From a6ad0a80fd19608200e95c69bb256c5557c2bd9a Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 6 Nov 2025 19:06:55 +0400 Subject: [PATCH 1/7] add cell ratio docs + refactor cell group response --- openapi/v1/integrationCurator.yaml | 46 +++++++++++++++++++ openapi/v1/integrationUser.yaml | 46 +++++++++++++++++++ openapi/v1/schemas/cell/CellGroupRequest.yaml | 32 +++++++++++++ openapi/v1/schemas/cell/CellRatioRequest.yaml | 7 +++ .../v1/schemas/cell/CellRatioResponse.yaml | 17 +++++++ openapi/v1/schemas/cell/DERequest.yaml | 39 +--------------- .../v1/schemas/cell/GeneSummaryRequest.yaml | 37 +-------------- 7 files changed, 151 insertions(+), 73 deletions(-) create mode 100644 openapi/v1/schemas/cell/CellGroupRequest.yaml create mode 100644 openapi/v1/schemas/cell/CellRatioRequest.yaml create mode 100644 openapi/v1/schemas/cell/CellRatioResponse.yaml diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 529bd9c8..ef7f5516 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -7062,6 +7062,48 @@ paths: security: - Access-token: [ ] - Genestack-API-Token: [ ] + /api/v1/as-curator/omics/cells/analytics/cell-ratio: + post: + operationId: cellRatioAsCurator + summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." + tags: + - "[BETA] Analysis omics queries as Curator" + description: |+ + This endpoint calculates cell ratio statistics based on single-cell metadata. + It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population defined by study, samples, library, or preparation metadata + Request and response parameters are subject to change as this feature is in BETA. + + The endpoint supports grouping by Study, Sample, Library, or Preparation metadata and filtering by cell expression or cell metadata fields. + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CellRatioRequest" + required: true + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/CellRatioResponse" + description: Cell ratio result + "400": + content: { } + description: Entities cannot be retrieved. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] /api/v1/as-curator/integration/studies/{id}/tasks/publish-versions: post: description: This endpoint publishes information from staging and creates new @@ -7421,6 +7463,10 @@ components: $ref: "./schemas/cell/GeneSummaryRequest.yaml" GeneSummaryResponse: $ref: "./schemas/cell/GeneSummaryResponse.yaml" + CellRatioRequest: + $ref: "./schemas/cell/CellRatioRequest.yaml" + CellRatioResponse: + $ref: "./schemas/cell/CellRatioResponse.yaml" securitySchemes: Access-token: in: header diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index b09c8079..efdcb297 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5513,6 +5513,48 @@ paths: security: - Access-token: [ ] - Genestack-API-Token: [ ] + /api/v1/as-curator/omics/cells/analytics/cell-ratio: + post: + operationId: cellRatioAsUser + summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." + tags: + - "[BETA] Analysis omics queries as Curator" + description: |+ + This endpoint calculates cell ratio statistics based on single-cell metadata. + It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population defined by study, samples, library, or preparation metadata + Request and response parameters are subject to change as this feature is in BETA. + + The endpoint supports grouping by Study, Sample, Library, or Preparation metadata and filtering by cell expression or cell metadata fields. + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CellRatioRequest" + required: true + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/CellRatioResponse" + description: Cell ratio result + "400": + content: { } + description: Entities cannot be retrieved. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] /api/v1/as-user/integration/link/files/by/study/{id}: get: operationId: getFilesByStudyAsUser @@ -5640,6 +5682,10 @@ components: $ref: "./schemas/cell/GeneSummaryRequest.yaml" GeneSummaryResponse: $ref: "./schemas/cell/GeneSummaryResponse.yaml" + CellRatioRequest: + $ref: "./schemas/cell/CellRatioRequest.yaml" + CellRatioResponse: + $ref: "./schemas/cell/CellRatioResponse.yaml" securitySchemes: Access-token: in: header diff --git a/openapi/v1/schemas/cell/CellGroupRequest.yaml b/openapi/v1/schemas/cell/CellGroupRequest.yaml new file mode 100644 index 00000000..81b6128e --- /dev/null +++ b/openapi/v1/schemas/cell/CellGroupRequest.yaml @@ -0,0 +1,32 @@ +type: object +properties: + studyFilter: + type: string + example: '"Study Source"=ArrayExpress' + studyQuery: + type: string + example: 'RNA-Seq of human dendritic cells' + sampleFilter: + type: string + example: '"Species or strain"="Homo sapiens"' + sampleQuery: + type: string + example: 'Clozapine' + libraryFilter: + type: string + example: '"Library Type"=RNA-Seq-1' + libraryQuery: + type: string + example: 'illumina