refact: remove mentions of tables

src/components/ServiceContent.js

@@ -40,7 +40,6 @@ const ServiceContent = () => {
                                 />
                             </Spin>
                         </Col>
-                        {/* TODO: Tables */}
                     </Row>
                     <Typography.Title level={3}>Services</Typography.Title>
                     <ServiceList />

src/components/datasets/Dataset.js

@@ -76,7 +76,6 @@ class Dataset extends Component {
             contact_info: value.contact_info || "",
             data_use: simpleDeepCopy(value.data_use || INITIAL_DATA_USE_VALUE),
             linked_field_sets: value.linked_field_sets || [],
-            tables: value.tables || [],
 
             fieldSetAdditionModalVisible: false,
 
@@ -87,7 +86,6 @@ class Dataset extends Component {
             },
 
             selectedTab: "overview",
-            selectedTable: null,
         };
 
         this.handleFieldSetDeletion = this.handleFieldSetDeletion.bind(this);
@@ -294,7 +292,6 @@ Dataset.propTypes = {
     mode: PropTypes.oneOf(["public", "private"]),
 
     project: projectPropTypesShape,
-    strayTables: PropTypes.arrayOf(PropTypes.object),
 
     value: datasetPropTypesShape,
 

src/components/manager/ManagerDropBoxContent.js

@@ -459,7 +459,7 @@ const ManagerDropBoxContent = () => {
     const [fileDeleteModal, setFileDeleteModal] = useState(false);
 
     const [selectedWorkflow, setSelectedWorkflow] = useState(null);
-    const [tableSelectionModal, setTableSelectionModal] = useState(false);
+    const [datasetSelectionModal, setDatasetSelectionModal] = useState(false);
 
     const showUploadModal = useCallback(() => setUploadModal(true), []);
     const hideUploadModal = useCallback(() => setUploadModal(false), []);
@@ -468,11 +468,11 @@ const ManagerDropBoxContent = () => {
     const showFileContentsModal = useCallback(() => setFileContentsModal(true), []);
     const hideFileContentsModal = useCallback(() => setFileContentsModal(false), []);
 
-    const showTableSelectionModal = useCallback(workflow => {
+    const showDatasetSelectionModal = useCallback(workflow => {
         setSelectedWorkflow(workflow);
-        setTableSelectionModal(true);
+        setDatasetSelectionModal(true);
     }, []);
-    const hideTableSelectionModal = useCallback(() => setTableSelectionModal(false), []);
+    const hideDatasetSelectionModal = useCallback(() => setDatasetSelectionModal(false), []);
 
     const getWorkflowFit = useCallback(w => {
         let workflowSupported = true;
@@ -482,7 +482,7 @@ const ManagerDropBoxContent = () => {
         for (const i of w.inputs.filter(i => i.type.startsWith("file"))) {
             const isFileArray = i.type.endsWith("[]");
 
-            // Find tables that support the data type
+            // Find datasets that support the data type
             // TODO
 
             // Find files where 1+ of the valid extensions (e.g. jpeg or jpg) match.
@@ -535,7 +535,7 @@ const ManagerDropBoxContent = () => {
             {ingestionWorkflows.map(w => (
                 <Menu.Item key={w.id}
                            disabled={workflowsSupported.findIndex(w2 => w2.id === w.id) === -1}
-                           onClick={() => showTableSelectionModal(w)}>
+                           onClick={() => showDatasetSelectionModal(w)}>
                     Ingest with Workflow &ldquo;{w.name}&rdquo;
                 </Menu.Item>
             ))}
@@ -544,7 +544,7 @@ const ManagerDropBoxContent = () => {
 
     const handleIngest = useCallback(() => {
         if (workflowsSupported.length !== 1) return;
-        showTableSelectionModal(workflowsSupported[0]);
+        showDatasetSelectionModal(workflowsSupported[0]);
     }, [workflowsSupported]);
 
     const hasUploadPermission = permissions.includes(ingestDropBox);
@@ -647,9 +647,9 @@ const ManagerDropBoxContent = () => {
 
             <DatasetSelectionModal
                 dataType={selectedWorkflow?.data_type || null}
-                visible={tableSelectionModal}
-                title="Select a Table to Ingest Into"
-                onCancel={hideTableSelectionModal}
+                visible={datasetSelectionModal}
+                title="Select a Dataset to Ingest Into"
+                onCancel={hideDatasetSelectionModal}
                 onOk={ingestIntoDataset}
             />
 

src/components/manager/projects/Project.js

@@ -190,8 +190,6 @@ class Project extends Component {
 
 Project.propTypes = {
     value: projectPropTypesShape,
-    tables: PropTypes.arrayOf(PropTypes.object),  // TODO: shape
-    strayTables: PropTypes.arrayOf(PropTypes.object),  // TODO: shape (this is currently heterogeneous)
 
     editing: PropTypes.bool,
     saving: PropTypes.bool,

src/components/manager/projects/RoutedProject.js

@@ -29,7 +29,7 @@ class RoutedProject extends Component {
         this.showDatasetAdditionModal = this.showDatasetAdditionModal.bind(this);
         this.hideDatasetAdditionModal = this.hideDatasetAdditionModal.bind(this);
         this.hideDatasetEditModal = this.hideDatasetEditModal.bind(this);
-        this.ingestIntoTable = this.ingestIntoDataset.bind(this);
+        this.ingestIntoDataset = this.ingestIntoDataset.bind(this);
         this.handleDeleteProject = this.handleDeleteProject.bind(this);
     }
 
