From 8c2daf6b5b4d2858903fd53a724498eab78ae661 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Thu, 23 Oct 2025 12:21:58 +0400 Subject: [PATCH 1/4] change the description of cellQuery --- openapi/v1/integrationCurator.yaml | 16 ++++++++++++++++ openapi/v1/integrationUser.yaml | 16 ++++++++++++++++ 2 files changed, 32 insertions(+) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index c072f3ff..4ac57271 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -4504,6 +4504,22 @@ paths: * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2. * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000. * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query. + + Embedding constraints: + + * UMAP + - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**. + - If exactly **1** UMAP dimension is provided, the request is invalid. + - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. + + * PCA + - Allowed number of components per cell: **0** (absent) or **≥ 2**. + - If exactly **1** PCA component is provided, the request is invalid. + - At most **100** PCA components are stored; components beyond 100 are ignored. + + Notes: + - “Dimensions/components” refer to the length of the embedding vector for each cell. + - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. in: query name: cellQuery schema: diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index 033ae61f..be24c789 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -2951,6 +2951,22 @@ paths: * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2. * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000. * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query. + + Embedding constraints: + + * UMAP + - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**. + - If exactly **1** UMAP dimension is provided, the request is invalid. + - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. + + * PCA + - Allowed number of components per cell: **0** (absent) or **≥ 2**. + - If exactly **1** PCA component is provided, the request is invalid. + - At most **100** PCA components are stored; components beyond 100 are ignored. + + Notes: + - “Dimensions/components” refer to the length of the embedding vector for each cell. + - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. in: query name: cellQuery schema: From 52785488156b3bbbd13e180fdf160230984a7889 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Tue, 28 Oct 2025 14:08:45 +0400 Subject: [PATCH 2/4] fix build --- Earthfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Earthfile b/Earthfile index 08980a08..4ded0b2d 100644 --- a/Earthfile +++ b/Earthfile @@ -84,7 +84,7 @@ r-api-client: RUN \ apt update && \ apt-get install -y \ - libssl-dev libcurl4-gnutls-dev curl libcurl4t64:amd64=8.16.0-4 --allow-downgrades && \ + libssl-dev libcurl4-gnutls-dev curl && \ Rscript requirements.R COPY +build/generated generated From caa2ead03295e484e66c76485e5bcad1b2062b32 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Wed, 29 Oct 2025 13:49:26 +0400 Subject: [PATCH 3/4] move constraints description to job endpoints --- openapi/v1/integrationCurator.yaml | 8 -------- openapi/v1/integrationUser.yaml | 15 -------------- openapi/v1/job.yaml | 32 ++++++++++++++++++++++++++++++ 3 files changed, 32 insertions(+), 23 deletions(-) diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml index 4ac57271..71efc650 100644 --- a/openapi/v1/integrationCurator.yaml +++ b/openapi/v1/integrationCurator.yaml @@ -4512,14 +4512,6 @@ paths: - If exactly **1** UMAP dimension is provided, the request is invalid. - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. - * PCA - - Allowed number of components per cell: **0** (absent) or **≥ 2**. - - If exactly **1** PCA component is provided, the request is invalid. - - At most **100** PCA components are stored; components beyond 100 are ignored. - - Notes: - - “Dimensions/components” refer to the length of the embedding vector for each cell. - - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. in: query name: cellQuery schema: diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml index be24c789..99944485 100644 --- a/openapi/v1/integrationUser.yaml +++ b/openapi/v1/integrationUser.yaml @@ -2952,21 +2952,6 @@ paths: * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000. * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query. - Embedding constraints: - - * UMAP - - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**. - - If exactly **1** UMAP dimension is provided, the request is invalid. - - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. - - * PCA - - Allowed number of components per cell: **0** (absent) or **≥ 2**. - - If exactly **1** PCA component is provided, the request is invalid. - - At most **100** PCA components are stored; components beyond 100 are ignored. - - Notes: - - “Dimensions/components” refer to the length of the embedding vector for each cell. - - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. in: query name: cellQuery schema: diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index 53c9e682..23234dc5 100644 --- a/openapi/v1/job.yaml +++ b/openapi/v1/job.yaml @@ -308,6 +308,22 @@ paths: "groupAccession": "GSF1234567" } ``` + + Embedding constraints: + + * UMAP + - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**. + - If exactly **1** UMAP dimension is provided, the request is invalid. + - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. + + * PCA + - Allowed number of components per cell: **0** (absent) or **≥ 2**. + - If exactly **1** PCA component is provided, the request is invalid. + - At most **100** PCA components are stored; components beyond 100 are ignored. + + Notes: + - “Dimensions/components” refer to the length of the embedding vector for each cell. + - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. operationId: startImportCells parameters: - description: "Load duplicate data: the data from the link(s) has already been\ @@ -351,6 +367,22 @@ paths: "groupAccession": "GSF1234567" } ``` + + Embedding constraints: + + * UMAP + - Allowed number of dimensions per cell: **0** (absent) or **≥ 2**. + - If exactly **1** UMAP dimension is provided, the request is invalid. + - At most **3** UMAP dimensions are stored; if more than 3 are provided, only the first 3 are kept and the rest are ignored. + + * PCA + - Allowed number of components per cell: **0** (absent) or **≥ 2**. + - If exactly **1** PCA component is provided, the request is invalid. + - At most **100** PCA components are stored; components beyond 100 are ignored. + + Notes: + - “Dimensions/components” refer to the length of the embedding vector for each cell. + - Ignoring excess dimensions/components does not cause an error; validation errors occur only when the number is exactly **1**. operationId: startImportCellsMultipart requestBody: content: From 7689658a8560d345fde8ea1d71882adbbbfdf6d7 Mon Sep 17 00:00:00 2001 From: oleg parkhomenko Date: Wed, 29 Oct 2025 13:49:46 +0400 Subject: [PATCH 4/4] Revert "fix build" This reverts commit 52785488156b3bbbd13e180fdf160230984a7889. --- Earthfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Earthfile b/Earthfile index 4ded0b2d..08980a08 100644 --- a/Earthfile +++ b/Earthfile @@ -84,7 +84,7 @@ r-api-client: RUN \ apt update && \ apt-get install -y \ - libssl-dev libcurl4-gnutls-dev curl && \ + libssl-dev libcurl4-gnutls-dev curl libcurl4t64:amd64=8.16.0-4 --allow-downgrades && \ Rscript requirements.R COPY +build/generated generated