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gencove-client

API for Gencove REST service. Visit gencove.com and docs.gencove.com for more information.


To work with Insomnia, you can generate a Gencove API key by clicking here. Once you have the API key and have imported the project in Insomnia as a Request Collection, enter the key in Insomnia under Manage Environment.

Run in Insomnia

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: v2
  • Package version: 1.0.0
  • Generator version: 7.10.0-SNAPSHOT
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.7+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git)

Then import the package:

import gencove_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import gencove_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import gencove_client
from gencove_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://api.gencove.com/api/v2
# See configuration.py for a list of all supported configuration parameters.
configuration = gencove_client.Configuration(
    host = "https://api.gencove.com/api/v2"
)

# 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.

# Configure API key authorization: API key
configuration.api_key['API key'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['API key'] = 'Bearer'

# Configure API key authorization: JWT
configuration.api_key['JWT'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['JWT'] = 'Bearer'


# Enter a context with an instance of the API client
with gencove_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = gencove_client.BasespaceApi(api_client)
    data = gencove_client.BaseSpaceBioSamplesImport() # BaseSpaceBioSamplesImport |

    try:
        api_response = api_instance.basespace_biosamples_import_create(data)
        print("The response of BasespaceApi->basespace_biosamples_import_create:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling BasespaceApi->basespace_biosamples_import_create: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://api.gencove.com/api/v2

