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feat: improve review page loading times #3189

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feat: improve review page loading times #3189

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f2a455c
implement
fhennig Nov 12, 2024
d8e24f4
Update backend/src/main/kotlin/org/loculus/backend/api/SubmissionType…
fhennig Nov 18, 2024
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2 changes: 1 addition & 1 deletion backend/docs/plantuml/statusChange.svg
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9 changes: 9 additions & 0 deletions backend/src/main/kotlin/org/loculus/backend/api/SubmissionTypes.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -229,6 +229,15 @@ data class SequenceEntryStatus(
val isRevocation: Boolean = false,
val submissionId: String,
val dataUseTerms: DataUseTerms,
val processedData: ProcessedData<GeneticSequence>?,
val originalData: OriginalData<GeneticSequence>?,
@Schema(description = "The preprocessing will be considered failed if this is not empty")
val errors: List<PreprocessingAnnotation>? = null,
@Schema(
description =
"Issues where data is not necessarily wrong, but the user might want to look into those warnings.",
fhennig marked this conversation as resolved.
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)
val warnings: List<PreprocessingAnnotation>? = null,
) : AccessionVersionInterface

data class EditedSequenceEntryData(
Expand Down
6 changes: 6 additions & 0 deletions backend/src/main/kotlin/org/loculus/backend/service/submission/CompressionService.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,9 @@ class CompressionService(private val backendConfig: BackendConfig) {
getDictionaryForAminoAcidSequence(gene, organism),
)

fun maybeDecompressSequencesInOriginalData(originalData: OriginalData<CompressedSequence>?, organism: Organism) =
if (originalData != null) decompressSequencesInOriginalData(originalData, organism) else null

fun decompressSequencesInOriginalData(originalData: OriginalData<CompressedSequence>, organism: Organism) =
OriginalData(
originalData.metadata,
Expand All @@ -84,6 +87,9 @@ class CompressionService(private val backendConfig: BackendConfig) {
},
)

fun maybeDecompressSequencesInProcessedData(processedData: ProcessedData<CompressedSequence>?, organism: Organism) =
if (processedData != null) decompressSequencesInProcessedData(processedData, organism) else null

fun decompressSequencesInProcessedData(processedData: ProcessedData<CompressedSequence>, organism: Organism) =
ProcessedData(
processedData.metadata,
Expand Down
14 changes: 13 additions & 1 deletion backend/src/main/kotlin/org/loculus/backend/service/submission/SubmissionDatabaseService.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -655,14 +655,16 @@ class SubmissionDatabaseService(
SequenceEntriesView.versionColumn,
SequenceEntriesView.submissionIdColumn,
SequenceEntriesView.statusColumn,
SequenceEntriesView.processingResultColumn,
SequenceEntriesView.isRevocationColumn,
SequenceEntriesView.groupIdColumn,
SequenceEntriesView.submitterColumn,
SequenceEntriesView.organismColumn,
SequenceEntriesView.submittedAtTimestampColumn,
SequenceEntriesView.errorsColumn,
SequenceEntriesView.warningsColumn,
SequenceEntriesView.processingResultColumn,
SequenceEntriesView.processedDataColumn,
SequenceEntriesView.originalDataColumn,
DataUseTermsTable.dataUseTermsTypeColumn,
DataUseTermsTable.restrictedUntilColumn,
)
Expand Down Expand Up @@ -710,6 +712,16 @@ class SubmissionDatabaseService(
DataUseTermsType.fromString(row[DataUseTermsTable.dataUseTermsTypeColumn]),
row[DataUseTermsTable.restrictedUntilColumn],
),
processedData = compressionService.maybeDecompressSequencesInProcessedData(
row[SequenceEntriesView.processedDataColumn],
organism,
),
originalData = compressionService.maybeDecompressSequencesInOriginalData(
row[SequenceEntriesView.originalDataColumn],
organism,
),
errors = row[SequenceEntriesView.errorsColumn],
warnings = row[SequenceEntriesView.warningsColumn],
)
}

