mgnipy.emgapi_v2_client.api.studies package

Contains endpoint functions for accessing the API

Submodules

mgnipy.emgapi_v2_client.api.studies.get_mgnify_study module

mgnipy.emgapi_v2_client.api.studies.get_mgnify_study.sync_detailed(accession, *, client)

Get the detail of a single study analysed by MGnify

MGnify studies inherit directly from studies (or projects) 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[MGnifyStudyDetail]

Return type:

Response[MGnifyStudyDetail]

mgnipy.emgapi_v2_client.api.studies.get_mgnify_study.sync(accession, *, client)

Get the detail of a single study analysed by MGnify

MGnify studies inherit directly from studies (or projects) 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:

MGnifyStudyDetail

Return type:

MGnifyStudyDetail | None

async mgnipy.emgapi_v2_client.api.studies.get_mgnify_study.asyncio_detailed(accession, *, client)

Get the detail of a single study analysed by MGnify

MGnify studies inherit directly from studies (or projects) 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[MGnifyStudyDetail]

Return type:

Response[MGnifyStudyDetail]

async mgnipy.emgapi_v2_client.api.studies.get_mgnify_study.asyncio(accession, *, client)

Get the detail of a single study analysed by MGnify

MGnify studies inherit directly from studies (or projects) 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:

MGnifyStudyDetail

Return type:

MGnifyStudyDetail | None

mgnipy.emgapi_v2_client.api.studies.get_super_study module

mgnipy.emgapi_v2_client.api.studies.get_super_study.sync_detailed(slug, *, client)

Get the detail of a single Super Study

A Super Study is a collection of MGnify Studies all related to a single large initiative. They may

also reference Genome Catalogues that were assembled from the Studies or as part of the Super Study initiative.

Parameters:

• slug (str )

• 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[SuperStudyDetail]

Return type:

Response[SuperStudyDetail]

mgnipy.emgapi_v2_client.api.studies.get_super_study.sync(slug, *, client)

Get the detail of a single Super Study

A Super Study is a collection of MGnify Studies all related to a single large initiative. They may

also reference Genome Catalogues that were assembled from the Studies or as part of the Super Study initiative.

Parameters:

• slug (str )

• 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:

SuperStudyDetail

Return type:

SuperStudyDetail | None

async mgnipy.emgapi_v2_client.api.studies.get_super_study.asyncio_detailed(slug, *, client)

Get the detail of a single Super Study

A Super Study is a collection of MGnify Studies all related to a single large initiative. They may

also reference Genome Catalogues that were assembled from the Studies or as part of the Super Study initiative.

Parameters:

• slug (str )

• 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[SuperStudyDetail]

Return type:

Response[SuperStudyDetail]

async mgnipy.emgapi_v2_client.api.studies.get_super_study.asyncio(slug, *, client)

Get the detail of a single Super Study

A Super Study is a collection of MGnify Studies all related to a single large initiative. They may

also reference Genome Catalogues that were assembled from the Studies or as part of the Super Study initiative.

Parameters:

• slug (str )

• 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:

SuperStudyDetail

Return type:

SuperStudyDetail | None

mgnipy.emgapi_v2_client.api.studies.list_mgnify_studies module

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

List all studies analysed by MGnify

MGnify studies inherit directly from studies (or projects) in ENA.

Parameters:

• order (ListMgnifyStudiesOrderType0 | None | Unset)

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

• has_analyses_from_pipeline (None | PipelineVersions | Unset) – If set, will only show studies with analyses from the specified MGnify pipeline version

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

• 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[NinjaPaginationResponseSchemaMGnifyStudy]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyStudy]

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

List all studies analysed by MGnify

MGnify studies inherit directly from studies (or projects) in ENA.

Parameters:

• order (ListMgnifyStudiesOrderType0 | None | Unset)

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

• has_analyses_from_pipeline (None | PipelineVersions | Unset) – If set, will only show studies with analyses from the specified MGnify pipeline version

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

• 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:

NinjaPaginationResponseSchemaMGnifyStudy

Return type:

NinjaPaginationResponseSchemaMGnifyStudy | None

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

List all studies analysed by MGnify

MGnify studies inherit directly from studies (or projects) in ENA.

Parameters:

• order (ListMgnifyStudiesOrderType0 | None | Unset)

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

• has_analyses_from_pipeline (None | PipelineVersions | Unset) – If set, will only show studies with analyses from the specified MGnify pipeline version

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

• 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[NinjaPaginationResponseSchemaMGnifyStudy]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyStudy]

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

List all studies analysed by MGnify

MGnify studies inherit directly from studies (or projects) in ENA.