Class Method HTTP request Description
BasespaceApi basespace_biosamples_import_create POST /basespace-biosamples-import/
BasespaceApi basespace_project_biosamples_read GET /basespace-project-biosamples/{basespace_project_id}
BasespaceApi basespace_projects_autoimport_create POST /basespace-projects-autoimport/
BasespaceApi basespace_projects_autoimport_delete DELETE /basespace-projects-autoimport/{basespace_project_import_id}
BasespaceApi basespace_projects_autoimport_list GET /basespace-projects-autoimport/
BasespaceApi basespace_projects_import_create POST /basespace-projects-import/
BasespaceApi basespace_projects_list GET /basespace-projects/
BatchApi batches_read GET /batches/{batch_id}
BillingApi billing_portal_create POST /billing-portal/
ExitApi exit POST /project-share-exit/
ExplorerApi explorer_access_url_create POST /explorer-access-url/
ExplorerApi explorer_cost_reporting_list GET /explorer-cost-reporting/
ExplorerApi explorer_data_credentials_create POST /explorer-data-credentials/
ExplorerApi explorer_instances_inactivity_stop_create POST /explorer-instances-inactivity-stop/
ExplorerApi explorer_instances_inactivity_stop_organization_create POST /explorer-instances-inactivity-stop-organization/
ExplorerApi explorer_instances_inactivity_stop_organization_list GET /explorer-instances-inactivity-stop-organization/
ExplorerApi explorer_instances_list GET /explorer-instances/
ExplorerApi explorer_shell_session_credentials_create POST /explorer-shell-session-credentials/
ExplorerApi explorer_start_instances_create POST /explorer-start-instances/
ExplorerApi explorer_stop_instances_create POST /explorer-stop-instances/
FileApi file_types_list GET /file-types/
FileApi files_read GET /files/{file_id}.sha256
FirstmileApi firstmile_s3_role_element_create POST /firstmile-s3-role-element/
FirstmileApi firstmile_s3_role_element_read GET /firstmile-s3-role-element/
FirstmileApi firstmile_validate_illumina_samplesheet_create POST /firstmile-validate-illumina-samplesheet/
InvitationApi invitations_create POST /invitations/
InvitationApi invitations_delete DELETE /invitations/{invitation_id} Invitation details and management.
InvitationApi invitations_list GET /invitations/
InvitationApi invitations_token_read GET /invitations-token/{token}
InvitationApi invitations_token_update PATCH /invitations-token/{token}
JwtApi jwt_create_create POST /jwt-create/
JwtApi jwt_logout_create POST /jwt-logout/
JwtApi jwt_refresh_create POST /jwt-refresh/
JwtApi jwt_verify_create POST /jwt-verify/
MfaApi mfa_disable_delete DELETE /mfa-disable/
MfaApi mfa_setup_create POST /mfa-setup/
MfaApi mfa_status_list GET /mfa-status/
MfaApi mfa_validate_create POST /mfa-validate/
NotificationApi notifications_read GET /notifications/{notification_id}
OrganizationApi organization_monthly_usage_report_list GET /organization-monthly-usage-report/
OrganizationApi organization_partial_update PATCH /organization/
OrganizationApi organization_read GET /organization/
OrganizationApi organization_roles_read GET /organization-roles/{role_id}
OrganizationApi organization_users_create POST /organization-users/
OrganizationApi organization_users_list GET /organization-users/
OrganizationApi organization_users_partial_update PATCH /organization-users/{user_id}
PipelineApi pipeline_capabilities_read GET /pipeline-capabilities/{pipeline_capabilities_id}
PipelineApi pipeline_latest_read GET /pipeline-latest/
PipelineApi pipeline_list GET /pipeline/
PipelineApi pipeline_read GET /pipeline/{pipeline_id}
ProjectApi project_batch_types_read GET /project-batch-types/{project_id}
ProjectApi project_batches_create POST /project-batches/{project_id}
ProjectApi project_batches_read GET /project-batches/{project_id}
ProjectApi project_cancel_samples_create POST /project-cancel-samples/{project_id}
ProjectApi project_delete_samples_delete DELETE /project-delete-samples/{project_id}
ProjectApi project_hide_samples_create POST /project-hide-samples/{project_id}
ProjectApi project_merge_vcfs_create POST /project-merge-vcfs/{project_id}
ProjectApi project_merge_vcfs_read GET /project-merge-vcfs/{project_id}
ProjectApi project_organization_users_list GET /project-organization-users/{project_id}
ProjectApi project_qc_report_read GET /project-qc-report/{project_id}
ProjectApi project_qc_types_read GET /project-qc-types/{project_id}
ProjectApi project_quality_control_histogram_read GET /project-quality-control-histogram/{project_id}
ProjectApi project_restore_samples_create POST /project-restore-samples/{project_id}
ProjectApi project_roles_delete DELETE /project-roles/{role_id}
ProjectApi project_roles_read GET /project-roles/{role_id}
ProjectApi project_sample_manifests_create POST /project-sample-manifests/{project_id}
ProjectApi project_sample_manifests_read GET /project-sample-manifests/{project_id}
ProjectApi project_samples_create POST /project-samples/{project_id} Add samples to the project.
ProjectApi project_samples_import_create POST /project-samples-import/
