Index

A

abort_analysis() (in module wrapica.project_analysis) add_data_to_bundle() (in module wrapica.bundle) add_pipeline_file() (in module wrapica.project_pipelines) add_pipeline_to_bundle() (in module wrapica.bundle)

add_project_data_to_bundle() (in module wrapica.bundle) add_tag_to_analysis() (in module wrapica.project_analysis) add_tag_to_data_object() (in module wrapica.project_data) analysis_step_to_dict() (in module wrapica.project_analysis)

C

check_file_exists() (in module wrapica.project_data) check_folder_exists() (in module wrapica.project_data) check_project_has_data_sharing_enabled() (in module wrapica.project) check_uri_exists() (in module wrapica.project_data) coerce_analysis_id_or_user_reference_to_analysis_id() (in module wrapica.project_analysis) coerce_analysis_id_or_user_reference_to_analysis_obj() (in module wrapica.project_analysis) coerce_analysis_storage_id_or_size_to_analysis_storage() (in module wrapica.project_pipelines) coerce_bundle_id_or_name_to_bundle_id() (in module wrapica.bundle) coerce_bundle_id_or_name_to_bundle_obj() (in module wrapica.bundle) coerce_data_id_icav2_uri_or_path_to_project_data_obj() (in module wrapica.project_data) coerce_data_id_or_icav2_uri_to_project_data_obj() (in module wrapica.project_data) coerce_data_id_or_uri_to_project_data_obj() (in module wrapica.project_data) coerce_data_id_path_or_icav2_uri_to_data_obj() (in module wrapica.data) coerce_data_id_uri_or_path_to_project_data_obj() (in module wrapica.project_data) coerce_pipeline_id_or_code_to_pipeline_id() (in module wrapica.pipelines) coerce_pipeline_id_or_code_to_pipeline_obj() (in module wrapica.pipelines) coerce_pipeline_id_or_code_to_project_pipeline_obj() (in module wrapica.project_pipelines) coerce_project_id_or_name_to_project_id() (in module wrapica.project) coerce_project_id_or_name_to_project_obj() (in module wrapica.project) coerce_region_id_or_city_name_to_region_id() (in module wrapica.region) coerce_region_id_or_city_name_to_region_obj() (in module wrapica.region) coerce_user_id_or_name_to_user_id() (in module wrapica.user) coerce_user_id_or_name_to_user_obj() (in module wrapica.user) convert_data_obj_to_icav2_uri() (in module wrapica.data) convert_icav2_uri_to_data_obj() (in module wrapica.data) (in module wrapica.project_data)

convert_icav2_uri_to_project_data_obj() (in module wrapica.project_data) convert_icav2_uri_to_s3_uri() (in module wrapica.storage_configuration) convert_icav2_uris_to_data_ids_from_cwl_input_json() (in module wrapica.project_pipelines) convert_project_data_obj_to_icav2_uri() (in module wrapica.project_data) convert_project_data_obj_to_s3_uri() (in module wrapica.storage_configuration) convert_project_data_obj_to_uri() (in module wrapica.project_data) convert_project_id_and_data_path_to_icav2_uri() (in module wrapica.project_data) convert_project_id_and_data_path_to_uri() (in module wrapica.project_data) convert_s3_uri_to_icav2_uri() (in module wrapica.storage_configuration) convert_s3_uri_to_project_data_obj() (in module wrapica.storage_configuration) convert_uri_to_project_data_obj() (in module wrapica.project_data) convert_uris_to_data_ids_from_cwl_input_json() (in module wrapica.project_pipelines) create_blank_params_xml() (in module wrapica.project_pipelines) create_cwl_input_json_analysis_obj() (in module wrapica.project_pipelines) create_cwl_project_pipeline() (in module wrapica.project_pipelines) create_cwl_workflow_from_zip() (in module wrapica.project_pipelines) create_data_in_project() (in module wrapica.project_data) create_download_url() (in module wrapica.project_data) create_download_urls() (in module wrapica.project_data) create_file_in_project() (in module wrapica.project_data) create_file_with_upload_url() (in module wrapica.project_data) create_folder_in_project() (in module wrapica.project_data) create_nextflow_pipeline_from_nf_core_zip() (in module wrapica.project_pipelines) create_nextflow_pipeline_from_zip() (in module wrapica.project_pipelines) create_nextflow_project_pipeline() (in module wrapica.project_pipelines) create_params_xml() (in module wrapica.project_pipelines)

