ecotaxa_py_client.TaxonomyTreeApi

All URIs are relative to https://ecotaxa.obs-vlfr.fr/api

Method	HTTP request	Description
add_taxon_in_central	PUT /taxon/central	Add Taxon In Central
get_taxon_in_central	GET /taxon/central/{taxon_id}	Get Taxon In Central
pull_taxa_update_from_central	GET /taxa/pull_from_central	Pull Taxa Update From Central
push_taxa_stats_in_central	GET /taxa/stats/push_to_central	Push Taxa Stats In Central
query_root_taxa	GET /taxa	Query Root Taxa
query_taxa	GET /taxon/{taxon_id}	Query Taxa
query_taxa_set	GET /taxon_set/query	Query Taxa Set
query_taxa_usage	GET /taxon/{taxon_id}/usage	Query Taxa Usage
reclassif_project_stats	GET /taxa/reclassification_history/{project_id}	Reclassif Project Stats
reclassif_stats	GET /taxa/reclassification_stats	Reclassif Stats
search_taxa	GET /taxon_set/search	Search Taxa
taxa_tree_status	GET /taxa/status	Taxa Tree Status

add_taxon_in_central

object add_taxon_in_central(name, parent_id, taxotype, creator_email, source_desc=source_desc, source_url=source_url)

Add Taxon In Central

Create a taxon on EcoTaxoServer. 🔒 Logged user must be manager (on any project) or application admin.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    name = 'Echinodermata' # str | The taxon/category verbatim name.
    parent_id = 2367 # int | It's not possible to create a root taxon.
    taxotype = 'P' # str | The taxon type, 'M' for Morpho or 'P' for Phylo.
    creator_email = 'user.creator@email.com' # str | The email of the taxo creator.
    source_desc = 'null' # str | The source description. (optional)
    source_url = 'http://www.google.fr/' # str | The source url. (optional)

    try:
        # Add Taxon In Central
        api_response = api_instance.add_taxon_in_central(name, parent_id, taxotype, creator_email, source_desc=source_desc, source_url=source_url)
        print("The response of TaxonomyTreeApi->add_taxon_in_central:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->add_taxon_in_central: %s\n" % e)

Parameters

Name	Type	Description	Notes
name	str	The taxon/category verbatim name.
parent_id	int	It's not possible to create a root taxon.
taxotype	str	The taxon type, 'M' for Morpho or 'P' for Phylo.
creator_email	str	The email of the taxo creator.
source_desc	str	The source description.	[optional]
source_url	str	The source url.	[optional]

Return type

object

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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get_taxon_in_central

List[TaxonCentral] get_taxon_in_central(taxon_id)

Get Taxon In Central

Return EcoTaxoServer full record for this taxon.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_central import TaxonCentral
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    taxon_id = 12876 # int | Internal, the unique numeric id of this taxon.

    try:
        # Get Taxon In Central
        api_response = api_instance.get_taxon_in_central(taxon_id)
        print("The response of TaxonomyTreeApi->get_taxon_in_central:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->get_taxon_in_central: %s\n" % e)

Parameters

Name	Type	Description	Notes
taxon_id	int	Internal, the unique numeric id of this taxon.

Return type

List[TaxonCentral]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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pull_taxa_update_from_central

object pull_taxa_update_from_central()

Pull Taxa Update From Central

Returns what changed in EcoTaxoServer managed tree and update local tree accordingly. i.e. : the number of inserts as nbr_inserts, updates as nbr_updates and errors as errors.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)

    try:
        # Pull Taxa Update From Central
        api_response = api_instance.pull_taxa_update_from_central()
        print("The response of TaxonomyTreeApi->pull_taxa_update_from_central:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->pull_taxa_update_from_central: %s\n" % e)

Parameters

This endpoint does not need any parameter.

Return type

object

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-

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push_taxa_stats_in_central

object push_taxa_stats_in_central()

Push Taxa Stats In Central

Push present instance stats, into EcoTaxoServer.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)

    try:
        # Push Taxa Stats In Central
        api_response = api_instance.push_taxa_stats_in_central()
        print("The response of TaxonomyTreeApi->push_taxa_stats_in_central:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->push_taxa_stats_in_central: %s\n" % e)

Parameters

This endpoint does not need any parameter.

Return type

object

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-

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query_root_taxa

List[TaxonModel] query_root_taxa()

Query Root Taxa

Return all taxa with no parent.

Example

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_model import TaxonModel
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)


# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)

    try:
        # Query Root Taxa
        api_response = api_instance.query_root_taxa()
        print("The response of TaxonomyTreeApi->query_root_taxa:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->query_root_taxa: %s\n" % e)

Parameters

This endpoint does not need any parameter.

Return type

List[TaxonModel]

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-

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query_taxa

TaxonModel query_taxa(taxon_id)

Query Taxa

Returns information about the taxon corresponding to the given id, including its lineage.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_model import TaxonModel
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    taxon_id = 12876 # int | Internal, the unique numeric id of this taxon.

    try:
        # Query Taxa
        api_response = api_instance.query_taxa(taxon_id)
        print("The response of TaxonomyTreeApi->query_taxa:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->query_taxa: %s\n" % e)

Parameters

Name	Type	Description	Notes
taxon_id	int	Internal, the unique numeric id of this taxon.