HiSeq500' + preparationFilter: + type: string + example: 'Digestion=Trypsin' + preparationQuery: + type: string + example: 'reversed-phase liquid chromatography' + cellQuery: + type: string + example: 'cellType=Macrophage,Monocyte' + searchSpecificTerms: + type: boolean + example: false diff --git a/openapi/v1/schemas/cell/CellRatioRequest.yaml b/openapi/v1/schemas/cell/CellRatioRequest.yaml new file mode 100644 index 00000000..c357ac70 --- /dev/null +++ b/openapi/v1/schemas/cell/CellRatioRequest.yaml @@ -0,0 +1,7 @@ +type: object +properties: + cellGroup: + $ref: 'CellGroupRequest.yaml' + exQuery: + type: string + example: '-3 < value < 3' diff --git a/openapi/v1/schemas/cell/CellRatioResponse.yaml b/openapi/v1/schemas/cell/CellRatioResponse.yaml new file mode 100644 index 00000000..04c434a6 --- /dev/null +++ b/openapi/v1/schemas/cell/CellRatioResponse.yaml @@ -0,0 +1,17 @@ +type: object +properties: + countSelected: + type: integer + format: int32 + description: Count of Cells selected with all queries. + example: 8968167 + countAvailable: + type: integer + format: int32 + description: Count of all available Cells limited by Study and SLP queries and filters. + example: 9234945 + ratio: + type: number + format: double + description: Ratio value + example: 0.13465 diff --git a/openapi/v1/schemas/cell/DERequest.yaml b/openapi/v1/schemas/cell/DERequest.yaml index 52005e11..f63bb125 100644 --- a/openapi/v1/schemas/cell/DERequest.yaml +++ b/openapi/v1/schemas/cell/DERequest.yaml @@ -1,9 +1,9 @@ type: object properties: caseGroup: - $ref: '#/components/schemas/CellGroupRequest' + $ref: 'CellGroupRequest.yaml' controlGroup: - $ref: '#/components/schemas/CellGroupRequest' + $ref: 'CellGroupRequest.yaml' exQuery: type: string example: 'feature=ENSG00000230368,ENSG00000188976' @@ -20,38 +20,3 @@ properties: required: - caseGroup - controlGroup -components: - schemas: - CellGroupRequest: - type: object - properties: - studyFilter: - type: string - example: '"Study Source"=ArrayExpress' - studyQuery: - type: string - example: 'RNA-Seq of human dendritic cells' - sampleFilter: - type: string - example: '"Species or strain"="Homo sapiens"' - sampleQuery: - type: string - example: 'Clozapine' - libraryFilter: - type: string - example: '"Library Type"=RNA-Seq-1' - libraryQuery: - type: string - example: 'illumina HiSeq500' - preparationFilter: - type: string - example: 'Digestion=Trypsin' - preparationQuery: - type: string - example: 'reversed-phase liquid chromatography' - cellQuery: - type: string - example: 'cellType=Macrophage,Monocyte' - searchSpecificTerms: - type: boolean - example: false diff --git a/openapi/v1/schemas/cell/GeneSummaryRequest.yaml b/openapi/v1/schemas/cell/GeneSummaryRequest.yaml index 86b90d2e..f771f156 100644 --- a/openapi/v1/schemas/cell/GeneSummaryRequest.yaml +++ b/openapi/v1/schemas/cell/GeneSummaryRequest.yaml @@ -1,7 +1,7 @@ type: object properties: cellGroup: - $ref: '#/components/schemas/CellGroupRequest' + $ref: 'CellGroupRequest.yaml' geneNames: type: array items: @@ -15,38 +15,3 @@ properties: example: '-3 < value < 3' required: - geneNames -components: - schemas: - CellGroupRequest: - type: object - properties: - studyFilter: - type: string - example: '"Study Source"=ArrayExpress' - studyQuery: - type: string - example: 'RNA-Seq of human dendritic cells' - sampleFilter: - type: string - example: '"Species or strain"="Homo sapiens"' - sampleQuery: - type: string - example: 'Clozapine' - libraryFilter: - type: string - example: '"Library Type"=RNA-Seq-1' - libraryQuery: - type: string - example: 'illumina HiSeq500' - preparationFilter: - type: string - example: 'Digestion=Trypsin' - preparationQuery: - type: string - example: 'reversed-phase liquid chromatography' - cellQuery: - type: string - example: 'cellType=Macrophage,Monocyte' - searchSpecificTerms: - type: boolean - example: false From 7848391c6322210398ef02d80c7921aa9568793a Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 6 Nov 2025 19:16:53 +0400 Subject: [PATCH 2/7] fix tag --- openapi/v1/integrationUser.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index efdcb297..6df2153a 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5518,7 +5518,7 @@ paths: operationId: cellRatioAsUser summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." tags: - - "[BETA] Analysis omics queries as Curator" + - "[BETA] Analysis omics queries as User" description: |+ This endpoint calculates cell ratio statistics based on single-cell metadata. It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) From 02981c8d11d0df4b3e6d68e72e8375d7c85c2030 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 6 Nov 2025 19:18:55 +0400 Subject: [PATCH 3/7] fix example to make sense --- openapi/v1/schemas/cell/CellRatioResponse.