Expand Down
44 changes: 8 additions & 36 deletions website/src/components/ReviewPage/ReviewCard.tsx
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
import { type FC } from 'react';
import { Tooltip } from 'react-tooltip';

import { backendClientHooks } from '../../services/serviceHooks.ts';
import {
type DataUseTerms,
processedStatus,
Expand All @@ -11,12 +10,9 @@ import {
restrictedDataUseTermsType,
type SequenceEntryStatus,
type SequenceEntryStatusNames,
type SequenceEntryToEdit,
errorsProcessingResult,
warningsProcessingResult,
} from '../../types/backend.ts';
import type { ClientConfig } from '../../types/runtimeConfig.ts';
import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader.ts';
import { displayMetadataField } from '../../utils/displayMetadataField.ts';
import { getAccessionVersionString } from '../../utils/extractAccessionVersion.ts';
import BiTrash from '~icons/bi/trash';
Expand All @@ -34,21 +30,14 @@ type ReviewCardProps = {
deleteAccessionVersion: () => void;
approveAccessionVersion: () => void;
editAccessionVersion: () => void;
clientConfig: ClientConfig;
organism: string;
accessToken: string;
};

export const ReviewCard: FC<ReviewCardProps> = ({
sequenceEntryStatus,
approveAccessionVersion,
deleteAccessionVersion,
editAccessionVersion,
clientConfig,
organism,
accessToken,
}) => {
const { isLoading, data } = useGetMetadataAndAnnotations(organism, clientConfig, accessToken, sequenceEntryStatus);
return (
<div className='px-3 py-2 relative transition-all duration-500'>
<div className='flex'>
Expand All @@ -65,7 +54,7 @@ export const ReviewCard: FC<ReviewCardProps> = ({
keyName={getAccessionVersionString(sequenceEntryStatus)}
value={sequenceEntryStatus.submissionId}
/>
{data !== undefined && <MetadataList data={data} isLoading={isLoading} />}
<MetadataList data={sequenceEntryStatus} />
{sequenceEntryStatus.isRevocation && (
<KeyValueComponent
accessionVersion={getAccessionVersionString(sequenceEntryStatus)}
Expand All @@ -83,11 +72,11 @@ export const ReviewCard: FC<ReviewCardProps> = ({
/>
</div>

{data?.errors?.length !== undefined && data.errors.length > 0 && (
<Errors errors={data.errors} accession={sequenceEntryStatus.accession} />
{sequenceEntryStatus.errors?.length !== undefined && sequenceEntryStatus.errors.length > 0 && (
<Errors errors={sequenceEntryStatus.errors} accession={sequenceEntryStatus.accession} />
)}
{data?.warnings?.length !== undefined && data.warnings.length > 0 && (
<Warnings warnings={data.warnings} accession={sequenceEntryStatus.accession} />
{sequenceEntryStatus.warnings?.length !== undefined && sequenceEntryStatus.warnings.length > 0 && (
<Warnings warnings={sequenceEntryStatus.warnings} accession={sequenceEntryStatus.accession} />
)}
</div>
);
Expand Down Expand Up @@ -171,15 +160,14 @@ const ButtonBar: FC<ButtonBarProps> = ({
};

type MetadataListProps = {
data: SequenceEntryToEdit;
isLoading: boolean;
data: SequenceEntryStatus;
};

const isAnnotationPresent = (metadataField: string) => (item: ProcessingAnnotation) =>
item.source[0].name === metadataField;

const MetadataList: FC<MetadataListProps> = ({ data, isLoading }) =>
!isLoading &&
const MetadataList: FC<MetadataListProps> = ({ data }) =>
data.processedData !== null &&
Object.entries(data.processedData.metadata).map(([metadataName, value], index) =>
value === null ? null : (
<KeyValueComponent
Expand Down Expand Up @@ -412,19 +400,3 @@ function getTextColorAndMessages(
secondaryMessages: undefined,
};
}

function useGetMetadataAndAnnotations(
organism: string,
clientConfig: ClientConfig,
accessToken: string,
sequenceEntryStatus: SequenceEntryStatus,
) {
const { status, accession, version } = sequenceEntryStatus;
return backendClientHooks(clientConfig).useGetDataToEdit(
{
headers: createAuthorizationHeader(accessToken),
params: { organism, accession, version },
},
{ enabled: status !== receivedStatus && status !== inProcessingStatus },
);
}
74 changes: 74 additions & 0 deletions website/src/components/ReviewPage/ReviewPage.spec.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ import {
noIssuesProcessingResult,
warningsProcessingResult,
errorsProcessingResult,
type ProcessingAnnotation,
} from '../../types/backend.ts';

const unreleasedSequencesRegex = /You do not currently have any unreleased sequences awaiting review.*/;
Expand All @@ -31,6 +32,63 @@ function renderReviewPage() {
);
}

