Add the first production-ready version of the external project overview - #1185
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nabalma wants to merge 8 commits into
Open
Add the first production-ready version of the external project overview#1185nabalma wants to merge 8 commits into
nabalma wants to merge 8 commits into
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…view with submissions, readsets, dashboards, filters, and CSV exports
nafiz1001
reviewed
Aug 29, 2026
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| def _get_readsets_queryset(self, parent_project): | ||
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Collaborator
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a type annotation would be nice parent_project: ParentProject
nafiz1001
reviewed
Aug 29, 2026
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| @action(detail=True, methods=["get"],url_path="readsets") | ||
| def overview_readsets(self, request, pk=None): |
Collaborator
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space after comma (methods=["get"],)
nafiz1001
reviewed
Aug 29, 2026
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| class ParentProjectReadsetSerializer(serializers.Serializer): | ||
| id = serializers.IntegerField() | ||
| name = serializers.CharField() | ||
| readset_sample_name = serializers.CharField() | ||
| biosample_id = serializers.IntegerField(allow_null=True) | ||
| external_id = serializers.CharField() | ||
| run_name = serializers.CharField() | ||
| lane = serializers.IntegerField() | ||
| reference_genome_id = serializers.IntegerField(allow_null=True,) | ||
| reference_genome_assembly_name = serializers.CharField(allow_null=True,) | ||
| sequencing_index_name = serializers.CharField(allow_null=True) | ||
| run_start_date = serializers.DateField() | ||
| alias = serializers.CharField(allow_null=True) | ||
| cohort = serializers.CharField(allow_blank=True,allow_null=True,) | ||
| library_type = serializers.CharField(allow_null=True,) | ||
| container_barcodes = serializers.ListField(child=serializers.CharField(allow_null=True),allow_empty=True,) | ||
| number_of_reads = serializers.IntegerField(allow_null=True,) | ||
| number_of_bases = serializers.IntegerField(allow_null=True,) | ||
| average_quality = serializers.DecimalField( | ||
| max_digits=40, | ||
| decimal_places=20, | ||
| allow_null=True, | ||
| ) | ||
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| pf_reads_aligned = serializers.DecimalField( | ||
| max_digits=40, | ||
| decimal_places=20, | ||
| allow_null=True, | ||
| ) | ||
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| duplicate_aligned = serializers.DecimalField( | ||
| max_digits=40, | ||
| decimal_places=20, | ||
| allow_null=True, | ||
| ) | ||
| readset_files = serializers.ListField( | ||
| child=serializers.DictField(), | ||
| required=False, | ||
| ) | ||
| run_validation_status = serializers.IntegerField(allow_null=True,) |
Collaborator
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@UlysseFG Personally I feel this serializer should be a composition of models rather than individual fields. Like we could have a field for parent_project, derived_sample, readset, etc. So that way, we know where each fields come from.
nafiz1001
reviewed
Aug 29, 2026
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| const openCount = data.filter((project) => project.status === "Open").length | ||
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| const uniquePIs = new Set(data.map((project) => project.principal_investigator).filter(Boolean)) | ||
| .size | ||
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| const uniqueRequestors = new Set(data.map((project) => project.requestor_name).filter(Boolean)) | ||
| .size |
Collaborator
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These should be memoized. Otherwise, they would get recomputed at each re-render of the component.
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Especially if these values are passed to child components.
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Author
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Fixed ...
const ExternalIDProjectsDashboard = ({ data }: ExternalIDProjectsDashboardProps) => {
const total = data.length
const openCount = useMemo(() => data.filter((project) => project.status === "Open").length, [data])
const uniquePIs = useMemo(() => new Set(data.map((project) => project.principal_investigator).filter(Boolean)).size, [data])
const uniqueRequestors = useMemo(() => new Set(data.map((project) => project.requestor_name).filter(Boolean)).size, [data])
nafiz1001
reviewed
Aug 29, 2026
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| const iconStyle = (color: string, backgroundColor: string): React.CSSProperties => ({ | ||
| color, | ||
| backgroundColor, | ||
| fontSize: 18, | ||
| padding: 6, | ||
| borderRadius: 8, | ||
| marginRight: 4, | ||
| }) |
Collaborator
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This can be outside the component definition.
Collaborator
Author
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This style is now out of the component definition ...
const iconStyle = (color: string, backgroundColor: string): React.CSSProperties => ({
color,
backgroundColor,
fontSize: 18,
padding: 6,
borderRadius: 8,
marginRight: 4,
})
function ExternalIDReadSetDashboard({ readsets }: { readsets: ProjectOverviewReadset[] }) {
nafiz1001
reviewed
Aug 29, 2026
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| <Route | ||
| path="/external-projects-overview/*" | ||
| element={ | ||
| <PrivateNavigate> | ||
| <ExternalProjectsPage /> | ||
| </PrivateNavigate> | ||
| } | ||
| /> | ||
| <Route | ||
| path="/external-projects-overview/:parentProjectId" | ||
| element={ | ||
| <PrivateNavigate> | ||
| <ExternalProjectDetailsPage /> | ||
| </PrivateNavigate> | ||
| } | ||
| /> |
Collaborator
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We normally have nested Routes for specific pages like with frontend/src/components/projects/ProjectsPage.js. But since it's just two pages for now, we can keep it like this.
nafiz1001
reviewed
Aug 29, 2026
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| expandedRowRender: (parentProject) => { | ||
| const internalProjects = (parentProject.projects ?? []).reduce<FMSProject[]>( | ||
| (projects, projectID) => { | ||
| const project = internalProjectsByID[projectID] | ||
| if (project) { | ||
| projects.push(project) | ||
| } | ||
| return projects | ||
| }, | ||
| [], | ||
| ) | ||
| return ( | ||
| <Table | ||
| size="small" | ||
| rowKey="id" | ||
| dataSource={internalProjects} | ||
| columns={internalProjectColumns} | ||
| pagination={false} | ||
| /> | ||
| ) | ||
| }, | ||
| }} |
Collaborator
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This makes me a little uncomfortable because dataSource is getting generated on the fly without memoization. But, so far, the performance is fine, so it's not so important to address this.
This was referenced Sep 3, 2026
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Summary
This PR introduces the first production-ready version of the External Project Overview,
Review comments from the previous stacked PRs have been addressed and incorporated in this PR.
This PR includes :
Review comments from the previous stacked PRs have been addressed and incorporated.