D

delete_pipeline_file() (in module wrapica.project_pipelines) delete_project_data() (in module wrapica.project_data) deprecate_bundle() (in module wrapica.bundle)

download_pipeline_file() (in module wrapica.pipelines) download_pipeline_to_directory() (in module wrapica.pipelines) download_pipeline_to_zip() (in module wrapica.pipelines)

F

filter_bundle_data_to_top_level_only() (in module wrapica.bundle) filter_bundles() (in module wrapica.bundle)

find_project_data_bulk() (in module wrapica.project_data) find_project_data_recursively() (in module wrapica.project_data)

G

generate_empty_bundle() (in module wrapica.bundle) get_analysis_input_object_from_analysis_input_code() (in module wrapica.project_analysis) get_analysis_log_from_analysis_step() (in module wrapica.project_analysis) get_analysis_obj_from_analysis_id() (in module wrapica.project_analysis) get_analysis_obj_from_user_reference() (in module wrapica.project_analysis) get_analysis_output_object_from_analysis_output_code() (in module wrapica.project_analysis) get_analysis_steps() (in module wrapica.project_analysis) get_analysis_storage_from_analysis_storage_id() (in module wrapica.project_pipelines) get_analysis_storage_from_analysis_storage_size() (in module wrapica.project_pipelines) get_analysis_storage_id_from_analysis_storage_size() (in module wrapica.project_pipelines) get_analysis_usage() (in module wrapica.project_analysis) get_aws_credentials_access_for_project_folder() (in module wrapica.project_data) get_bundle_obj_from_bundle_id() (in module wrapica.bundle) get_bundle_obj_from_bundle_name() (in module wrapica.bundle) get_credentials_access_for_project_folder() (in module wrapica.project_data) get_cwl_analysis_input_json() (in module wrapica.project_analysis) get_cwl_analysis_output_json() (in module wrapica.project_analysis) get_cwl_obj_from_pipeline_id() (in module wrapica.pipelines) get_cwl_outputs_json_from_analysis_id() (in module wrapica.project_analysis) get_data_obj_from_data_id() (in module wrapica.data) get_default_analysis_storage_id_from_project_pipeline() (in module wrapica.project_pipelines) get_default_analysis_storage_obj_from_project_pipeline() (in module wrapica.project_pipelines) get_default_region() (in module wrapica.region) get_file_by_file_name_from_project_data_list() (in module wrapica.project_data) get_job() (in module wrapica.job) get_outputs_object_from_analysis_id() (in module wrapica.project_analysis) get_owning_project_id() (in module wrapica.data) get_pipeline_obj_from_pipeline_code() (in module wrapica.pipelines) get_pipeline_obj_from_pipeline_id() (in module wrapica.pipelines) get_project_analysis_inputs() (in module wrapica.project_analysis) get_project_data_file_id_from_project_id_and_path() (in module wrapica.project_data) get_project_data_folder_id_from_project_id_and_path() (in module wrapica.project_data) get_project_data_id_from_project_id_and_path() (in module wrapica.project_data)

