PySirius.CompoundsApi

All URIs are relative to http://localhost:8080

Method	HTTP request	Description
add_compounds	POST /api/projects/{projectId}/compounds	Import Compounds and its contained features.
delete_compound	DELETE /api/projects/{projectId}/compounds/{compoundId}	Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space.
get_compound	GET /api/projects/{projectId}/compounds/{compoundId}	Get compound (group of ion identities) with the given identifier from the specified project-space.
get_compounds	GET /api/projects/{projectId}/compounds	List of all available compounds (group of ion identities) in the given project-space.
get_compounds_paged	GET /api/projects/{projectId}/compounds/page	Page of available compounds (group of ion identities) in the given project-space.

add_compounds

List[Compound] add_compounds(project_id, compound_import, profile=profile, opt_fields=opt_fields, opt_fields_features=opt_fields_features)

Import Compounds and its contained features.

Import Compounds and its contained features. Compounds and Features must not exist in the project. Otherwise, they will exist twice.

Example

import PySirius
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.compound import Compound
from PySirius.models.compound_import import CompoundImport
from PySirius.models.compound_opt_field import CompoundOptField
from PySirius.models.instrument_profile import InstrumentProfile
from PySirius.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
    host = "http://localhost:8080"
)


# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = PySirius.CompoundsApi(api_client)
    project_id = 'project_id_example' # str | project-space to import into.
    compound_import = [PySirius.CompoundImport()] # List[CompoundImport] | the compound data to be imported
    profile = PySirius.InstrumentProfile() # InstrumentProfile | profile describing the instrument used to measure the data. Used to merge spectra. (optional)
    opt_fields = ["none"] # List[CompoundOptField] | set of optional fields to be included. Use 'none' to override defaults. (optional) (default to ["none"])
    opt_fields_features = ["none"] # List[AlignedFeatureOptField] | set of optional fields of the nested features to be included. Use 'none' to override defaults. (optional) (default to ["none"])

    try:
        # Import Compounds and its contained features.
        api_response = api_instance.add_compounds(project_id, compound_import, profile=profile, opt_fields=opt_fields, opt_fields_features=opt_fields_features)
        print("The response of CompoundsApi->add_compounds:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling CompoundsApi->add_compounds: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	str	project-space to import into.
compound_import	List[CompoundImport]	the compound data to be imported
profile	InstrumentProfile	profile describing the instrument used to measure the data. Used to merge spectra.	[optional]
opt_fields	List[CompoundOptField]	set of optional fields to be included. Use 'none' to override defaults.	[optional] [default to ["none"]]
opt_fields_features	List[AlignedFeatureOptField]	set of optional fields of the nested features to be included. Use 'none' to override defaults.	[optional] [default to ["none"]]

Return type

List[Compound]

Authorization

No authorization required

HTTP request headers

Content-Type: application/json
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	the Compounds that have been imported with specified optional fields	-

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delete_compound

delete_compound(project_id, compound_id)

Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space.

Example

import PySirius
from PySirius.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
    host = "http://localhost:8080"
)


# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = PySirius.CompoundsApi(api_client)
    project_id = 'project_id_example' # str | project-space to delete from.
    compound_id = 'compound_id_example' # str | identifier of the compound to delete.

    try:
        # Delete compound (group of ion identities) with the given identifier (and the included features) from the  specified project-space.
        api_instance.delete_compound(project_id, compound_id)
    except Exception as e:
        print("Exception when calling CompoundsApi->delete_compound: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	str	project-space to delete from.
compound_id	str	identifier of the compound to delete.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: Not defined

HTTP response details

Status code	Description	Response headers
200	OK	-

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get_compound

Compound get_compound(project_id, compound_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)

Get compound (group of ion identities) with the given identifier from the specified project-space.

