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fix: Never send empty argument objects to APIv2 (#1447)
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* fix sort
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@bchu1
bchu1 authored Jan 8, 2025
1 parent 3257850 commit 2087cf6
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Showing 4 changed files with 112 additions and 79 deletions.
20 changes: 12 additions & 8 deletions frontend/packages/data-portal/app/graphql/getDatasetByIdV2.server.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -218,8 +218,6 @@ function getRunFilter(
datasetId: {
_eq: datasetId,
},
tiltseries: {},
annotations: {},
}

// Deposition filter:
Expand All @@ -234,7 +232,8 @@ function getRunFilter(
const tiltRangeMin = parseFloat(filterState.tiltSeries.min)
const tiltRangeMax = parseFloat(filterState.tiltSeries.max)
if (Number.isFinite(tiltRangeMin) || Number.isFinite(tiltRangeMax)) {
where.tiltseries!.tiltRange = {
where.tiltseries ??= {}
where.tiltseries.tiltRange = {
_gte: Number.isFinite(tiltRangeMin)
? tiltRangeMin
: DEFAULT_TILT_RANGE_MIN,
Expand All @@ -244,7 +243,8 @@ function getRunFilter(
}
}
if (filterState.tiltSeries.qualityScore.length > 0) {
where.tiltseries!.tiltSeriesQuality = {
where.tiltseries ??= {}
where.tiltseries.tiltSeriesQuality = {
_in: filterState.tiltSeries.qualityScore
.map(parseInt)
.filter((val) => Number.isFinite(val)),
Expand All @@ -253,23 +253,27 @@ function getRunFilter(

// Annotation filters:
if (filterState.includedContents.isGroundTruthEnabled) {
where.annotations!.groundTruthStatus = { _eq: true }
where.annotations ??= {}
where.annotations.groundTruthStatus = { _eq: true }
}
if (filterState.annotation.objectNames.length > 0) {
where.annotations!.objectName = {
where.annotations ??= {}
where.annotations.objectName = {
_in: filterState.annotation.objectNames,
}
}
if (filterState.annotation.objectShapeTypes.length > 0) {
where.annotations!.annotationShapes = {
where.annotations ??= {}
where.annotations.annotationShapes = {
shapeType: {
_in: filterState.annotation
.objectShapeTypes as Annotation_File_Shape_Type_Enum[], // TODO(bchu): Remove typecast.
},
}
}
if (filterState.annotation.objectId !== null) {
where.annotations!.objectId = {
where.annotations ??= {}
where.annotations.objectId = {
_ilike: `%${filterState.annotation.objectId.replace(':', '_')}`, // _ is wildcard
}
}
Expand Down
51 changes: 33 additions & 18 deletions frontend/packages/data-portal/app/graphql/getDatasetsV2.server.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -87,9 +87,7 @@ function getFilter(
filterState: FilterState,
searchText?: string,
): DatasetWhereClause {
const where: DatasetWhereClause = {
runs: { annotations: {}, tiltseries: {}, tomograms: {} },
}
const where: DatasetWhereClause = {}

// Search by Dataset Name
if (searchText) {
Expand All @@ -101,7 +99,9 @@ function getFilter(
// INCLUDED CONTENTS SECTION
// Ground Truth Annotation
if (filterState.includedContents.isGroundTruthEnabled) {
where.runs!.annotations!.groundTruthStatus = {
where.runs ??= { annotations: {} }
where.runs.annotations ??= {}
where.runs.annotations.groundTruthStatus = {
_eq: true,
}
}
Expand Down Expand Up @@ -201,16 +201,15 @@ function getFilter(
}
}
// Dataset Author
if (filterState.author.name || filterState.author.orcid) {
where.authors = {}
}
if (filterState.author.name) {
where.authors!.name = {
where.authors ??= {}
where.authors.name = {
_ilike: `%${filterState.author.name}%`,
}
}
if (filterState.author.orcid) {
where.authors!.orcid = {
where.authors ??= {}
where.authors.orcid = {
_ilike: `%${filterState.author.orcid}%`,
}
}
Expand All @@ -235,21 +234,27 @@ function getFilter(

// ANNOTATION METADATA SECTION
const { objectNames, objectId, objectShapeTypes } = filterState.annotation
// Object Name
if (objectNames.length > 0) {
// Object Name
where.runs!.annotations!.objectName = {
where.runs ??= { annotations: {} }
where.runs.annotations ??= {}
where.runs.annotations.objectName = {
_in: objectNames,
}
}
// Object ID
if (objectId) {
where.runs!.annotations!.objectId = {
where.runs ??= { annotations: {} }
where.runs.annotations ??= {}
where.runs.annotations.objectId = {
_eq: objectId,
}
}
// Object Shape Type
if (objectShapeTypes.length > 0) {
where.runs!.annotations!.annotationShapes = {
where.runs ??= { annotations: {} }
where.runs.annotations ??= {}
where.runs.annotations.annotationShapes = {
shapeType: {
_in: objectShapeTypes as Annotation_File_Shape_Type_Enum[], // TODO(bchu): Remove typecast.
},
Expand All @@ -258,7 +263,9 @@ function getFilter(