export const metadataKey = 'originalMetaDataField';
export const editableEntry = 'originalMetaDataValue';
const testErrors: ProcessingAnnotation[] = [
{
source: [
{
name: metadataKey,
type: 'Metadata',
},
],
message: 'errorMessage',
},
];

const testWarnings: ProcessingAnnotation[] = [
{
source: [
{
name: metadataKey,
type: 'Metadata',
},
],
message: 'warningMessage',
},
];

const testOriginalData = {
metadata: {
[metadataKey]: editableEntry,
},
unalignedNucleotideSequences: {
originalSequenceName: 'originalUnalignedNucleotideSequencesValue',
},
};

const testProcessedData = {
metadata: {
processedMetaDataField: 'processedMetaDataValue',
nullField: null,
},
unalignedNucleotideSequences: {
unalignedProcessedSequenceName: 'processedUnalignedNucleotideSequencesValue',
},
alignedNucleotideSequences: {
alignedProcessedSequenceName: 'processedAlignedNucleotideSequencesValue',
},
nucleotideInsertions: {
processedInsertionSequenceName: ['nucleotideInsertion1', 'nucleotideInsertion2'],
},
alignedAminoAcidSequences: {
alignedProcessedGeneName: 'processedAminoAcidSequencesValue',
},
aminoAcidInsertions: {
processedInsertionGeneName: ['aminoAcidInsertion1', 'aminoAcidInsertion2'],
},
};

const receivedTestData: SequenceEntryStatus = {
submissionId: 'custom1',
status: receivedStatus,
Expand All @@ -41,6 +99,10 @@ const receivedTestData: SequenceEntryStatus = {
dataUseTerms: openDataUseTerms,
groupId: 42,
submitter: 'submitter',
originalData: testOriginalData,
processedData: testProcessedData,
errors: testErrors,
warnings: testWarnings,
};

const processingTestData: SequenceEntryStatus = {
Expand All @@ -53,6 +115,10 @@ const processingTestData: SequenceEntryStatus = {
dataUseTerms: openDataUseTerms,
groupId: 42,
submitter: 'submitter',
originalData: testOriginalData,
processedData: testProcessedData,
errors: testErrors,
warnings: testWarnings,
};

const erroneousTestData: SequenceEntryStatus = {
Expand All @@ -65,6 +131,10 @@ const erroneousTestData: SequenceEntryStatus = {
dataUseTerms: openDataUseTerms,
groupId: 42,
submitter: 'submitter',
originalData: testOriginalData,
processedData: testProcessedData,
errors: testErrors,
warnings: testWarnings,
};

const awaitingApprovalTestData: SequenceEntryStatus = {
Expand All @@ -77,6 +147,10 @@ const awaitingApprovalTestData: SequenceEntryStatus = {
dataUseTerms: openDataUseTerms,
groupId: 42,
submitter: 'submitter',
originalData: testOriginalData,
processedData: testProcessedData,
errors: testErrors,
warnings: testWarnings,
};

const emptyStatusCounts = {
Expand Down
3 changes: 0 additions & 3 deletions website/src/components/ReviewPage/ReviewPage.tsx
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Expand Up @@ -367,9 +367,6 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
editAccessionVersion={() => {
window.location.href = routes.editPage(organism, sequence);
}}
clientConfig={clientConfig}
organism={organism}
accessToken={accessToken}
/>
</div>
);
Expand Down
18 changes: 18 additions & 0 deletions website/src/types/backend.ts
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I think that if we were to make the changes in this PR we need to not send sequences in the endpoint used on the review page. This is is because:

  • sequences for some viruses are 200 kb, 100 per page = 20 MB, polling constantly = a lot of bandwidth

We may want to delay making any change here for now for simplicity to avoid having to add extra types etc.

Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,24 @@ export const sequenceEntryStatus = accessionVersion.merge(
dataUseTerms,
groupId: z.number(),
submitter: z.string(),
errors: z.array(processingAnnotation).nullable(),
warnings: z.array(processingAnnotation).nullable(),
originalData: z
.object({
metadata: unprocessedMetadataRecord,
unalignedNucleotideSequences: z.record(z.string()),
})
.nullable(),
processedData: z
.object({
metadata: metadataRecord,
unalignedNucleotideSequences: z.record(z.string().nullable()),
alignedNucleotideSequences: z.record(z.string().nullable()),
nucleotideInsertions: z.record(z.array(z.string())),
alignedAminoAcidSequences: z.record(z.string().nullable()),
aminoAcidInsertions: z.record(z.array(z.string())),
})
.nullable(),
}),
);

Expand Down
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