ProjectApi project_samples_list GET /project-samples/{project_id}
ProjectApi project_share_revoke_create POST /project-share-revoke/{project_share_id}
ProjectApi project_shares_create POST /project-shares/
ProjectApi project_shares_list GET /project-shares/
ProjectApi project_shares_read GET /project-shares/{project_share_id}
ProjectApi project_stats_read GET /project-stats/{project_id}
ProjectApi project_subscription_details_delete DELETE /project-subscription-details/{subscription_id}
ProjectApi project_subscription_details_read GET /project-subscription-details/{subscription_id}
ProjectApi project_subscription_event_types_list GET /project-subscription-event-types/
ProjectApi project_subscription_notifications_list GET /project-subscription-notifications/{subscription_id}
ProjectApi project_subscription_secret_create POST /project-subscription-secret/{subscription_id} Set webhook secret for given subscription.
ProjectApi project_subscription_test_create POST /project-subscription-test/{subscription_id}
ProjectApi project_subscriptions_create POST /project-subscriptions/{project_id}
ProjectApi project_subscriptions_list GET /project-subscriptions/{project_id}
ProjectApi project_unhide_samples_create POST /project-unhide-samples/{project_id}
ProjectApi project_users_create POST /project-users/{project_id}
ProjectApi project_users_list GET /project-users/{project_id}
ProjectApi projects_create POST /projects/
ProjectApi projects_delete_delete DELETE /projects-delete/
ProjectApi projects_hide_create POST /projects-hide/
ProjectApi projects_list GET /projects/
ProjectApi projects_partial_update PATCH /projects/{project_id}
ProjectApi projects_read GET /projects/{project_id}
ProjectApi projects_unhide_create POST /projects-unhide/
RoleApi roles_list GET /roles/{applies_to}
S3Api s3_external_id_create POST /s3-external-id/
S3Api s3_external_id_read GET /s3-external-id/
S3Api s3_role_create POST /s3-role/
S3Api s3_role_delete DELETE /s3-role/
S3Api s3_role_read GET /s3-role/
S3Api s3_uri_autoimport_create POST /s3-uri-autoimport/
S3Api s3_uri_autoimport_delete DELETE /s3-uri-autoimport/{s3_uri_import_id}
S3Api s3_uri_autoimport_list GET /s3-uri-autoimport/
S3Api s3_uri_import_create POST /s3-uri-import/
SampleApi sample_ancestry_read GET /sample-ancestry/{sample_id}
SampleApi sample_manifests_csv_template_list GET /sample-manifests-csv-template/
SampleApi sample_manifests_read GET /sample-manifests/{sample_manifest_id}
SampleApi sample_manifests_xlsx_template_list GET /sample-manifests-xlsx-template/
SampleApi sample_metadata_create POST /sample-metadata/{sample_id}
SampleApi sample_metadata_read GET /sample-metadata/{sample_id}
SampleApi sample_quality_controls_read GET /sample-quality-controls/{sample_id}
SampleApi sample_restore_group_read GET /sample-restore-group/{restore_group_id}
SampleApi sample_sheet_list GET /sample-sheet/
SampleApi sample_stats_read GET /sample-stats/{sample_id}
SampleApi sample_statuses_read GET /sample-statuses/{sample_id}
SampleApi sample_trait_scores_read GET /sample-trait-scores/{sample_id}
SampleApi samples_read GET /samples/{sample_id}
SocialApi social_disconnect_create POST /social-disconnect/
SocialApi social_providers_list GET /social-providers/
SocialApi social_signup_create POST /social-signup/ Associate Social user with logged in Django user.
UploadApi upload_credentials_create POST /upload-credentials/
UploadApi uploads_delete_unassigned_create POST /uploads-delete-unassigned/
UploadApi uploads_list GET /uploads/
UploadApi uploads_post_data_create POST /uploads-post-data/
UploadApi uploads_presigned_post_data_create POST /uploads-presigned-post-data/
UploadApi uploads_read GET /uploads/{upload_id}
UploadApi uploads_url_create POST /uploads-url/
UserApi resend_activation POST /user-activate-resend/
UserApi reset_password POST /user-password-reset/
UserApi reset_password_confirm POST /user-password-reset-confirm/
UserApi set_password POST /user-password-set/
UserApi user_activate_create POST /user-activate/
UserApi user_api_keys_create POST /user-api-keys/
UserApi user_api_keys_list GET /user-api-keys/
UserApi user_api_keys_partial_update PATCH /user-api-keys/{api_key_id}
UserApi user_change_email_create POST /user-change-email/
UserApi user_config_read GET /user-config/
UserApi user_config_update PATCH /user-config/
UserApi user_partial_update PATCH /user/
UserApi user_projects_list GET /user-projects/{user_id}
UserApi user_read GET /user/
UserApi user_register_create POST /user-register/
UserApi user_update PUT /user/

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

JWT

  • Type: API key
  • API key parameter name: Authorization
  • Location: HTTP header

API key

  • Type: API key
  • API key parameter name: Authorization
  • Location: HTTP header

Author

info@gencove.com

About

Gencove API Python Client (auto-generated with openapi-generator-cli from https://api.gencove.com/api/v2/docs/?format=openapi)

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