Return type

TaxonModel

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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query_taxa_set

List[TaxonModel] query_taxa_set(ids)

Query Taxa Set

Returns information about several taxa, including their lineage.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_model import TaxonModel
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    ids = '1:2:3' # str | The separator between numbers is arbitrary non-digit, e.g. ':', '|' or ','.

    try:
        # Query Taxa Set
        api_response = api_instance.query_taxa_set(ids)
        print("The response of TaxonomyTreeApi->query_taxa_set:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->query_taxa_set: %s\n" % e)

Parameters

Name	Type	Description	Notes
ids	str	The separator between numbers is arbitrary non-digit, e.g. ':', '	' or ','.

Return type

List[TaxonModel]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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query_taxa_usage

List[TaxonUsageModel] query_taxa_usage(taxon_id)

Query Taxa Usage

Where a given taxon is used. Only validated uses are returned.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_usage_model import TaxonUsageModel
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    taxon_id = 12876 # int | Internal, the unique numeric id of this taxon.

    try:
        # Query Taxa Usage
        api_response = api_instance.query_taxa_usage(taxon_id)
        print("The response of TaxonomyTreeApi->query_taxa_usage:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->query_taxa_usage: %s\n" % e)

Parameters

Name	Type	Description	Notes
taxon_id	int	Internal, the unique numeric id of this taxon.

Return type

List[TaxonUsageModel]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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reclassif_project_stats

List[object] reclassif_project_stats(project_id)

Reclassif Project Stats

Dig into reclassification logs and return the associations (source → target) for previous reclassifications.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    project_id = 1 # int | Internal, numeric id of the project.

    try:
        # Reclassif Project Stats
        api_response = api_instance.reclassif_project_stats(project_id)
        print("The response of TaxonomyTreeApi->reclassif_project_stats:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->reclassif_project_stats: %s\n" % e)

Parameters

Name	Type	Description	Notes
project_id	int	Internal, numeric id of the project.

Return type

List[object]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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reclassif_stats

List[TaxonModel] reclassif_stats(taxa_ids)

Reclassif Stats

Dig into reclassification logs and, for each input category id, determine the most chosen target category, excluding the advised one. By convention, if nothing relevant is found, the input category itself is returned. So one can expect that the returned list has the same size as the required one.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxon_model import TaxonModel
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    taxa_ids = '12876' # str | String containing the list of one or more taxa id separated by non-num char.

    try:
        # Reclassif Stats
        api_response = api_instance.reclassif_stats(taxa_ids)
        print("The response of TaxonomyTreeApi->reclassif_stats:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->reclassif_stats: %s\n" % e)

Parameters

Name	Type	Description	Notes
taxa_ids	str	String containing the list of one or more taxa id separated by non-num char.

Return type

List[TaxonModel]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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search_taxa

List[TaxaSearchRsp] search_taxa(query, project_id=project_id)

Search Taxa

Search for taxa by name. Queries can be 'small', i.e. of length ﹤3 and even zero-length. 🔓 For a public, unauthenticated call : - zero-length and small queries always return nothing. - otherwise, a full search is done and results are returned in alphabetical order. 🔒 For an authenticated call : - zero-length queries: return the MRU list in full. - small queries: the MRU list is searched, so that taxa in the recent list are returned, if matching. - otherwise, a full search is done. Results are ordered so that taxa in the project list are in first, and are signalled as such in the response.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxa_search_rsp import TaxaSearchRsp
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)
    query = 'Ban' # str | Use this query for matching returned taxa names.
    project_id = 1 # int | Internal, numeric id of the project. (optional)

    try:
        # Search Taxa
        api_response = api_instance.search_taxa(query, project_id=project_id)
        print("The response of TaxonomyTreeApi->search_taxa:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->search_taxa: %s\n" % e)

Parameters

Name	Type	Description	Notes
query	str	Use this query for matching returned taxa names.
project_id	int	Internal, numeric id of the project.	[optional]

Return type

List[TaxaSearchRsp]

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-
422	Validation Error	-

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taxa_tree_status

TaxonomyTreeStatus taxa_tree_status()

Taxa Tree Status

Return the status of taxonomy tree w/r to freshness.

Example

OAuth Authentication (BearerOrCookieAuth):

import ecotaxa_py_client
from ecotaxa_py_client.models.taxonomy_tree_status import TaxonomyTreeStatus
from ecotaxa_py_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://ecotaxa.obs-vlfr.fr/api
# See configuration.py for a list of all supported configuration parameters.
configuration = ecotaxa_py_client.Configuration(
    host = "https://ecotaxa.obs-vlfr.fr/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

configuration.access_token = os.environ["ACCESS_TOKEN"]

# Enter a context with an instance of the API client
with ecotaxa_py_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ecotaxa_py_client.TaxonomyTreeApi(api_client)

    try:
        # Taxa Tree Status
        api_response = api_instance.taxa_tree_status()
        print("The response of TaxonomyTreeApi->taxa_tree_status:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling TaxonomyTreeApi->taxa_tree_status: %s\n" % e)

Parameters

This endpoint does not need any parameter.

Return type

TaxonomyTreeStatus

Authorization

BearerOrCookieAuth

HTTP request headers

Content-Type: Not defined
Accept: application/json

HTTP response details

Status code	Description	Response headers
200	Successful Response	-

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Files

TaxonomyTreeApi.md

Latest commit

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TaxonomyTreeApi.md

File metadata and controls

ecotaxa_py_client.TaxonomyTreeApi

add_taxon_in_central

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

get_taxon_in_central

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

pull_taxa_update_from_central

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

push_taxa_stats_in_central

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

query_root_taxa

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

query_taxa

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

query_taxa_set

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

query_taxa_usage

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

reclassif_project_stats

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

reclassif_stats

Example

Parameters

Return type

Authorization

HTTP request headers

HTTP response details

search_taxa

Example

Parameters