mgnipy.emgapi_v2_client.api.samples package

Contains endpoint functions for accessing the API

Submodules

mgnipy.emgapi_v2_client.api.samples.get_mgnify_sample module

mgnipy.emgapi_v2_client.api.samples.get_mgnify_sample.sync_detailed(accession, *, client)

Get the detail of a single sample analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• accession (str )

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[MGnifySampleDetail]

Return type:

Response[MGnifySampleDetail]

mgnipy.emgapi_v2_client.api.samples.get_mgnify_sample.sync(accession, *, client)

Get the detail of a single sample analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• accession (str )

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

MGnifySampleDetail

Return type:

MGnifySampleDetail | None

async mgnipy.emgapi_v2_client.api.samples.get_mgnify_sample.asyncio_detailed(accession, *, client)

Get the detail of a single sample analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• accession (str )

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[MGnifySampleDetail]

Return type:

Response[MGnifySampleDetail]

async mgnipy.emgapi_v2_client.api.samples.get_mgnify_sample.asyncio(accession, *, client)

Get the detail of a single sample analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• accession (str )

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

MGnifySampleDetail

Return type:

MGnifySampleDetail | None

mgnipy.emgapi_v2_client.api.samples.list_mgnify_samples module

mgnipy.emgapi_v2_client.api.samples.list_mgnify_samples.sync_detailed(*, client, biome_lineage=<mgnipy.emgapi_v2_client.types.Unset object>, search=<mgnipy.emgapi_v2_client.types.Unset object>, order=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all samples analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• biome_lineage (None | str | Unset) – The lineage to match, including all descendant biomes

• search (None | str | Unset) – Search within sample titles and accessions

• order (ListMgnifySamplesOrderType0 | None | Unset)

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaMGnifySample]

Return type:

Response[NinjaPaginationResponseSchemaMGnifySample]

mgnipy.emgapi_v2_client.api.samples.list_mgnify_samples.sync(*, client, biome_lineage=<mgnipy.emgapi_v2_client.types.Unset object>, search=<mgnipy.emgapi_v2_client.types.Unset object>, order=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all samples analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• biome_lineage (None | str | Unset) – The lineage to match, including all descendant biomes

• search (None | str | Unset) – Search within sample titles and accessions

• order (ListMgnifySamplesOrderType0 | None | Unset)

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaMGnifySample

Return type:

NinjaPaginationResponseSchemaMGnifySample | None

async mgnipy.emgapi_v2_client.api.samples.list_mgnify_samples.asyncio_detailed(*, client, biome_lineage=<mgnipy.emgapi_v2_client.types.Unset object>, search=<mgnipy.emgapi_v2_client.types.Unset object>, order=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all samples analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• biome_lineage (None | str | Unset) – The lineage to match, including all descendant biomes

• search (None | str | Unset) – Search within sample titles and accessions

• order (ListMgnifySamplesOrderType0 | None | Unset)

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaMGnifySample]

Return type:

Response[NinjaPaginationResponseSchemaMGnifySample]

async mgnipy.emgapi_v2_client.api.samples.list_mgnify_samples.asyncio(*, client, biome_lineage=<mgnipy.emgapi_v2_client.types.Unset object>, search=<mgnipy.emgapi_v2_client.types.Unset object>, order=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all samples analysed by MGnify

MGnify samples inherit directly from samples (or BioSamples) in ENA.

Parameters:

• biome_lineage (None | str | Unset) – The lineage to match, including all descendant biomes

• search (None | str | Unset) – Search within sample titles and accessions

• order (ListMgnifySamplesOrderType0 | None | Unset)

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaMGnifySample

Return type:

NinjaPaginationResponseSchemaMGnifySample | None

mgnipy.emgapi_v2_client.api.samples.list_sample_runs module

mgnipy.emgapi_v2_client.api.samples.list_sample_runs.sync_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List ENA Runs associated with this sample

Samples may be associated with one or more ENA runs. ENA runs ‘Hold raw read files and sequencing

methods’

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAnalysedRun]

Return type:

Response[NinjaPaginationResponseSchemaAnalysedRun]

mgnipy.emgapi_v2_client.api.samples.list_sample_runs.sync(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List ENA Runs associated with this sample

Samples may be associated with one or more ENA runs. ENA runs ‘Hold raw read files and sequencing

methods’

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAnalysedRun

Return type:

NinjaPaginationResponseSchemaAnalysedRun | None

async mgnipy.emgapi_v2_client.api.samples.list_sample_runs.asyncio_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List ENA Runs associated with this sample

Samples may be associated with one or more ENA runs. ENA runs ‘Hold raw read files and sequencing

methods’

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAnalysedRun]

Return type:

Response[NinjaPaginationResponseSchemaAnalysedRun]

async mgnipy.emgapi_v2_client.api.samples.list_sample_runs.asyncio(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List ENA Runs associated with this sample

Samples may be associated with one or more ENA runs. ENA runs ‘Hold raw read files and sequencing

methods’

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAnalysedRun

Return type:

NinjaPaginationResponseSchemaAnalysedRun | None