// HARDWARE SECTION
if (filterState.hardware.cameraManufacturer) {
where.runs!.tiltseries!.cameraManufacturer = {
where.runs ??= { tiltseries: {} }
where.runs.tiltseries ??= {}
where.runs.tiltseries.cameraManufacturer = {
_eq: filterState.hardware.cameraManufacturer,
}
}
Expand All @@ -267,7 +274,9 @@ function getFilter(
const tiltRangeMin = parseFloat(filterState.tiltSeries.min)
const tiltRangeMax = parseFloat(filterState.tiltSeries.max)
if (Number.isFinite(tiltRangeMin) || Number.isFinite(tiltRangeMax)) {
where.runs!.tiltseries!.tiltRange = {
where.runs ??= { tiltseries: {} }
where.runs.tiltseries ??= {}
where.runs.tiltseries.tiltRange = {
_gte: Number.isFinite(tiltRangeMin)
? tiltRangeMin
: DEFAULT_TILT_RANGE_MIN,
Expand All @@ -280,7 +289,9 @@ function getFilter(
// TOMOGRAM METADATA SECTION
// Fiducial Alignment Status
if (filterState.tomogram.fiducialAlignmentStatus) {
where.runs!.tomograms!.fiducialAlignmentStatus = {
where.runs ??= { tomograms: {} }
where.runs.tomograms ??= {}
where.runs.tomograms.fiducialAlignmentStatus = {
_eq:
filterState.tomogram.fiducialAlignmentStatus === 'true'
? Fiducial_Alignment_Status_Enum.Fiducial
Expand All @@ -289,15 +300,19 @@ function getFilter(
}
// Reconstruction Method
if (filterState.tomogram.reconstructionMethod) {
where.runs!.tomograms!.reconstructionMethod = {
where.runs ??= { tomograms: {} }
where.runs.tomograms ??= {}
where.runs.tomograms.reconstructionMethod = {
_eq: convertReconstructionMethodToV2(
filterState.tomogram.reconstructionMethod,
),
}
}
// Reconstruction Software
if (filterState.tomogram.reconstructionSoftware) {
where.runs!.tomograms!.reconstructionSoftware = {
where.runs ??= { tomograms: {} }
where.runs.tomograms ??= {}
where.runs.tomograms.reconstructionSoftware = {
_eq: filterState.tomogram.reconstructionSoftware,
}
}
Expand Down
96 changes: 51 additions & 45 deletions frontend/packages/data-portal/app/graphql/getRunByIdDiffer.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@ export function logIfHasDiff(
methodLinkA.node.link.localeCompare(methodLinkB.node.link),
)
}
// Tomograms are currently being sorted by the FE.
v2.tomograms.sort((tomogramA, tomogramB) => tomogramB.id - tomogramA.id)
for (const tomogram of v2.tomograms) {
// Delete fields that don't exist in V1.
delete tomogram.alignment
Expand Down Expand Up @@ -295,50 +297,52 @@ export function logIfHasDiff(
},
},
})),
tomograms: v1.tomograms.map((tomogram) => ({
ctfCorrected: tomogram.ctf_corrected,
fiducialAlignmentStatus:
tomogram.fiducial_alignment_status as Fiducial_Alignment_Status_Enum,
httpsMrcFile: tomogram.https_mrc_scale0,
id: tomogram.id,
isPortalStandard: false,
isAuthorSubmitted: tomogram.is_canonical,
keyPhotoThumbnailUrl: tomogram.key_photo_thumbnail_url,
keyPhotoUrl: tomogram.key_photo_url,
name: tomogram.name,
neuroglancerConfig: tomogram.neuroglancer_config,
processing: tomogram.processing as Tomogram_Processing_Enum,
processingSoftware: tomogram.processing_software,
reconstructionMethod: (tomogram.reconstruction_method ===
'Weighted back projection'
? 'WBP'
: tomogram.reconstruction_method) as Tomogram_Reconstruction_Method_Enum,
reconstructionSoftware: tomogram.reconstruction_software,
s3MrcFile: tomogram.s3_mrc_scale0,
s3OmezarrDir: tomogram.s3_omezarr_dir,
sizeX: tomogram.size_x,
sizeY: tomogram.size_y,
sizeZ: tomogram.size_z,
voxelSpacing: tomogram.voxel_spacing,
tomogramVoxelSpacing:
tomogram.tomogram_voxel_spacing != null
? {
id: tomogram.tomogram_voxel_spacing.id,
s3Prefix: tomogram.tomogram_voxel_spacing.s3_prefix!,
}
: undefined,
authors: {
edges: tomogram.authors.map((author) => ({
node: {
primaryAuthorStatus: author.primary_author_status,
correspondingAuthorStatus: author.corresponding_author_status,
name: author.name,
email: author.email,
orcid: author.orcid,
},
})),
},
})),
tomograms: v1.tomograms
.map((tomogram) => ({
ctfCorrected: tomogram.ctf_corrected,
fiducialAlignmentStatus:
tomogram.fiducial_alignment_status as Fiducial_Alignment_Status_Enum,
httpsMrcFile: tomogram.https_mrc_scale0,
id: tomogram.id,
isPortalStandard: false,
isAuthorSubmitted: tomogram.is_canonical,
keyPhotoThumbnailUrl: tomogram.key_photo_thumbnail_url,
keyPhotoUrl: tomogram.key_photo_url,
name: tomogram.name,
neuroglancerConfig: tomogram.neuroglancer_config,
processing: tomogram.processing as Tomogram_Processing_Enum,
processingSoftware: tomogram.processing_software,
reconstructionMethod: (tomogram.reconstruction_method ===
'Weighted back projection'
? 'WBP'
: tomogram.reconstruction_method) as Tomogram_Reconstruction_Method_Enum,
reconstructionSoftware: tomogram.reconstruction_software,
s3MrcFile: tomogram.s3_mrc_scale0,
s3OmezarrDir: tomogram.s3_omezarr_dir,
sizeX: tomogram.size_x,
sizeY: tomogram.size_y,
sizeZ: tomogram.size_z,
voxelSpacing: tomogram.voxel_spacing,
tomogramVoxelSpacing:
tomogram.tomogram_voxel_spacing != null
? {
id: tomogram.tomogram_voxel_spacing.id,
s3Prefix: tomogram.tomogram_voxel_spacing.s3_prefix!,
}
: undefined,
authors: {
edges: tomogram.authors.map((author) => ({
node: {
primaryAuthorStatus: author.primary_author_status,
correspondingAuthorStatus: author.corresponding_author_status,
name: author.name,
email: author.email,
orcid: author.orcid,
},
})),
},
}))
.sort((tomogramA, tomogramB) => tomogramB.id - tomogramA.id),
uniqueAnnotationSoftwares: {
aggregate: v1.annotations_for_softwares
.map((annotation) => ({
Expand Down Expand Up @@ -443,7 +447,9 @@ export function logIfHasDiff(
console.log(
`DIFF AT ${url} ======================================== ${JSON.stringify(
v1Transformed,
)} ======================================== ${JSON.stringify(v2)}`,
)} ================================================================================ ${JSON.stringify(
v2,
)}`,
)
}
}
24 changes: 16 additions & 8 deletions frontend/packages/data-portal/app/graphql/getRunByIdV2.server.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,6 @@ function getAnnotationShapesFilter(
_eq: runId,
},
},
authors: {},
},
}