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi/v1/schemas/cell/CellRatioResponse.yaml b/openapi/v1/schemas/cell/CellRatioResponse.yaml index 04c434a6..8c5859a1 100644 --- a/openapi/v1/schemas/cell/CellRatioResponse.yaml +++ b/openapi/v1/schemas/cell/CellRatioResponse.yaml @@ -4,7 +4,7 @@ properties: type: integer format: int32 description: Count of Cells selected with all queries. - example: 8968167 + example: 1243393 countAvailable: type: integer format: int32 From 7a4d9f7d107b9a1c6e1b9f6eea7ad0c0897152d1 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Wed, 12 Nov 2025 23:35:35 +0400 Subject: [PATCH 4/7] fix review comments --- openapi/v1/integrationCurator.yaml | 12 ++++++------ openapi/v1/integrationUser.yaml | 12 ++++++------ .../cell/{CellRatioRequest.yaml => CRRequest.yaml} | 0 .../cell/{CellRatioResponse.yaml => CRResponse.yaml} | 6 +++++- 4 files changed, 17 insertions(+), 13 deletions(-) rename openapi/v1/schemas/cell/{CellRatioRequest.yaml => CRRequest.yaml} (100%) rename openapi/v1/schemas/cell/{CellRatioResponse.yaml => CRResponse.yaml} (73%) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index c8e35e82..df4d36a0 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -7144,14 +7144,14 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/CellRatioRequest" + $ref: "#/components/schemas/CRRequest" required: true responses: "200": content: application/json: schema: - $ref: "#/components/schemas/CellRatioResponse" + $ref: "#/components/schemas/CRResponse" description: Cell ratio result "400": content: { } @@ -7528,10 +7528,10 @@ components: $ref: "./schemas/cell/GSRequest.yaml" GSResponse: $ref: "./schemas/cell/GSResponse.yaml" - CellRatioRequest: - $ref: "./schemas/cell/CellRatioRequest.yaml" - CellRatioResponse: - $ref: "./schemas/cell/CellRatioResponse.yaml" + CRRequest: + $ref: "./schemas/cell/CRRequest.yaml" + CRResponse: + $ref: "./schemas/cell/CRResponse.yaml" securitySchemes: Access-token: in: header diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index 62398f10..b93f6018 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5595,14 +5595,14 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/CellRatioRequest" + $ref: "#/components/schemas/CRRequest" required: true responses: "200": content: application/json: schema: - $ref: "#/components/schemas/CellRatioResponse" + $ref: "#/components/schemas/CRResponse" description: Cell ratio result "400": content: { } @@ -5747,10 +5747,10 @@ components: $ref: "./schemas/cell/GSRequest.yaml" GSResponse: $ref: "./schemas/cell/GSResponse.yaml" - CellRatioRequest: - $ref: "./schemas/cell/CellRatioRequest.yaml" - CellRatioResponse: - $ref: "./schemas/cell/CellRatioResponse.yaml" + CRRequest: + $ref: "./schemas/cell/CRRequest.yaml" + CRResponse: + $ref: "./schemas/cell/CRResponse.yaml" securitySchemes: Access-token: in: header diff --git a/openapi/v1/schemas/cell/CellRatioRequest.yaml b/openapi/v1/schemas/cell/CRRequest.yaml similarity index 100% rename from openapi/v1/schemas/cell/CellRatioRequest.yaml rename to openapi/v1/schemas/cell/CRRequest.yaml diff --git a/openapi/v1/schemas/cell/CellRatioResponse.yaml b/openapi/v1/schemas/cell/CRResponse.yaml similarity index 73% rename from openapi/v1/schemas/cell/CellRatioResponse.yaml rename to openapi/v1/schemas/cell/CRResponse.yaml index 8c5859a1..afa265f4 100644 --- a/openapi/v1/schemas/cell/CellRatioResponse.yaml +++ b/openapi/v1/schemas/cell/CRResponse.yaml @@ -1,9 +1,13 @@ type: object +required: + - countSelected + - countAvailable + - ratio properties: countSelected: type: integer format: int32 - description: Count of Cells selected with all queries. + description: Count of Cells selected with all queries and filters. example: 1243393 countAvailable: type: integer From 182e3f11e3ba4d0e68ab6375cffc45ce849ef73f Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 13 Nov 2025 19:44:28 +0400 Subject: [PATCH 5/7] fix tag --- openapi/v1/integrationCurator.yaml | 2 +- openapi/v1/integrationUser.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 16276173..1f8fd28f 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -7133,7 +7133,7 @@ paths: operationId: cellRatioAsCurator summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." tags: - - "[BETA] Analysis omics queries as Curator" + - "[BETA] Analytics omics queries as Curator" description: |+ This endpoint calculates cell ratio statistics based on single-cell metadata. It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index f69fb7d4..95565e12 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5584,7 +5584,7 @@ paths: operationId: cellRatioAsUser summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." tags: - - "[BETA] Analysis omics queries as User" + - "[BETA] Analytics omics queries as User" description: |+ This endpoint calculates cell ratio statistics based on single-cell