DataImportJobsApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| StartImportAFile | POST /api/v1/jobs/import/file | Import file as an attachment |
| StartImportCells | POST /api/v1/jobs/import/cells | Import a group of cell data objects from a TSV file |
| StartImportExpression | POST /api/v1/jobs/import/expression | Import any tabular data from TSV or GCT files |
| StartImportFlowCytometry | POST /api/v1/jobs/import/flow-cytometry | Import flow-cytometry data and metadata from FACS and TSV files |
| StartImportLibraries | POST /api/v1/jobs/import/libraries | Import a group of library metadata objects from a TSV file |
| StartImportPreparations | POST /api/v1/jobs/import/preparations | Import a group of preparation metadata objects from a TSV file |
| StartImportSamples | POST /api/v1/jobs/import/samples | Import a group of sample metadata objects from a TSV file |
| StartImportStudy | POST /api/v1/jobs/import/study | Import study metadata from a TSV file |
| StartImportVariant | POST /api/v1/jobs/import/variant | Import variation data and metadata from VCF and TSV files |
StartImportAFile¶
Info StartImportAFile(body = var.body)
Import file as an attachment
In order to import a file as an attachment to a study, please fill in the following fields: * source - The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link. * dataLink - a link to a file to import as an attachment. The file will be associated with a study and will be searchable by its name and metadata. * metadataLink - an optional URL of a metadata file to be used as the original metadata for the created objects. The file must contain a single record describing the uploaded attachment. * studyAccession - an accession of a study the file will be associated with. * dataClass - file data class with the following possible values: Bulk transcriptomics, Single-cell transcriptomics, Differential abundance (FC, pval, etc.), Pathway analysis, Proteomics, Single-cell proteomics, Metabolomics, Lipidomics, Epigenomics, DNA methylation, Chemoinformatics, Imaging features, Gene panel data, Biomarker data, Physical measures, Blood counts, Other body fluid counts, Long-read sequencing (Nanopore, PacBio), Flow Cytometry (FCS), Spatial transcriptomics, Phenomics, Copy number alterations, Microbiome / Metagenomics, Immune repertoire, Genetic screens (CRISPR / RNAi), Cell imaging, Document, Other. When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"accession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import file as an attachment
#
# prepare function argument(s)
var_body <- ImportAFileRequest$new("dataLink_example", "studyAccession_example", "dataClass_example", "S3", "metadataLink_example") # ImportAFileRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportAFile(body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportAFile(body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| body | ImportAFileRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportCells¶
Info StartImportCells(allow_dups = FALSE, body = var.body)
Import a group of cell data objects from a TSV file
The endpoint initiates a job to import cell data and creates a Cell Group to manage it. When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" } Embedding constraints: * UMAP/t-SNE - Allowed number of dimensions per cell: 0 (absent) or ≥ 2. - If exactly 1 UMAP/t-SNE dimension is provided, the request is invalid. - At most 3 UMAP/t-SNE 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.
Example¶
library(odmApi)
# Import a group of cell data objects from a TSV file
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportCellsRequest$new("dataLink_example") # ImportCellsRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportCells(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportCells(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportCellsRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportExpression¶
Info StartImportExpression(allow_dups = FALSE, body = var.body)
Import any tabular data from TSV or GCT files
Data This operation necessitates the URL of a tabular data file, which must be either in TSV or GCT 1.2 format. Consult the user guide for a comprehensive understanding of the file content requirements. The endpoint is capable of handling uploads of any data type, which can be detailed in the parameters section, not only Gene Expression data. ## Metadata It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file. ## Data file format * Format: Gene Cluster Text (GCT) and Tab-separated format (TSV), attribute names and record values are separated with tabs (U+0009), lines are separated with CRLF sequence (U+000D U+000A) * Extension: .zip, .gz, .br, .lz4 are supported, treated as archives and get decompressed * Header: the first line is treated as table header that contains attribute names * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the \"pipe\" | (U+007C) separator. Values are trimmed of whitespace before parsing, and a literal | (U+007C) character may be escaped by repeating it twice. * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data.¶
Example¶
library(odmApi)
# Import any tabular data from TSV or GCT files
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportExpressionSignalRunRequest$new("dataLink_example", "S3", "metadataLink_example", "templateId_example", "previousVersion_example", 123, "dataClass_example", "measurementSeparator_example") # ImportExpressionSignalRunRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportExpression(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportExpression(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportExpressionSignalRunRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportFlowCytometry¶
Info StartImportFlowCytometry(allow_dups = FALSE, body = var.body)
Import flow-cytometry data and metadata from FACS and TSV files
This operation necessitates the URL of a gated flow cytometry data file, which must be in FACS format. Consult the user guide for a comprehensive understanding of the file content requirements. For flow cytometry data in FCS format use expression endpoint. When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import flow-cytometry data and metadata from FACS and TSV files
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- startImportVariant_request$new("dataLink_example", "S3", "metadataLink_example", "templateId_example", "previousVersion_example") # StartImportVariantRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportFlowCytometry(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportFlowCytometry(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | StartImportVariantRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportLibraries¶
Info StartImportLibraries(allow_dups = FALSE, body = var.body)
Import a group of library metadata objects from a TSV file
When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import a group of library metadata objects from a TSV file
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportMetadataRequest$new("metadataLink_example", "S3", "templateId_example") # ImportMetadataRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportLibraries(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportLibraries(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportMetadataRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json, multipart/form-data
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportPreparations¶
Info StartImportPreparations(allow_dups = FALSE, body = var.body)
Import a group of preparation metadata objects from a TSV file
When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import a group of preparation metadata objects from a TSV file
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportMetadataRequest$new("metadataLink_example", "S3", "templateId_example") # ImportMetadataRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportPreparations(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportPreparations(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportMetadataRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportSamples¶
Info StartImportSamples(allow_dups = FALSE, body = var.body)
Import a group of sample metadata objects from a TSV file
When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import a group of sample metadata objects from a TSV file
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportMetadataRequest$new("metadataLink_example", "S3", "templateId_example") # ImportMetadataRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportSamples(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportSamples(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportMetadataRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportStudy¶
Info StartImportStudy(allow_dups = FALSE, body = var.body)
Import study metadata from a TSV file
When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import study metadata from a TSV file
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- ImportMetadataRequest$new("metadataLink_example", "S3", "templateId_example") # ImportMetadataRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportStudy(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportStudy(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | ImportMetadataRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |
StartImportVariant¶
Info StartImportVariant(allow_dups = FALSE, body = var.body)
Import variation data and metadata from VCF and TSV files
When job finishes successfully the following result object can be obtained using GET /job/{id}/output request: { \"groupAccession\": \"GSF1234567\" }
Example¶
library(odmApi)
# Import variation data and metadata from VCF and TSV files
#
# prepare function argument(s)
var_allow_dups <- FALSE # character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for **testing purposes**, you need to load this data again. (Optional)
var_body <- startImportVariant_request$new("dataLink_example", "S3", "metadataLink_example", "templateId_example", "previousVersion_example") # StartImportVariantRequest | (Optional)
api_instance <- DataImportJobsApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$StartImportVariant(allow_dups = var_allow_dups, body = var_bodydata_file = "result.txt")
result <- api_instance$StartImportVariant(allow_dups = var_allow_dups, body = var_body)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| allow_dups | character | Load duplicate data: the data from the link(s) has already been previously loaded into ODM, and for testing purposes, you need to load this data again. | [optional] [default to FALSE] |
| body | StartImportVariantRequest | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | successful operation | - |