Merge pull request #1105 from sennetconsortium/libpitt/1090-dataset_type

Libpitt/1090 dataset type
sennetconsortium · Dec 14, 2023 · 5ada11d · 5ada11d
2 parents daf4027 + 6f7bcdb
commit 5ada11d
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Showing 25 changed files with 147 additions and 229 deletions.
diff --git a/src/components/custom/TableResultsEntities.jsx b/src/components/custom/TableResultsEntities.jsx
@@ -115,9 +115,9 @@ function TableResultsEntities({children, filters, onRowClicked, forData = false,
 
     const datasetColumns = [
         {
-            name: 'Data Types',
+            name: 'Dataset Type',
             selector: row => {
-                let val = raw(row.data_types)
+                let val = raw(row.dataset_type)
                 if (val) {
                     return Array.isArray(val) ? getUBKGFullName(val[0]) : val
                 }

diff --git a/src/components/custom/TableResultsFiles.jsx b/src/components/custom/TableResultsFiles.jsx
@@ -73,7 +73,7 @@ function TableResultsFiles({children, filters, forData = false, rowFn, inModal =
         for (let file of rawResponse.records.files) {
             if (!results.hasOwnProperty(file.dataset_uuid)) {
                 results[file.dataset_uuid] = {
-                    data_types: file.data_types,
+                    dataset_type: file.dataset_type,
                     dataset_sennet_id: file.dataset_sennet_id,
                     dataset_uuid: file.dataset_uuid,
                     donors: file.donors,
@@ -243,9 +243,9 @@ function TableResultsFiles({children, filters, forData = false, rowFn, inModal =
 
         cols.push(
             {
-                name: 'Data Types',
+                name: 'Dataset Type',
                 selector: row => {
-                    let val = raw(row.data_types)
+                    let val = raw(row.dataset_types)
                     if (val) {
                         return Array.isArray(val) ? getUBKGFullName(val[0]) : val
                     }

diff --git a/src/components/custom/bulk/BulkCreate.js b/src/components/custom/bulk/BulkCreate.js
@@ -388,7 +388,7 @@ export default function BulkCreate({
             typeCol = 'sample_category'
             labIdCol = 'lab_tissue_sample_id'
         } else {
-            typeCol = 'data_types'
+            typeCol = 'dataset_type'
             labIdCol = 'lab_dataset_id'
         }
         return {typeCol, labIdCol}

diff --git a/src/components/custom/edit/dataset/AncestorIds.jsx b/src/components/custom/edit/dataset/AncestorIds.jsx
@@ -56,7 +56,7 @@ export default function AncestorIds({values, onChange, fetchAncestors, deleteAnc
         // const excludeDataTypes = getDataTypesByProperty("vis-only", true)
         const excludeNonPrimaryTypes = getDataTypesByProperty("primary", false)
         valid_dataset_ancestor_config['searchQuery']['excludeFilters'].push({
-            keyword: "data_types.keyword",
+            keyword: "dataset_type.keyword",
             value: excludeNonPrimaryTypes
         });
     }, [])