get_project_data_obj_by_id() (in module wrapica.project_data) get_project_data_obj_from_data_id() (in module wrapica.data) get_project_data_obj_from_project_id_and_path() (in module wrapica.project_data) get_project_data_path_by_id() (in module wrapica.project_data) get_project_data_upload_url() (in module wrapica.project_data) get_project_id() (in module wrapica.project) get_project_id_by_s3_key_prefix() (in module wrapica.storage_configuration) get_project_id_from_project_name() (in module wrapica.project) get_project_name_from_project_id() (in module wrapica.project) get_project_obj_from_project_id() (in module wrapica.project) get_project_obj_from_project_name() (in module wrapica.project) get_project_pipeline_configuration_parameters() (in module wrapica.project_pipelines) get_project_pipeline_description_from_pipeline_id() (in module wrapica.project_pipelines) get_project_pipeline_id_from_pipeline_code() (in module wrapica.project_pipelines) get_project_pipeline_input_parameters() (in module wrapica.project_pipelines) get_project_pipeline_obj() (in module wrapica.project_pipelines) get_project_pipeline_obj_from_pipeline_code() (in module wrapica.project_pipelines) get_project_to_storage_configuration_mapping_list() (in module wrapica.storage_configuration) get_rclone_credentials_access_for_project_folder() (in module wrapica.project_data) get_region_from_bundle_id() (in module wrapica.region) get_region_obj_from_city_name() (in module wrapica.region) get_region_obj_from_project_id() (in module wrapica.region) get_region_obj_from_region_id() (in module wrapica.region) get_regions() (in module wrapica.region) get_relative_path_from_credentials_prefix() (in module wrapica.storage_credentials) get_s3_key_prefix_by_project_id() (in module wrapica.storage_configuration) get_storage_configuration_list() (in module wrapica.storage_configuration) get_storage_credential_id_from_s3_uri() (in module wrapica.storage_credentials) get_tenant_id_for_user() (in module wrapica.user) get_user_id_from_configuration() (in module wrapica.user) get_user_name_from_user_id() (in module wrapica.user) get_user_obj_from_user_id() (in module wrapica.user) get_user_obj_from_user_name() (in module wrapica.user)

I

is_data_id_format() (in module wrapica.project_data) is_file_id_format() (in module wrapica.project_data)

is_folder_id_format() (in module wrapica.project_data) is_pipeline_in_project() (in module wrapica.project_pipelines)

L

launch_cwl_workflow() (in module wrapica.project_pipelines) launch_nextflow_workflow() (in module wrapica.project_pipelines) link_bundle_to_project() (in module wrapica.bundle) list_all_pipelines() (in module wrapica.pipelines) list_analyses() (in module wrapica.project_analysis) list_bundles_in_project() (in module wrapica.bundle)

list_data_in_bundle() (in module wrapica.bundle) list_pipeline_files() (in module wrapica.pipelines) list_pipelines_in_bundle() (in module wrapica.bundle) list_project_data_non_recursively() (in module wrapica.project_data) list_project_pipelines() (in module wrapica.project_pipelines) list_projects() (in module wrapica.project) list_projects_with_pipeline() (in module wrapica.project_pipelines)

M

module wrapica.bundle wrapica.data wrapica.job wrapica.pipelines wrapica.project wrapica.project_analysis wrapica.project_data wrapica.project_pipelines wrapica.region wrapica.storage_configuration wrapica.storage_credentials wrapica.user

move_project_data() (in module wrapica.project_data)

P

presign_cwl_directory() (in module wrapica.project_data) presign_cwl_directory_with_external_data_mounts() (in module wrapica.project_data)

presign_folder() (in module wrapica.project_data) project_data_copy_batch_handler() (in module wrapica.project_data)

R

read_icav2_file_contents() (in module wrapica.project_data) read_icav2_file_contents_to_string() (in module wrapica.project_data)

release_bundle() (in module wrapica.bundle) release_project_pipeline() (in module wrapica.project_pipelines)

S

set_default_region() (in module wrapica.region)

U

unlink_bundle_from_project() (in module wrapica.bundle) unpack_icav2_uri() (in module wrapica.project_data) unpack_s3_uri() (in module wrapica.storage_configuration)

unpack_uri() (in module wrapica.project_data) update_analysis_obj() (in module wrapica.project_analysis) update_pipeline_file() (in module wrapica.project_pipelines)

W

wait_for_job_completion() (in module wrapica.job) wrapica.bundle module wrapica.data module wrapica.job module wrapica.pipelines module wrapica.project module wrapica.project_analysis module

wrapica.project_data module wrapica.project_pipelines module wrapica.region module wrapica.storage_configuration module wrapica.storage_credentials module wrapica.user module write_analysis_step_logs() (in module wrapica.project_analysis) write_icav2_file_contents() (in module wrapica.project_data)