metadata. It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) From 57fad32f4e2acbc223244a5fd8e8c5391bb8e414 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 13 Nov 2025 20:09:33 +0400 Subject: [PATCH 6/7] update description --- openapi/v1/integrationCurator.yaml | 12 ++++++++---- openapi/v1/integrationUser.yaml | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 1f8fd28f..7065d792 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -7136,11 +7136,15 @@ paths: - "[BETA] Analytics omics queries as Curator" description: |+ This endpoint calculates cell ratio statistics based on single-cell metadata. - It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) - relative to a defined reference group or the total cell population defined by study, samples, library, or preparation metadata - Request and response parameters are subject to change as this feature is in BETA. - The endpoint supports grouping by Study, Sample, Library, or Preparation metadata and filtering by cell expression or cell metadata fields. + It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. + + `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. + In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. + + The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. + requestBody: content: application/json: diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index 95565e12..37fd7eaf 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5587,11 +5587,15 @@ paths: - "[BETA] Analytics omics queries as User" description: |+ This endpoint calculates cell ratio statistics based on single-cell metadata. - It allows quantifying the proportion of cells that meet specific criteria (e.g. expression threshold, cell type, or cluster) - relative to a defined reference group or the total cell population defined by study, samples, library, or preparation metadata - Request and response parameters are subject to change as this feature is in BETA. - The endpoint supports grouping by Study, Sample, Library, or Preparation metadata and filtering by cell expression or cell metadata fields. + It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. + + `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. + In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. + + The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. + requestBody: content: application/json: From ec7092c970b79e50fedb1a5fde5b31a4bd8fcbd8 Mon Sep 17 00:00:00 2001 From: Mikhail Smazhevsky Date: Fri, 14 Nov 2025 12:55:37 +0100 Subject: [PATCH 7/7] !!ODM-12845: * order of endpoints * added [BETA] mark and a disclaimer * fixed address for user cell-ratio --- openapi/v1/integrationCurator.yaml | 95 +++++++++++++++--------------- openapi/v1/integrationUser.yaml | 95 +++++++++++++++--------------- 2 files changed, 98 insertions(+), 92 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 7065d792..66b7b0f2 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -7021,6 +7021,53 @@ paths: summary: Stream data from a given VCF file tags: - Omics queries as Curator + /api/v1/as-curator/omics/cells/analytics/cell-ratio: + post: + operationId: cellRatioAsCurator + summary: "[BETA] Compute cell ratio statistics across groups or metadata attributes in single-cell data." + tags: + - "[BETA] Analytics omics queries as Curator" + description: |+ + This endpoint calculates cell ratio statistics based on single-cell metadata. + + It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. + + `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. + In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. + + The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. + + Request and response parameters are subject to change as this feature is in BETA. + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CRRequest" + required: true + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/CRResponse" + description: Cell ratio result + "400": + content: { } + description: Entities cannot be retrieved. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] /api/v1/as-curator/omics/cells/analytics/differential-expression: post: operationId: differentialExpressionAsCurator @@ -7097,6 +7144,8 @@ paths: - `Minimum and maximum values` - range of expression across cells. Results are sorted by gene name. + + Request and response parameters are subject to change as this feature is in BETA. requestBody: required: true content: @@ -7128,52 +7177,6 @@ paths: security: - Access-token: [ ] - Genestack-API-Token: [ ] - /api/v1/as-curator/omics/cells/analytics/cell-ratio: - post: - operationId: cellRatioAsCurator - summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." - tags: - - "[BETA] Analytics omics queries as Curator" - description: |+ - This endpoint calculates cell ratio statistics based on single-cell