odm_api.DataImportJobsApi¶

All URIs are relative to http://localhost

Method	HTTP request	Description
start_import_a_file	POST /api/v1/jobs/import/file	Import file as an attachment
start_import_cells	POST /api/v1/jobs/import/cells	Import a group of cell data objects from a TSV file
start_import_expression	POST /api/v1/jobs/import/expression	Import any tabular data from TSV or GCT files
start_import_flow_cytometry	POST /api/v1/jobs/import/flow-cytometry	Import flow-cytometry data and metadata from FACS and TSV files
start_import_libraries	POST /api/v1/jobs/import/libraries	Import a group of library metadata objects from a TSV file
start_import_preparations	POST /api/v1/jobs/import/preparations	Import a group of preparation metadata objects from a TSV file
start_import_samples	POST /api/v1/jobs/import/samples	Import a group of sample metadata objects from a TSV file
start_import_study	POST /api/v1/jobs/import/study	Import study metadata from a TSV file
start_import_variant	POST /api/v1/jobs/import/variant	Import variation data and metadata from VCF and TSV files

start_import_a_file¶

Info start_import_a_file(body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_a_file_request import ImportAFileRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    body = odm_api.ImportAFileRequest() # ImportAFileRequest |  (optional)

    try:
        # Import file as an attachment
        api_response = api_instance.start_import_a_file(body=body)
        print("The response of DataImportJobsApi->start_import_a_file:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_a_file: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
body	ImportAFileRequest		[optional]

Return type¶

Info

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	-

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start_import_cells¶

Info start_import_cells(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_cells_request import ImportCellsRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportCellsRequest() # ImportCellsRequest |  (optional)

    try:
        # Import a group of cell data objects from a TSV file
        api_response = api_instance.start_import_cells(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_cells:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_cells: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

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start_import_expression¶

Info start_import_expression(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_expression_signal_run_request import ImportExpressionSignalRunRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportExpressionSignalRunRequest() # ImportExpressionSignalRunRequest |  (optional)

    try:
        # Import any tabular data from TSV or GCT files
        api_response = api_instance.start_import_expression(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_expression:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_expression: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

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start_import_flow_cytometry¶

Info start_import_flow_cytometry(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.info import Info
from odm_api.models.start_import_variant_request import StartImportVariantRequest
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.StartImportVariantRequest() # StartImportVariantRequest |  (optional)

    try:
        # Import flow-cytometry data and metadata from FACS and TSV files
        api_response = api_instance.start_import_flow_cytometry(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_flow_cytometry:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_flow_cytometry: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

start_import_libraries¶

Info start_import_libraries(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_metadata_request import ImportMetadataRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportMetadataRequest() # ImportMetadataRequest |  (optional)

    try:
        # Import a group of library metadata objects from a TSV file
        api_response = api_instance.start_import_libraries(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_libraries:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_libraries: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

start_import_preparations¶

Info start_import_preparations(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_metadata_request import ImportMetadataRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportMetadataRequest() # ImportMetadataRequest |  (optional)

    try:
        # Import a group of preparation metadata objects from a TSV file
        api_response = api_instance.start_import_preparations(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_preparations:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_preparations: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

start_import_samples¶

Info start_import_samples(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_metadata_request import ImportMetadataRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportMetadataRequest() # ImportMetadataRequest |  (optional)

    try:
        # Import a group of sample metadata objects from a TSV file
        api_response = api_instance.start_import_samples(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_samples:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_samples: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

start_import_study¶

Info start_import_study(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.import_metadata_request import ImportMetadataRequest
from odm_api.models.info import Info
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.ImportMetadataRequest() # ImportMetadataRequest |  (optional)

    try:
        # Import study metadata from a TSV file
        api_response = api_instance.start_import_study(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_study:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_study: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

[Back to top] [Back to API list] [Back to Model list] [Back to README]

start_import_variant¶

Info start_import_variant(allow_dups=allow_dups, body=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¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.info import Info
from odm_api.models.start_import_variant_request import StartImportVariantRequest
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.DataImportJobsApi(api_client)
    allow_dups = False # bool | 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 = odm_api.StartImportVariantRequest() # StartImportVariantRequest |  (optional)

    try:
        # Import variation data and metadata from VCF and TSV files
        api_response = api_instance.start_import_variant(allow_dups=allow_dups, body=body)
        print("The response of DataImportJobsApi->start_import_variant:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling DataImportJobsApi->start_import_variant: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
allow_dups	bool	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¶

Info

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	-

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