
 exports.useGetMDSQuery = useGetMDSQuery;
+exports.useGetMetadataByIdQuery = useGetMetadataByIdQuery;
 exports.useGetProjectsDetailsQuery = useGetProjectsDetailsQuery;
 exports.useGetProjectsQuery = useGetProjectsQuery;
 exports.useGetRawDataAndTotalCountsQuery = useGetRawDataAndTotalCountsQuery;