mgnipy.emgapi_v2_client.api.publications package

Contains endpoint functions for accessing the API

Submodules

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication module

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication.sync_detailed(pubmed_id, *, client)

Get the detail of a single publication

Get detailed information about a publication, including associated studies.

Parameters:

• pubmed_id (int )

• 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[MGnifyPublicationDetail]

Return type:

Response[MGnifyPublicationDetail]

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication.sync(pubmed_id, *, client)

Get the detail of a single publication

Get detailed information about a publication, including associated studies.

Parameters:

• pubmed_id (int )

• 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:

MGnifyPublicationDetail

Return type:

MGnifyPublicationDetail | None

async mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication.asyncio_detailed(pubmed_id, *, client)

Get the detail of a single publication

Get detailed information about a publication, including associated studies.

Parameters:

• pubmed_id (int )

• 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[MGnifyPublicationDetail]

Return type:

Response[MGnifyPublicationDetail]

async mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication.asyncio(pubmed_id, *, client)

Get the detail of a single publication

Get detailed information about a publication, including associated studies.

Parameters:

• pubmed_id (int )

• 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:

MGnifyPublicationDetail

Return type:

MGnifyPublicationDetail | None

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication_annotations module

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication_annotations.sync_detailed(pubmed_id, *, client)

Get any full-text annotations associated with the publication

Full-text annotations are retrieved from Europe PMC, text mined for relevant metagenomic metadata

terms

Parameters:

• pubmed_id (int )

• 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[PublicationAnnotations]

Return type:

Response[PublicationAnnotations]

mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication_annotations.sync(pubmed_id, *, client)

Get any full-text annotations associated with the publication

Full-text annotations are retrieved from Europe PMC, text mined for relevant metagenomic metadata

terms

Parameters:

• pubmed_id (int )

• 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:

PublicationAnnotations

Return type:

PublicationAnnotations | None

async mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication_annotations.asyncio_detailed(pubmed_id, *, client)

Get any full-text annotations associated with the publication

Full-text annotations are retrieved from Europe PMC, text mined for relevant metagenomic metadata

terms

Parameters:

• pubmed_id (int )

• 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[PublicationAnnotations]

Return type:

Response[PublicationAnnotations]

async mgnipy.emgapi_v2_client.api.publications.get_mgnify_publication_annotations.asyncio(pubmed_id, *, client)

Get any full-text annotations associated with the publication

Full-text annotations are retrieved from Europe PMC, text mined for relevant metagenomic metadata

terms

Parameters:

• pubmed_id (int )

• 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:

PublicationAnnotations

Return type:

PublicationAnnotations | None

mgnipy.emgapi_v2_client.api.publications.list_mgnify_publications module

mgnipy.emgapi_v2_client.api.publications.list_mgnify_publications.sync_detailed(*, client, order=<mgnipy.emgapi_v2_client.types.Unset object>, published_after=<mgnipy.emgapi_v2_client.types.Unset object>, published_before=<mgnipy.emgapi_v2_client.types.Unset object>, title=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all publications

List all publications in the MGnify database.

Parameters:

• order (ListMgnifyPublicationsOrderType0 | None | Unset)

• published_after (int | None | Unset) – Filter by minimum publication year

• published_before (int | None | Unset) – Filter by maximum publication year

• title (None | str | Unset) – Search within publication titles

• 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[NinjaPaginationResponseSchemaMGnifyPublication]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyPublication]

mgnipy.emgapi_v2_client.api.publications.list_mgnify_publications.sync(*, client, order=<mgnipy.emgapi_v2_client.types.Unset object>, published_after=<mgnipy.emgapi_v2_client.types.Unset object>, published_before=<mgnipy.emgapi_v2_client.types.Unset object>, title=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all publications

List all publications in the MGnify database.

Parameters:

• order (ListMgnifyPublicationsOrderType0 | None | Unset)

• published_after (int | None | Unset) – Filter by minimum publication year

• published_before (int | None | Unset) – Filter by maximum publication year

• title (None | str | Unset) – Search within publication titles

• 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:

NinjaPaginationResponseSchemaMGnifyPublication

Return type:

NinjaPaginationResponseSchemaMGnifyPublication | None

async mgnipy.emgapi_v2_client.api.publications.list_mgnify_publications.asyncio_detailed(*, client, order=<mgnipy.emgapi_v2_client.types.Unset object>, published_after=<mgnipy.emgapi_v2_client.types.Unset object>, published_before=<mgnipy.emgapi_v2_client.types.Unset object>, title=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all publications

List all publications in the MGnify database.

Parameters:

• order (ListMgnifyPublicationsOrderType0 | None | Unset)

• published_after (int | None | Unset) – Filter by minimum publication year

• published_before (int | None | Unset) – Filter by maximum publication year

• title (None | str | Unset) – Search within publication titles

• 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[NinjaPaginationResponseSchemaMGnifyPublication]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyPublication]

async mgnipy.emgapi_v2_client.api.publications.list_mgnify_publications.asyncio(*, client, order=<mgnipy.emgapi_v2_client.types.Unset object>, published_after=<mgnipy.emgapi_v2_client.types.Unset object>, published_before=<mgnipy.emgapi_v2_client.types.Unset object>, title=<mgnipy.emgapi_v2_client.types.Unset object>, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all publications

List all publications in the MGnify database.

Parameters:

• order (ListMgnifyPublicationsOrderType0 | None | Unset)

• published_after (int | None | Unset) – Filter by minimum publication year

• published_before (int | None | Unset) – Filter by maximum publication year

• title (None | str | Unset) – Search within publication titles

• 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:

NinjaPaginationResponseSchemaMGnifyPublication

Return type:

NinjaPaginationResponseSchemaMGnifyPublication | None