diff --git a/src/components/custom/edit/dataset/DataTypes.jsx b/src/components/custom/edit/dataset/DataTypes.jsx
diff --git a/src/components/custom/edit/dataset/DatasetType.jsx b/src/components/custom/edit/dataset/DatasetType.jsx
@@ -0,0 +1,49 @@
+import React from 'react';
+import {Col, Form, Row} from 'react-bootstrap';
+import {QuestionCircleFill} from "react-bootstrap-icons";
+import SenNetPopover from "../../../SenNetPopover";
+import {getUBKGFullName} from "../../js/functions";
+
+export default function DatasetType({datasetTypes, data, onChange}) {
+
+    return (
+        //Data Types
+        <>
+            <Form.Group className="mb-3" controlId="dataset_type">
+                <Form.Label>Dataset Type <span
+                    className="required">* </span>
+                    <SenNetPopover className={'dataset_type'}
+                                   text={<>The type of data contained in this <code>Dataset</code>. Choose from one
+                                       of the available options.</>}>
+                        <QuestionCircleFill/>
+                    </SenNetPopover>
+                </Form.Label>
+
+                {/*Check that there exists a data type for this dataset and if it is not a part of the list of primary assay types*/}
+                {data?.dataset_type && !datasetTypes.includes(data.dataset_type) ?
+                    (
+                        <Form.Select required aria-label="Dataset Type" disabled>
+                            <option
+                                value={data.dataset_type}>{getUBKGFullName(data.dataset_type)}</option>
+                        </Form.Select>
+                    ) : (
+                        <Form.Select required aria-label="Dataset Type"
+                                     onChange={(e) => onChange(e, 'dataset_type', e.target.value)}
+                                     name={'dataset_type'}
+                                     defaultValue={data?.dataset_type}>
+                            <option value="">----</option>
+                            {datasetTypes.map(data_type => {
+                                return (
+                                    <option key={data_type} value={data_type.trim()}>
+                                        {getUBKGFullName(data_type)}
+                                    </option>
+                                );
+                            })}
+                        </Form.Select>
+                    )}
+
+            </Form.Group>
+        </>
+    )
+
+}
diff --git a/src/components/custom/entities/sample/DerivedDatasetItem.jsx b/src/components/custom/entities/sample/DerivedDatasetItem.jsx
@@ -32,8 +32,7 @@ export default class DerivedDatasetItem extends React.Component {
                                 return (
                                     <>
                                         <td>
-                                            {Array.isArray(this.state.descendant_data.data_types) ?
-                                                this.state.descendant_data.data_types.join(', ') : this.state.descendant_data.data_types}
+                                            {this.state.descendant_data.dataset_type}
                                         </td>
                                         <td>
                                             <span className={`${getStatusColor(this.state.descendant_data.status)} badge`}>

diff --git a/src/components/custom/js/functions.js b/src/components/custom/js/functions.js
@@ -168,6 +168,10 @@ export function getDataTypesByProperty(property, value) {
     return window.UBKG_CACHE.dataTypesObj.filter(data_type => data_type[property] === value).map(data_type => data_type.data_type);
 }
 
+export function getIsPrimaryDataset(data) {
+    return equals(data.dataset_category, 'primary') || equals(data.creation_action, 'Create Dataset Activity')
+}
+
 export function getDOIPattern() {
     return "(^(http(s)?:\/\/)?dx.doi.org\/10.\\d{4,9}\/protocols\.io\..+)|(^(http(s)?:\/\/)?doi.org\/10.\\d{4,9}\/protocols\.io\..+)"
 }
@@ -308,27 +312,6 @@ export function checkMultipleFilterType(filters, field = 'entity_type') {
     return hasMultipleType;
 }
 
-export function isPrimaryAssay(data, verifyAll = false) {
-    let dict = {}
-    let result = false
-    for (let assay of window.UBKG_CACHE.dataTypesObj) {
-        dict[assay.data_type] = assay.primary
-    }
-    for (let assay of data.data_types) {
-        if (dict[assay]) {
-            result = true
-            if (!verifyAll) {
-                return true
-            }
-        } else {
-            if (verifyAll) {
-                return false
-            }
-        }
-    }
-    return result;
-}
-
 export function cleanJson(json) {
     Object.entries(json).forEach(([key, val]) =>
         (val && typeof val === 'object') && cleanJson(val) ||

diff --git a/src/components/custom/layout/entity/VersionsDropdown.jsx b/src/components/custom/layout/entity/VersionsDropdown.jsx
@@ -16,7 +16,7 @@ function VersionsDropdown({data}) {
     const buildOptions = (r) => {
         let results = []
         for (let s of r.uuids) {
-            results.push({value: s.uuid, label: `${s.sennet_id} (${s.data_types[0]})`, revision: r})
+            results.push({value: s.uuid, label: `${s.sennet_id} (${s.dataset_type})`, revision: r})
         }
         return results
     }