metadata. - - It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) - relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. - - `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. - In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. - - The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. - - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/CRRequest" - required: true - responses: - "200": - content: - application/json: - schema: - $ref: "#/components/schemas/CRResponse" - description: Cell ratio result - "400": - content: { } - description: Entities cannot be retrieved. - "401": - content: { } - description: |- - User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) - or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). - "500": - content: { } - description: "An internal server error occurred. This indicates an unexpected\ - \ failure in the Genestack system, please file a bug report to support@genestack.com,\ - \ including the error details." - security: - - Access-token: [ ] - - Genestack-API-Token: [ ] /api/v1/as-curator/integration/studies/{id}/tasks/publish-versions: post: description: This endpoint publishes information from staging and creates new diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index 37fd7eaf..8944dea1 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -5472,6 +5472,53 @@ paths: summary: Stream data from a given VCF file tags: - Omics queries as User + /api/v1/as-user/omics/cells/analytics/cell-ratio: + post: + operationId: cellRatioAsUser + summary: "[BETA] Compute cell ratio statistics across groups or metadata attributes in single-cell data." + tags: + - "[BETA] Analytics omics queries as User" + description: |+ + This endpoint calculates cell ratio statistics based on single-cell metadata. + + It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) + relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. + + `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. + In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. + + The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. + + Request and response parameters are subject to change as this feature is in BETA. + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CRRequest" + required: true + responses: + "200": + content: + application/json: + schema: + $ref: "#/components/schemas/CRResponse" + description: Cell ratio result + "400": + content: { } + description: Entities cannot be retrieved. + "401": + content: { } + description: |- + User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) + or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). + "500": + content: { } + description: "An internal server error occurred. This indicates an unexpected\ + \ failure in the Genestack system, please file a bug report to support@genestack.com,\ + \ including the error details." + security: + - Access-token: [ ] + - Genestack-API-Token: [ ] /api/v1/as-user/omics/cells/analytics/differential-expression: post: operationId: differentialExpressionAsUser @@ -5548,6 +5595,8 @@ paths: - `Minimum and maximum values` - range of expression across cells. Results are sorted by gene name. + + Request and response parameters are subject to change as this feature is in BETA. requestBody: required: true content: @@ -5579,52 +5628,6 @@ paths: security: - Access-token: [ ] - Genestack-API-Token: [ ] - /api/v1/as-curator/omics/cells/analytics/cell-ratio: - post: - operationId: cellRatioAsUser - summary: "Compute cell ratio statistics across groups or metadata attributes in single-cell data." - tags: - - "[BETA] Analytics omics queries as User" - description: |+ - This endpoint calculates cell ratio statistics based on single-cell metadata. - - It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster) - relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata. - - `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters. - In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter. - - The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields. - - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/CRRequest" - required: true - responses: - "200": - content: - application/json: - schema: - $ref: "#/components/schemas/CRResponse" - description: Cell ratio result - "400": - content: { } - description: Entities cannot be retrieved. - "401": - content: { } - description: |- - User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) - or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page). - "500": - content: { } - description: "An internal server error occurred. This indicates an unexpected\ - \ failure in the Genestack system, please file a bug report to support@genestack.com,\ - \ including the error details." - security: - - Access-token: [ ] - - Genestack-API-Token: [ ] /api/v1/as-user/integration/link/files/by/study/{id}: get: operationId: getFilesByStudyAsUser