Parameters:

• order (ListMgnifyStudiesOrderType0 | None | Unset)

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

• has_analyses_from_pipeline (None | PipelineVersions | Unset) – If set, will only show studies with analyses from the specified MGnify pipeline version

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

• 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:

NinjaPaginationResponseSchemaMGnifyStudy

Return type:

NinjaPaginationResponseSchemaMGnifyStudy | None

mgnipy.emgapi_v2_client.api.studies.list_mgnify_study_analyses module

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

List MGnify Analyses associated with this Study

MGnify analyses correspond to an individual Run or Assembly within this study,analysed by a MGnify

Pipelione.

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[NinjaPaginationResponseSchemaMGnifyAnalysis]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

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

List MGnify Analyses associated with this Study

MGnify analyses correspond to an individual Run or Assembly within this study,analysed by a MGnify

Pipelione.

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:

NinjaPaginationResponseSchemaMGnifyAnalysis

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysis | None

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

List MGnify Analyses associated with this Study

MGnify analyses correspond to an individual Run or Assembly within this study,analysed by a MGnify

Pipelione.

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[NinjaPaginationResponseSchemaMGnifyAnalysis]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

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

List MGnify Analyses associated with this Study

MGnify analyses correspond to an individual Run or Assembly within this study,analysed by a MGnify

Pipelione.

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:

NinjaPaginationResponseSchemaMGnifyAnalysis

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysis | None

mgnipy.emgapi_v2_client.api.studies.list_mgnify_study_publications module

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

List Publications associated with this Study

List all publications associated with this study.

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[NinjaPaginationResponseSchemaMGnifyPublication]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyPublication]

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

List Publications associated with this Study

List all publications associated with this study.

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:

NinjaPaginationResponseSchemaMGnifyPublication

Return type:

NinjaPaginationResponseSchemaMGnifyPublication | None

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

List Publications associated with this Study

List all publications associated with this study.

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[NinjaPaginationResponseSchemaMGnifyPublication]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyPublication]

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

List Publications associated with this Study

List all publications associated with this study.

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:

NinjaPaginationResponseSchemaMGnifyPublication

Return type:

NinjaPaginationResponseSchemaMGnifyPublication | None

mgnipy.emgapi_v2_client.api.studies.list_mgnify_study_samples module

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

List Samples associated with this Study

List all samples associated with this study.

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[NinjaPaginationResponseSchemaMGnifySampleWithMetadata]

Return type:

Response[NinjaPaginationResponseSchemaMGnifySampleWithMetadata]

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

List Samples associated with this Study

List all samples associated with this study.

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:

NinjaPaginationResponseSchemaMGnifySampleWithMetadata

Return type:

NinjaPaginationResponseSchemaMGnifySampleWithMetadata | None

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

List Samples associated with this Study

List all samples associated with this study.

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[NinjaPaginationResponseSchemaMGnifySampleWithMetadata]

Return type:

Response[NinjaPaginationResponseSchemaMGnifySampleWithMetadata]

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

List Samples associated with this Study

List all samples associated with this study.

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:

NinjaPaginationResponseSchemaMGnifySampleWithMetadata

Return type:

NinjaPaginationResponseSchemaMGnifySampleWithMetadata | None

mgnipy.emgapi_v2_client.api.studies.list_super_studies module

mgnipy.emgapi_v2_client.api.studies.list_super_studies.sync_detailed(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all Super Studies

Super Studies are collections of MGnify Studies associated with major initiatives.

Parameters:

• 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[NinjaPaginationResponseSchemaSuperStudy]

Return type:

Response[NinjaPaginationResponseSchemaSuperStudy]

mgnipy.emgapi_v2_client.api.studies.list_super_studies.sync(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all Super Studies

Super Studies are collections of MGnify Studies associated with major initiatives.

Parameters:

• 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:

NinjaPaginationResponseSchemaSuperStudy

Return type:

NinjaPaginationResponseSchemaSuperStudy | None

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

List all Super Studies

Super Studies are collections of MGnify Studies associated with major initiatives.

Parameters:

• 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[NinjaPaginationResponseSchemaSuperStudy]

Return type:

Response[NinjaPaginationResponseSchemaSuperStudy]

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

List all Super Studies

Super Studies are collections of MGnify Studies associated with major initiatives.

Parameters:

• 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:

NinjaPaginationResponseSchemaSuperStudy

Return type:

NinjaPaginationResponseSchemaSuperStudy | None