Expand All @@ -459,12 +458,16 @@ function getAnnotationShapesFilter(
// Author filters
const { name, orcid } = filterState.author
if (name) {
where.annotation!.authors!.name = {
where.annotation ??= { authors: {} }
where.annotation.authors ??= {}
where.annotation.authors.name = {
_ilike: `%${name}%`,
}
}
if (orcid) {
where.annotation!.authors!.orcid = {
where.annotation ??= { authors: {} }
where.annotation.authors ??= {}
where.annotation.authors.orcid = {
_ilike: `%${orcid}%`,
}
}
Expand All @@ -473,29 +476,34 @@ function getAnnotationShapesFilter(
const { objectNames, annotationSoftwares, methodTypes, objectId } =
filterState.annotation
if (objectNames.length > 0) {
where.annotation!.objectName = {
where.annotation ??= {}
where.annotation.objectName = {
_in: objectNames,
}
}
if (objectId) {
where.annotation!.objectId = {
where.annotation ??= {}
where.annotation.objectId = {
_ilike: `%${objectId.replace(':', '_')}`, // _ is wildcard
}
}
if (methodTypes.length > 0) {
where.annotation!.methodType = {
where.annotation ??= {}
where.annotation.methodType = {
_in: methodTypes as Annotation_Method_Type_Enum[],
}
}
if (annotationSoftwares.length > 0) {
where.annotation!.annotationSoftware = {
where.annotation ??= {}
where.annotation.annotationSoftware = {
_in: annotationSoftwares,
}
}

// Ground truth dividers
if (groundTruthStatus !== undefined) {
where.annotation!.groundTruthStatus = {
where.annotation ??= {}
where.annotation.groundTruthStatus = {
_eq: groundTruthStatus,
}
}
Expand Down

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