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Austenem/CAT-793 unified datasets attribution #3551

Merged
merged 11 commits into from
Oct 2, 2024
Merged

Austenem/CAT-793 unified datasets attribution #3551

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82e31e7
switch to creation action for contact info
austenem Sep 20, 2024
5787350
add attribution section
austenem Sep 26, 2024
9ee78ff
add changelog
austenem Sep 26, 2024
167b193
add section to table of contents
austenem Sep 26, 2024
02ebae5
add creation action type
austenem Sep 26, 2024
97b91e7
check for empty contributors and add group field
austenem Sep 27, 2024
f3368c8
Update context/app/static/js/pages/Dataset/hooks.ts
austenem Oct 1, 2024
b3de042
Update context/app/static/js/components/detailPage/ProcessedData/Proc…
austenem Oct 1, 2024
c29f038
Merge branch 'main' into austenem/cat-793-unified-datasets-attribution
austenem Oct 1, 2024
7014e9e
fix parentheses issue
austenem Oct 1, 2024
c0ca82e
switch to booelean syntax
austenem Oct 1, 2024
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1 change: 1 addition & 0 deletions CHANGELOG-unified-datasets-attribution.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
- Remove "Contact" section and add Attribution table with contributors for EPICs and Lab Processed datasets.
4 changes: 2 additions & 2 deletions context/app/static/js/components/detailPage/Attribution/Attribution.tsx
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Expand Up @@ -16,7 +16,7 @@ const tooltips = {
contact: 'This is the contact for this data.',
};

const DatasetAttribution = (
export const DatasetAttributionDescription = (
<SectionDescription>
Below is the information for the individuals who provided this dataset. For questions about this dataset, reach out
to the individuals listed as contacts, either via the email address listed in the table or via contact information
Expand Down Expand Up @@ -44,7 +44,7 @@ function Attribution({ children }: PropsWithChildren) {
return (
<CollapsibleDetailPageSection id="attribution" title="Attribution" icon={sectionIconMap.attribution}>
<Stack spacing={1}>
{isDataset && DatasetAttribution}
{isDataset && DatasetAttributionDescription}
<SummaryPaper>
<Stack direction="row" spacing={10}>
{sections.map((props) => (
Expand Down
68 changes: 48 additions & 20 deletions ...t/app/static/js/components/detailPage/ProcessedData/ProcessedDataset/ProcessedDataset.tsx
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@@ -1,36 +1,43 @@
import React, { useState } from 'react';
import LabelledSectionText from 'js/shared-styles/sections/LabelledSectionText';
import { formatDate } from 'date-fns/format';
import { Tabs, Tab, TabPanel } from 'js/shared-styles/tabs';

import FactCheckRounded from '@mui/icons-material/FactCheckRounded';
import SummarizeRounded from '@mui/icons-material/SummarizeRounded';
import AttributionRoundedIcon from '@mui/icons-material/AttributionRounded';
import InsertDriveFileRounded from '@mui/icons-material/InsertDriveFileRounded';
import Skeleton from '@mui/material/Skeleton';
import Stack from '@mui/material/Stack';

import LabelledSectionText from 'js/shared-styles/sections/LabelledSectionText';
import { Tabs, Tab, TabPanel } from 'js/shared-styles/tabs';
import { VisualizationIcon } from 'js/shared-styles/icons';
import { useVitessceConf } from 'js/pages/Dataset/hooks';
import { isSupport } from 'js/components/types';
import { useFlaskDataContext } from 'js/components/Contexts';
import Skeleton from '@mui/material/Skeleton';
import ContactUsLink from 'js/shared-styles/Links/ContactUsLink';
import Files from '../../files/Files';
import DataProducts from '../../files/DataProducts';
import VisualizationWrapper from '../../visualization/VisualizationWrapper';
import AnalysisDetails from '../../AnalysisDetails';
import Protocol from '../../Protocol';
import ContributorsTable from 'js/components/detailPage/ContributorsTable';
import { DatasetAttributionDescription } from 'js/components/detailPage/Attribution/Attribution';
import Files from 'js/components/detailPage/files/Files';
import DataProducts from 'js/components/detailPage/files/DataProducts';
import VisualizationWrapper from 'js/components/detailPage/visualization/VisualizationWrapper';
import AnalysisDetails from 'js/components/detailPage/AnalysisDetails';
import Protocol from 'js/components/detailPage/Protocol';
import { getDateLabelAndValue } from 'js/components/detailPage/utils';
import { useSelectedVersionStore } from 'js/components/detailPage/VersionSelect/SelectedVersionStore';
import { useVersions } from 'js/components/detailPage/VersionSelect/hooks';
import { useTrackEntityPageEvent } from 'js/components/detailPage/useTrackEntityPageEvent';

import { DatasetTitle } from './DatasetTitle';
import { ProcessedDatasetAccordion } from './ProcessedDatasetAccordion';
import { Subsection } from './Subsection';
import { SectionDescription } from './SectionDescription';
import useProcessedDataStore from '../store';
import { getDateLabelAndValue } from '../../utils';
import {
ProcessedDatasetContextProvider,
useProcessedDatasetContext,
ProcessedDataVisualizationProps,
} from './ProcessedDatasetContext';
import { useSelectedVersionStore } from '../../VersionSelect/SelectedVersionStore';
import { useProcessedDatasetDetails } from './hooks';
import { useVersions } from '../../VersionSelect/hooks';
import { useTrackEntityPageEvent } from '../../useTrackEntityPageEvent';
import { OldVersionAlert } from './OldVersionAlert';

function ProcessedDatasetDescription() {
Expand All @@ -47,12 +54,13 @@ function ProcessedDatasetDescription() {

function Contact() {
const {
dataset: { mapped_consortium },
dataset: { creation_action },
} = useProcessedDatasetContext();

if (mapped_consortium !== 'HuBMAP') {
if (creation_action !== 'Central Process') {
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Use a constant here as well.