@@ -41,13 +41,16 @@ class RoutedProject extends Component {
     }
 
     ingestIntoDataset(p, d, dt) {
-        this.props.history.push("/admin/data/manager/ingestion",
-            {workflowSelectionValues: {
-                selectedProject: p.identifier,
-                selectedDataset: d.identifier,
-                selectedDataType: dt.id,
+        this.props.history.push(
+            "/admin/data/manager/ingestion",
+            {
+                workflowSelectionValues: {
+                    selectedProject: p.identifier,
+                    selectedDataset: d.identifier,
+                    selectedDataType: dt.id,
+                },
             },
-            });
+        );
     }
 
     handleProjectSave(project) {
@@ -101,16 +104,6 @@ class RoutedProject extends Component {
         const project = this.props.projectsByID[this.props.match.params.project];
         if (!project) return <ProjectSkeleton />;
 
-        /**
-         * @typedef {Object} ProjectTable
-         * @property {string} table_id
-         * @property {string} service_id
-         * @property {string} dataset
-         * @property {string} data_type
-         * @property {string} sample
-         * @type {ProjectTable[]}
-         */
-
         return <>
             <DatasetFormModal mode={FORM_MODE_ADD}
                               project={project}
@@ -163,15 +156,9 @@ RoutedProject.propTypes = {
         isFetching: PropTypes.bool,
     })),
 
-    serviceTables: PropTypes.arrayOf(PropTypes.object),  // TODO: Shape
-    serviceTablesByServiceID: PropTypes.objectOf(PropTypes.object),  // TODO: Shape
-
     projects: PropTypes.arrayOf(projectPropTypesShape),
     projectsByID: PropTypes.objectOf(projectPropTypesShape),
 
-    projectTables: PropTypes.arrayOf(PropTypes.object),  // TODO: Shape
-    projectTablesByProjectID: PropTypes.objectOf(PropTypes.arrayOf(PropTypes.object)),  // TODO: Shape
-
     loadingProjects: PropTypes.bool,
 
     isDeletingProject: PropTypes.bool,
@@ -193,9 +180,6 @@ const mapStateToProps = state => ({
 
     serviceDataTypesByServiceID: state.serviceDataTypes.dataTypesByServiceID,
 
-    serviceTables: state.serviceTables.items,
-    serviceTablesByServiceID: state.serviceTables.itemsByServiceID,
-
     projects: state.projects.items,
     projectsByID: state.projects.itemsByID,
 

src/modules/auth/actions.js

@@ -57,7 +57,6 @@ export const fetchUserDependentData = (servicesCb) => async (dispatch, getState)
     try {
         if (idTokenContents) {
             // If we're newly authenticated as an owner, we run all actions that need authentication (via the callback).
-            // TODO: refactor to remove tables
             await dispatch(fetchServicesWithMetadataAndDataTypesIfNeeded(
                 () => dispatch(fetchServiceDependentData())));
             await (servicesCb || nop)();

src/modules/metadata/actions.js

@@ -11,7 +11,6 @@ import {jsonRequest} from "../../utils/requests";
 
 
 export const FETCH_PROJECTS = createNetworkActionTypes("FETCH_PROJECTS");
-export const FETCH_PROJECT_TABLES = createNetworkActionTypes("FETCH_PROJECT_TABLES");
 
 export const CREATE_PROJECT = createNetworkActionTypes("CREATE_PROJECT");
 export const DELETE_PROJECT = createNetworkActionTypes("DELETE_PROJECT");
@@ -27,9 +26,6 @@ export const ADD_DATASET_LINKED_FIELD_SET = createNetworkActionTypes("ADD_DATASE
 export const SAVE_DATASET_LINKED_FIELD_SET = createNetworkActionTypes("SAVE_DATASET_LINKED_FIELD_SET");
 export const DELETE_DATASET_LINKED_FIELD_SET = createNetworkActionTypes("DELETE_DATASET_LINKED_FIELD_SET");
 
-export const PROJECT_TABLE_ADDITION = createFlowActionTypes("PROJECT_TABLE_ADDITION");
-export const PROJECT_TABLE_DELETION = createFlowActionTypes("PROJECT_TABLE_DELETION");
-
 export const FETCH_INDIVIDUAL = createNetworkActionTypes("FETCH_INDIVIDUAL");
 export const FETCH_OVERVIEW_SUMMARY = createNetworkActionTypes("FETCH_OVERVIEW_SUMMARY");
 
@@ -121,8 +117,6 @@ export const deleteProject = networkAction(project => (dispatch, getState) => ({
 export const deleteProjectIfPossible = project => (dispatch, getState) => {
     if (getState().projects.isDeleting) return;
     return dispatch(deleteProject(project));
-
-    // TODO: Do we need to delete project tables as well? What to do here??
 };
 