diff --git a/src/components/custom/layout/entity/ViewHeaderBadges.jsx b/src/components/custom/layout/entity/ViewHeaderBadges.jsx
@@ -52,7 +52,7 @@ function ViewHeaderBadges({data, uniqueHeader, uniqueHeaderUrl, isMetadataHeader
                     ) : (
                         <h5 className={"title_badge"}>
                             <span className="badge bg-secondary ms-2">
-                                    {getUBKGFullName(data.data_types[0])}
+                                    {getUBKGFullName(data.dataset_type)}
                             </span>
                         </h5>
                     )

diff --git a/src/config/search/entities.js b/src/config/search/entities.js
@@ -10,10 +10,15 @@ const connector = new SearchAPIConnector({
 export const SEARCH_ENTITIES = {
     alwaysSearchOnInitialLoad: true,
     searchQuery: {
-        excludeFilters: [ {
-            keyword: "entity_type.keyword",
-            value: "Publication"
-        }
+        excludeFilters: [
+            {
+                keyword: "entity_type.keyword",
+                value: "Publication"
+            },
+            {
+                keyword: "dataset_category.keyword",
+                value: ["codcc-processed", "lab-processed"]
+            }
         ],
         facets: {
             entity_type: {
@@ -67,16 +72,16 @@ export const SEARCH_ENTITIES = {
                 filterType: 'any',
                 isFilterable: false,
             },
-            data_types: {
-                label: 'Data Type',
+            dataset_type: {
+                label: 'Dataset Type',
                 type: 'value',
-                field: 'data_types.keyword',
+                field: 'dataset_type.keyword',
                 isExpanded: false,
                 filterType: 'any',
                 isFilterable: false,
             },
             has_rui_information: {
-                label: 'Has Location Information',
+                label: 'Is Spatially Registered',
                 type: 'value',
                 field: 'has_rui_information.keyword',
                 isExpanded: false,
@@ -156,7 +161,8 @@ export const SEARCH_ENTITIES = {
             lab_name: {type: 'value'},
             lab_tissue_sample_id: {type: 'value'},
             source_type: {type: 'value'},
-            data_types: {type: 'value'},
+            dataset_type: {type: 'value'},
+            dataset_category: {type: 'value'},
             sample_category: {type: 'value'},
             lab_dataset_id: {type: 'value'},
             created_by_user_displayname: {type: 'value'},
@@ -182,7 +188,8 @@ export const SEARCH_ENTITIES = {
             'source_type',
             'source.source_type',
             'last_modified_timestamp',
-            'data_types',
+            'dataset_type',
+            'dataset_category',
             'status',
             'origin_sample.organ',
             'organ',

diff --git a/src/config/search/files.js b/src/config/search/files.js
@@ -12,7 +12,7 @@ const sourceItems = [
     'sennet_id',
     'dataset_sennet_id',
     'checksum',
-    'data_types',
+    'dataset_type',
     'description',
     'dataset_uuid',
     'donors',
@@ -45,10 +45,10 @@ export const SEARCH_FILES = {
                 filterType: 'any',
                 isFilterable: false,
             },
-            data_types: {
-                label: 'Data Type',
+            dataset_type: {
+                label: 'Dataset Type',
                 type: 'value',
-                field: 'data_types.keyword',
+                field: 'dataset_type.keyword',
                 isExpanded: false,
                 filterType: 'any',
                 isFilterable: false,
@@ -72,7 +72,7 @@ export const SEARCH_FILES = {
             'organs.type': {type: 'value'},
             'samples.type': {type: 'value'},
             dataset_sennet_id: {type: 'value'},
-            data_types: {type: 'value'}
+            dataset_type: {type: 'value'}
         },
         source_fields: sourceItems,
     },