return null;
}

return (
<LabelledSectionText label="Contact" iconTooltipText="This is the contact for this data.">
<ContactUsLink>HuBMAP Help Desk</ContactUsLink>
Expand All @@ -65,12 +73,14 @@ function SummaryAccordion() {
const [dateLabel, dateValue] = getDateLabelAndValue(dataset);
return (
<Subsection title="Summary" icon={<SummarizeRounded />}>
<ProcessedDatasetDescription />
<LabelledSectionText label="Consortium">{dataset.group_name}</LabelledSectionText>
<Contact />
<LabelledSectionText label={dateLabel}>
{dateValue ? formatDate(new Date(dateValue), 'yyyy-MM-dd') : 'N/A'}
</LabelledSectionText>
<Stack spacing={1}>
<ProcessedDatasetDescription />
<LabelledSectionText label="Consortium">{dataset.group_name}</LabelledSectionText>
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Is 'Consortium' the right label for group name? Should group_name be mapped_consortium? Do we also want to display the group_name? @tsliaw

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Consortium should be the label for mapped_consortium. I didn't include the group field initially since I assumed that the group should be the same for both the raw and processed, but that's probably not true. @austenem Let's add the group field before the consortium field in the summary section. Can you also replace the consortium field in the mini processed data detail section (the pop-up thing on the right) with group instead? That field should be more useful than consortium.

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@tsliaw Will do! Would it make sense to also replace the "Consortium" field in the summary view top bar, or to add a "Group" field?

<Contact />
<LabelledSectionText label={dateLabel}>
{dateValue ? formatDate(new Date(dateValue), 'yyyy-MM-dd') : 'N/A'}
</LabelledSectionText>
</Stack>
</Subsection>
);
}
Expand Down Expand Up @@ -182,6 +192,23 @@ function AnalysisDetailsAccordion() {
);
}

function AttributionAccordion() {
const {
dataset: { creation_action, contributors, contacts },
} = useProcessedDatasetContext();

if (creation_action === 'Central Process' || !contributors) {
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Constant here as well.

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return null;
}

return (
<Subsection title="Attribution" idTitleOverride="attribution" icon={<AttributionRoundedIcon />}>
{DatasetAttributionDescription}
<ContributorsTable contributors={contributors} contacts={contacts} />
</Subsection>
);
}

export default function ProcessedDataset({ sectionDataset }: ProcessedDataVisualizationProps) {
const selectedDatasetVersionUUID =
useSelectedVersionStore((state) => state.selectedVersions.get(sectionDataset.uuid))?.uuid ?? sectionDataset.uuid;
Expand Down Expand Up @@ -213,6 +240,7 @@ export default function ProcessedDataset({ sectionDataset }: ProcessedDataVisual
<VisualizationAccordion />
<FilesAccordion />
<AnalysisDetailsAccordion />
<AttributionAccordion />
</ProcessedDatasetAccordion>
</ProcessedDatasetContextProvider>
);
Expand Down
2 changes: 2 additions & 0 deletions context/app/static/js/components/detailPage/ProcessedData/ProcessedDataset/hooks.ts
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Expand Up @@ -53,6 +53,8 @@ export function useProcessedDatasetDetails(uuid: string) {
'dataset_type',
'creation_action',
'mapped_consortium',
'contributors',
'contacts',
],
size: 10000,
};
Expand Down
8 changes: 6 additions & 2 deletions context/app/static/js/pages/Dataset/hooks.ts
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Expand Up @@ -55,6 +55,8 @@ export type ProcessedDatasetInfo = Pick<
| 'dbgap_sra_experiment_url'
| 'is_component'
| 'visualization'
| 'contributors'
| 'contacts'
>;

type VitessceConf = object | undefined;
Expand Down Expand Up @@ -106,6 +108,7 @@ function useProcessedDatasets(includeComponents?: boolean) {
'dbgap_sra_experiment_url',
'is_component',
'visualization',
'contributors',
],
size: 10000,
};
Expand All @@ -128,13 +131,14 @@ function getProcessedDatasetSection({
hit: Required<SearchHit<ProcessedDatasetInfo>>;
conf?: VitessceConf;
}) {
const { pipeline, hubmap_id, files, metadata, visualization } = hit._source;
const { pipeline, hubmap_id, files, metadata, visualization, creation_action, contributors } = hit._source;

const shouldDisplaySection = {
summary: true,
visualization: visualization || Boolean(conf && 'data' in conf && conf?.data),
files: Boolean(files),
files: Boolean(files?.length !== 0),
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analysis: Boolean(metadata?.dag_provenance_list),
attribution: creation_action !== 'Central Process' && Boolean(contributors),
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Let's introduce constants for creation_action.

  • Create Dataset Activity
  • Central Process
  • Multi-Assay Split
  • Lab Process
  • Create Publication Activity
  • External Process

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Good idea - I wrote up a type CreationAction that represents that set of strings. Is that what you had in mind, or would creating individually named constants to represent these strings/an enum be preferable?

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};

const sectionsToDisplay = Object.entries(shouldDisplaySection).filter(([_k, v]) => v === true);
Expand Down
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