 
@@ -174,7 +168,6 @@ export const deleteProjectDataset = networkAction((project, dataset) => (dispatc
     url: `${getState().services.metadataService.url}/api/datasets/${dataset.identifier}`,
     req: {method: "DELETE"},
     err: `Error deleting dataset '${dataset.title}'`,
-    // TODO: Do we need to delete project tables as well? What to do here??
 }));
 
 export const deleteProjectDatasetIfPossible = (project, dataset) => (dispatch, getState) => {

src/modules/metadata/reducers.js

@@ -2,7 +2,6 @@ import {objectWithoutProp} from "../../utils/misc";
 
 import {
     FETCH_PROJECTS,
-    FETCH_PROJECT_TABLES,
 
     CREATE_PROJECT,
     DELETE_PROJECT,
@@ -16,9 +15,6 @@ import {
     SAVE_DATASET_LINKED_FIELD_SET,
     DELETE_DATASET_LINKED_FIELD_SET,
 
-    PROJECT_TABLE_ADDITION,
-    PROJECT_TABLE_DELETION,
-
     FETCH_INDIVIDUAL,
 
     FETCH_OVERVIEW_SUMMARY,
@@ -33,7 +29,6 @@ const projectSort = (a, b) => a.title.localeCompare(b.title);
 export const projects = (
     state = {
         isFetching: false,
-        isFetchingWithTables: false,
         isCreating: false,
         isDeleting: false,
         isSaving: false,
@@ -249,109 +244,6 @@ export const projects = (
 };
 
 
-export const projectTables = (
-    state = {
-        isFetching: false,
-        isFetchingAll: false,
-        isAdding: false,
-        isDeleting: false,
-        items: [],
-        itemsByProjectID: {},
-    },
-    action,
-) => {
-    switch (action.type) {
-        case CREATE_PROJECT.RECEIVE:
-            // TODO: Might want to re-fetch upon project creation instead...
-            return {
-                ...state,
-                itemsByProjectID: {
-                    ...state.itemsByProjectID,
-                    [action.data.id]: [],
-                },
-            };
-
-        case DELETE_PROJECT.RECEIVE:
-            return {
-                ...state,
-                items: state.items.filter(t => t.project_id !== action.project.identifier),
-                itemsByProjectID: objectWithoutProp(state.itemsByProjectID, action.project.identifier),
-            };
-
-        case FETCH_PROJECT_TABLES.REQUEST:
-            return {...state, isFetching: true};
-
-        case FETCH_PROJECT_TABLES.RECEIVE:
-            return {
-                ...state,
-                isFetching: false,
-                items: [
-                    ...state.items,
-                    ...action.data
-                        .map(t => ({
-                            ...t,
-                            project_id: (Object.entries(action.projectsByID)
-                                .filter(([_, project]) => project.datasets.map(d => d.identifier)
-                                    .includes(t.dataset))[0] || [])[0] || null,
-                        }))
-                        .filter(t => t.project_id !== null && !state.items.map(t => t.table_id).includes(t.table_id)),
-                ],
-                itemsByProjectID: {  // TODO: Improve performance by maybe returning project ID on server side?
-                    ...state.itemsByProjectID,
-                    ...Object.fromEntries(Object.entries(action.projectsByID).map(([projectID, project]) =>
-                        [projectID, action.data.filter(t => project.datasets
-                            .map(d => d.identifier)
-                            .includes(t.dataset))],
-                    )),
-                },
-            };
-
-        case FETCH_PROJECT_TABLES.FINISH:
-            return {...state, isFetching: false};
-
-        case PROJECT_TABLE_ADDITION.BEGIN:
-            return {...state, isAdding: true};
-
-        case PROJECT_TABLE_ADDITION.END:
-            // TODO
-            return {
-                ...state,
-                isAdding: false,
-                items: [...state.items, action.table],
-                itemsByProjectID: {
-                    ...state.itemsByProjectID,
-                    [action.project.identifier]: [...(state.itemsByProjectID[action.project.identifier] || []),
-                        action.table],
-                },
-            };
-
-        case PROJECT_TABLE_ADDITION.TERMINATE:
-            return {...state, isAdding: false};
-
-        case PROJECT_TABLE_DELETION.BEGIN:
-            return {...state, isDeleting: true};
-
-        case PROJECT_TABLE_DELETION.END:
-            return {
-                ...state,
-                isDeleting: false,
-                items: state.items.filter(t => t.table_id !== action.tableID),
-                itemsByProjectID: {
-                    ...state.itemsByProjectID,
-                    [action.project.identifier]: (state.itemsByProjectID[action.project.identifier] || [])
-                        .filter(t => t.id !== action.tableID),
-                },
-            };
-
-        case PROJECT_TABLE_DELETION.TERMINATE:
-            return {...state, isDeleting: false};
-
-        default:
-            return state;
-    }
-};
-
-
 export const biosamples = (
     state = {
         itemsByID: {},