Index

A

add_alias_prefix() (igvf_utils.connection.Connection method) add_to_set() (in module igvf_utils.utils) after_submit_file_cloud_upload() (igvf_utils.connection.Connection method) after_submit_hooks() (igvf_utils.connection.Connection method)

ALIAS_PROP_NAME (in module igvf_utils) auth (igvf_utils.connection.Connection property) AWARD (in module igvf_utils) AWARD_PROP_NAME (in module igvf_utils)

B

before_post_fastq_file() (igvf_utils.connection.Connection method) before_post_file() (igvf_utils.connection.Connection method)

before_submit_alias() (igvf_utils.connection.Connection method) before_submit_attachment() (igvf_utils.connection.Connection method) before_submit_hooks() (igvf_utils.connection.Connection method)

C

calculate_file_size() (in module igvf_utils.utils) calculate_md5sum() (in module igvf_utils.utils) check_dry_run() (igvf_utils.connection.Connection method)

clean_aliases() (in module igvf_utils.utils) Connection (class in igvf_utils.connection) create_subprocess() (in module igvf_utils.utils)

D

debug_logger (igvf_utils.connection.Connection attribute) (in module igvf_utils) DEBUG_LOGGER (in module igvf_utils.profiles)

DEBUG_LOGGER_NAME (in module igvf_utils) download() (igvf_utils.connection.Connection method) dry_run (igvf_utils.connection.Connection attribute)

E

err_context() (in module igvf_utils.utils) error_logger (igvf_utils.connection.Connection attribute) (in module igvf_utils)

ERROR_LOGGER (in module igvf_utils.profiles) ERROR_LOGGER_NAME (in module igvf_utils) extract_aws_upload_credentials() (igvf_utils.connection.Connection method)

F

FILE_PROFILE_ID (igvf_utils.profiles.Profiles attribute)

FILE_SIZE_PROP_NAME (igvf_utils.profiles.Profiles attribute)

G

gcp_transfer_from_aws() (igvf_utils.connection.Connection method) gcp_transfer_urllist() (igvf_utils.connection.Connection method) get() (igvf_utils.connection.Connection method) get_aliases() (igvf_utils.connection.Connection method) get_fastqfile_replicate_hash() (igvf_utils.connection.Connection method) get_fastqfiles_on_exp() (igvf_utils.connection.Connection method)

get_lookup_ids_from_payload() (igvf_utils.connection.Connection method) get_platforms_on_experiment() (igvf_utils.connection.Connection method) get_profile_from_id() (igvf_utils.profiles.Profiles method) get_profile_from_payload() (igvf_utils.connection.Connection method) get_record_id() (in module igvf_utils.utils) get_upload_credentials() (igvf_utils.connection.Connection method)

I

igvf_modes (igvf_utils.connection.Connection attribute) IGVF_MODES (in module igvf_utils) igvf_utils module igvf_utils.aws_storage module igvf_utils.connection module

igvf_utils.profiles module igvf_utils.utils module IGVFID_KEY (igvf_utils.connection.Connection attribute) indexing() (igvf_utils.connection.Connection method) is_jpg_or_tiff() (in module igvf_utils.utils)

L

LAB (in module igvf_utils) LAB_PREFIX (in module igvf_utils)

LAB_PROP_NAME (in module igvf_utils) LOG_DIR (in module igvf_utils.connection) log_error() (igvf_utils.connection.Connection method)

M

make_search_url() (igvf_utils.connection.Connection method) md5sum() (igvf_utils.aws_storage.S3Object method) MD5SUM_NAME_PROP_NAME (igvf_utils.profiles.Profiles attribute) module igvf_utils igvf_utils.aws_storage igvf_utils.connection igvf_utils.profiles igvf_utils.utils

O

orient_jpg() (in module igvf_utils.utils)

P

PATCH (igvf_utils.connection.Connection attribute) patch() (igvf_utils.connection.Connection method) POST (igvf_utils.connection.Connection attribute) post() (igvf_utils.connection.Connection method) post_document() (igvf_utils.connection.Connection method) post_logger (igvf_utils.connection.Connection attribute)

POST_LOGGER_NAME (in module igvf_utils) print_format_dict() (in module igvf_utils.utils) PROFILE_KEY (igvf_utils.connection.Connection attribute) Profiles (class in igvf_utils.profiles) profiles (igvf_utils.profiles.Profiles property) PROFILES_URL (in module igvf_utils) profiles_with_property() (igvf_utils.profiles.Profiles method)

R

regenerate_aws_upload_creds() (igvf_utils.connection.Connection method) remove_and_patch() (igvf_utils.connection.Connection method) remove_duplicate_associations() (igvf_utils.profiles.Profiles method)

remove_duplicate_objects() (in module igvf_utils.utils) remove_props() (igvf_utils.connection.Connection method) REQUEST_HEADERS_JSON (in module igvf_utils.utils)

S

s3_object_path() (igvf_utils.connection.Connection method) S3Object (class in igvf_utils.aws_storage) S3Upload (class in igvf_utils.aws_storage) search() (igvf_utils.connection.Connection method) set_attachment() (igvf_utils.connection.Connection method)

set_dry_run() (igvf_utils.connection.Connection method) set_live_run() (igvf_utils.connection.Connection method) set_submission() (igvf_utils.connection.Connection method) size() (igvf_utils.aws_storage.S3Object method) strip_alias_prefix() (in module igvf_utils.utils) SUBMITTED_FILE_PROP_NAME (igvf_utils.profiles.Profiles attribute)

T

TIMEOUT (in module igvf_utils)

truncate_long_strings_in_objects() (in module igvf_utils.utils)

U

UnknownProfile upload() (igvf_utils.aws_storage.S3Upload method)

upload_file() (igvf_utils.connection.Connection method) url_join() (in module igvf_utils.utils)