mgnipy.emgapi_v2_client.api.analyses package

mgnipy.emgapi_v2_client.api.analyses package#

Contains endpoint functions for accessing the API

Submodules#

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations module#

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations.sync_detailed(accession, *, client)[source]#

Get MGnify analysis by accession, with annotations and downloadable files

MGnify analyses have annotations (taxonomic and functional assignments), and downloadable files

(outputs from the pipeline execution).

Parameters:
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[MGnifyAnalysisWithAnnotations]

Return type:

Response[MGnifyAnalysisWithAnnotations]

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations.sync(accession, *, client)[source]#

Get MGnify analysis by accession, with annotations and downloadable files

MGnify analyses have annotations (taxonomic and functional assignments), and downloadable files

(outputs from the pipeline execution).

Parameters:
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:

MGnifyAnalysisWithAnnotations

Return type:

MGnifyAnalysisWithAnnotations | None

async mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations.asyncio_detailed(accession, *, client)[source]#

Get MGnify analysis by accession, with annotations and downloadable files

MGnify analyses have annotations (taxonomic and functional assignments), and downloadable files

(outputs from the pipeline execution).

Parameters:
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[MGnifyAnalysisWithAnnotations]

Return type:

Response[MGnifyAnalysisWithAnnotations]

async mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations.asyncio(accession, *, client)[source]#

Get MGnify analysis by accession, with annotations and downloadable files

MGnify analyses have annotations (taxonomic and functional assignments), and downloadable files

(outputs from the pipeline execution).

Parameters:
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:

MGnifyAnalysisWithAnnotations

Return type:

MGnifyAnalysisWithAnnotations | None

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations_of_type module#

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations_of_type.sync_detailed(accession, annotation_type, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

Get a named set of annotations for a MGnify analysis by accession.

List the annotations of a given type for a MGnify analysis referred to by its accession.

Parameters:
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[NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation]

mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations_of_type.sync(accession, annotation_type, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

Get a named set of annotations for a MGnify analysis by accession.

List the annotations of a given type for a MGnify analysis referred to by its accession.

Parameters:
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:

NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation | None

async mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations_of_type.asyncio_detailed(accession, annotation_type, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

Get a named set of annotations for a MGnify analysis by accession.

List the annotations of a given type for a MGnify analysis referred to by its accession.

Parameters:
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[NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation]

async mgnipy.emgapi_v2_client.api.analyses.analysis_get_mgnify_analysis_with_annotations_of_type.asyncio(accession, annotation_type, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

Get a named set of annotations for a MGnify analysis by accession.

List the annotations of a given type for a MGnify analysis referred to by its accession.

Parameters:
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:

NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysisTypedAnnotation | None

mgnipy.emgapi_v2_client.api.analyses.get_mgnify_analysis module#

mgnipy.emgapi_v2_client.api.analyses.get_mgnify_analysis.sync_detailed(accession, *, client)[source]#

Get MGnify analysis by accession

MGnify analyses are accessioned with an MYGA-prefixed identifier and correspond to an individual Run

or Assembly analysed by a Pipeline.

Parameters:
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[MGnifyAnalysisDetail]

Return type:

Response[MGnifyAnalysisDetail]

mgnipy.emgapi_v2_client.api.analyses.get_mgnify_analysis.sync(accession, *, client)[source]#

Get MGnify analysis by accession

MGnify analyses are accessioned with an MYGA-prefixed identifier and correspond to an individual Run

or Assembly analysed by a Pipeline.

Parameters:
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:

MGnifyAnalysisDetail

Return type:

MGnifyAnalysisDetail | None

async mgnipy.emgapi_v2_client.api.analyses.get_mgnify_analysis.asyncio_detailed(accession, *, client)[source]#

Get MGnify analysis by accession

MGnify analyses are accessioned with an MYGA-prefixed identifier and correspond to an individual Run

or Assembly analysed by a Pipeline.

Parameters:
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[MGnifyAnalysisDetail]

Return type:

Response[MGnifyAnalysisDetail]

async mgnipy.emgapi_v2_client.api.analyses.get_mgnify_analysis.asyncio(accession, *, client)[source]#

Get MGnify analysis by accession

MGnify analyses are accessioned with an MYGA-prefixed identifier and correspond to an individual Run

or Assembly analysed by a Pipeline.

Parameters:
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:

MGnifyAnalysisDetail

Return type:

MGnifyAnalysisDetail | None

mgnipy.emgapi_v2_client.api.analyses.list_mgnify_analyses module#

mgnipy.emgapi_v2_client.api.analyses.list_mgnify_analyses.sync_detailed(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

List all analyses (MGYAs) available from MGnify

Each analysis is the result of a Pipeline execution on a reads dataset (either a raw read-run, or an

assembly).

Parameters:
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[NinjaPaginationResponseSchemaMGnifyAnalysisDetail]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysisDetail]

mgnipy.emgapi_v2_client.api.analyses.list_mgnify_analyses.sync(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

List all analyses (MGYAs) available from MGnify

Each analysis is the result of a Pipeline execution on a reads dataset (either a raw read-run, or an

assembly).

Parameters:
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:

NinjaPaginationResponseSchemaMGnifyAnalysisDetail

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysisDetail | None

async mgnipy.emgapi_v2_client.api.analyses.list_mgnify_analyses.asyncio_detailed(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

List all analyses (MGYAs) available from MGnify

Each analysis is the result of a Pipeline execution on a reads dataset (either a raw read-run, or an

assembly).

Parameters:
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[NinjaPaginationResponseSchemaMGnifyAnalysisDetail]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysisDetail]

async mgnipy.emgapi_v2_client.api.analyses.list_mgnify_analyses.asyncio(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)[source]#

List all analyses (MGYAs) available from MGnify

Each analysis is the result of a Pipeline execution on a reads dataset (either a raw read-run, or an

assembly).

Parameters:
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:

NinjaPaginationResponseSchemaMGnifyAnalysisDetail

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysisDetail | None

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