Example

import PySirius
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.compound import Compound
from PySirius.models.compound_opt_field import CompoundOptField
from PySirius.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
    host = "http://localhost:8080"
)


# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = PySirius.CompoundsApi(api_client)
    project_id = 'project_id_example' # str | project-space to read from.
    compound_id = 'compound_id_example' # str | identifier of the compound (group of ion identities) to access.
    ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (optional) (default to False)
    opt_fields = ["none"] # List[CompoundOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
    opt_fields_features = ["none"] # List[AlignedFeatureOptField] |  (optional) (default to ["none"])

    try:
        # Get compound (group of ion identities) with the given identifier from the specified project-space.
        api_response = api_instance.get_compound(project_id, compound_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)
        print("The response of CompoundsApi->get_compound:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling CompoundsApi->get_compound: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	str	project-space to read from.
compound_id	str	identifier of the compound (group of ion identities) to access.
ms_data_search_prepared	bool	Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.	[optional] [default to False]
opt_fields	List[CompoundOptField]	set of optional fields to be included. Use 'none' only to override defaults.	[optional] [default to ["none"]]
opt_fields_features	List[AlignedFeatureOptField]		[optional] [default to ["none"]]

Return type

Compound

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Compounds with additional optional fields (if specified).	-

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get_compounds

List[Compound] get_compounds(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)

List of all available compounds (group of ion identities) in the given project-space.

Example

import PySirius
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.compound import Compound
from PySirius.models.compound_opt_field import CompoundOptField
from PySirius.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
    host = "http://localhost:8080"
)


# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = PySirius.CompoundsApi(api_client)
    project_id = 'project_id_example' # str | project-space to read from.
    ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (optional) (default to False)
    opt_fields = ["none"] # List[CompoundOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
    opt_fields_features = ["none"] # List[AlignedFeatureOptField] |  (optional) (default to ["none"])

    try:
        # List of all available compounds (group of ion identities) in the given project-space.
        api_response = api_instance.get_compounds(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)
        print("The response of CompoundsApi->get_compounds:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling CompoundsApi->get_compounds: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	str	project-space to read from.
ms_data_search_prepared	bool	Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.	[optional] [default to False]
opt_fields	List[CompoundOptField]	set of optional fields to be included. Use 'none' only to override defaults.	[optional] [default to ["none"]]
opt_fields_features	List[AlignedFeatureOptField]		[optional] [default to ["none"]]

Return type

List[Compound]

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Compounds with additional optional fields (if specified).	-

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get_compounds_paged

PagedModelCompound get_compounds_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)

Page of available compounds (group of ion identities) in the given project-space.

Example

import PySirius
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.compound_opt_field import CompoundOptField
from PySirius.models.paged_model_compound import PagedModelCompound
from PySirius.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
    host = "http://localhost:8080"
)


# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = PySirius.CompoundsApi(api_client)
    project_id = 'project_id_example' # str | project-space to read from.
    page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
    size = 20 # int | The size of the page to be returned (optional) (default to 20)
    sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
    ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast                             Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch                             peak assignments and reference spectra. (optional) (default to False)
    opt_fields = ["none"] # List[CompoundOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
    opt_fields_features = ["none"] # List[AlignedFeatureOptField] |  (optional) (default to ["none"])

    try:
        # Page of available compounds (group of ion identities) in the given project-space.
        api_response = api_instance.get_compounds_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features)
        print("The response of CompoundsApi->get_compounds_paged:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling CompoundsApi->get_compounds_paged: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	str	project-space to read from.
page	int	Zero-based page index (0..N)	[optional] [default to 0]
size	int	The size of the page to be returned	[optional] [default to 20]
sort	List[str]	Sorting criteria in the format: property,(asc	desc). Default sort order is ascending. Multiple sort criteria are supported.
ms_data_search_prepared	bool	Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.	[optional] [default to False]
opt_fields	List[CompoundOptField]	set of optional fields to be included. Use 'none' only to override defaults.	[optional] [default to ["none"]]
opt_fields_features	List[AlignedFeatureOptField]		[optional] [default to ["none"]]

Return type

PagedModelCompound

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Compounds with additional optional fields (if specified).	-

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PySirius.CompoundsApi

add_compounds

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

delete_compound

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compound

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compounds

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compounds_paged

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

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PySirius.CompoundsApi

add_compounds

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

delete_compound

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compound

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compounds

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_compounds_paged

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details