ENCODE Utils
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Connection class
Transferring files to GCP
registration
eu_add_controlled_by
eu_check_not_posted
eu_create_gcp_url_list
eu_generate_upload_creds.py
eu_get_aliases
eu_get_accessions
eu_get_replicate_fastq_encffs
eu_get_replicate_numbers
eu_report_fastq_content_errors
eu_s3_to_gcp.py
encode_utils.aws_storage
encode_utils.connection
encode_utils
encode_utils.profiles
encode_utils.transfer_to_gcp.py
encode_utils.utils
encode_utils.tests.test_utils
encode_utils.tests.test_connection
ENCODE Utils
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U
A
add_alias_prefix() (encode_utils.connection.Connection method)
add_to_set() (in module encode_utils.utils)
after_submit_file_cloud_upload() (encode_utils.connection.Connection method)
after_submit_hooks() (encode_utils.connection.Connection method)
ALIAS_PROP_NAME (in module encode_utils)
auth (encode_utils.connection.Connection attribute)
AWARD (in module encode_utils)
AWARD_PROP_NAME (in module encode_utils)
AwsCredentialsMissing
B
before_post_fastq_file() (encode_utils.connection.Connection method)
before_post_file() (encode_utils.connection.Connection method)
before_submit_alias() (encode_utils.connection.Connection method)
before_submit_attachment() (encode_utils.connection.Connection method)
before_submit_hooks() (encode_utils.connection.Connection method)
C
calculate_file_size() (in module encode_utils.utils)
calculate_md5sum() (in module encode_utils.utils)
check_dry_run() (encode_utils.connection.Connection method)
clean_aliases() (in module encode_utils.utils)
Connection (class in encode_utils.connection)
create_subprocess() (in module encode_utils.utils)
D
dcc_modes (encode_utils.connection.Connection attribute)
DCC_MODES (in module encode_utils)
debug_logger (encode_utils.connection.Connection attribute)
(in module encode_utils)
DEBUG_LOGGER (in module encode_utils.profiles)
DEBUG_LOGGER_NAME (in module encode_utils)
does_lib_replicate_exist() (in module encode_utils.utils)
download() (encode_utils.connection.Connection method)
dry_run (encode_utils.connection.Connection attribute)
E
ENCID_KEY (encode_utils.connection.Connection attribute)
encode_utils (module)
encode_utils.aws_storage (module)
encode_utils.connection (module)
encode_utils.profiles (module)
encode_utils.transfer_to_gcp (module)
encode_utils.utils (module)
err_context() (in module encode_utils.utils)
error_logger (encode_utils.connection.Connection attribute)
(in module encode_utils)
ERROR_LOGGER (in module encode_utils.profiles)
ERROR_LOGGER_NAME (in module encode_utils)
extract_aws_upload_credentials() (encode_utils.connection.Connection method)
F
FILE_PROFILE_ID (encode_utils.profiles.Profiles attribute)
FILE_SIZE_PROP_NAME (encode_utils.profiles.Profiles attribute)
from_s3() (encode_utils.transfer_to_gcp.Transfer method)
from_urllist() (encode_utils.transfer_to_gcp.Transfer method)
G
gcp_transfer_from_aws() (encode_utils.connection.Connection method)
gcp_transfer_urllist() (encode_utils.connection.Connection method)
get() (encode_utils.connection.Connection method)
get_aliases() (encode_utils.connection.Connection method)
get_biosample_type() (encode_utils.connection.Connection method)
get_experiments_with_biosample() (encode_utils.connection.Connection method)
get_fastqfile_replicate_hash() (encode_utils.connection.Connection method)
get_fastqfiles_on_exp() (encode_utils.connection.Connection method)
get_lookup_ids_from_payload() (encode_utils.connection.Connection method)
get_platforms_on_experiment() (encode_utils.connection.Connection method)
get_profile_from_id() (encode_utils.profiles.Profiles method)
get_profile_from_payload() (encode_utils.connection.Connection method)
get_record_id() (in module encode_utils.utils)
get_transfer_status() (encode_utils.transfer_to_gcp.Transfer method)
get_transfers_from_job() (encode_utils.transfer_to_gcp.Transfer method)
get_upload_credentials() (encode_utils.connection.Connection method)
I
indexing() (encode_utils.connection.Connection method)
is_jpg_or_tiff() (in module encode_utils.utils)
L
LAB (in module encode_utils)
LAB_PREFIX (in module encode_utils)
LAB_PROP_NAME (in module encode_utils)
LOG_DIR (in module encode_utils.connection)
log_error() (encode_utils.connection.Connection method)
M
make_search_url() (encode_utils.connection.Connection method)
md5sum() (encode_utils.aws_storage.S3Object method)
MD5SUM_NAME_PROP_NAME (encode_utils.profiles.Profiles attribute)
O
orient_jpg() (in module encode_utils.utils)
P
PATCH (encode_utils.connection.Connection attribute)
patch() (encode_utils.connection.Connection method)
POST (encode_utils.connection.Connection attribute)
post() (encode_utils.connection.Connection method)
post_document() (encode_utils.connection.Connection method)
post_logger (encode_utils.connection.Connection attribute)
POST_LOGGER_NAME (in module encode_utils)
print_format_dict() (in module encode_utils.utils)
PROFILE_KEY (encode_utils.connection.Connection attribute)
Profiles (class in encode_utils.profiles)
profiles (encode_utils.profiles.Profiles attribute)
PROFILES_URL (in module encode_utils)
profiles_with_property() (encode_utils.profiles.Profiles method)
R
regenerate_aws_upload_creds() (encode_utils.connection.Connection method)
remove_and_patch() (encode_utils.connection.Connection method)
remove_duplicate_associations() (encode_utils.profiles.Profiles method)
remove_duplicate_objects() (in module encode_utils.utils)
remove_props() (encode_utils.connection.Connection method)
REQUEST_HEADERS_JSON (in module encode_utils.utils)
S
s3_object_path() (encode_utils.connection.Connection method)
S3Object (class in encode_utils.aws_storage)
S3Upload (class in encode_utils.aws_storage)
search() (encode_utils.connection.Connection method)
send() (encode_utils.connection.Connection method)
set_attachment() (encode_utils.connection.Connection method)
set_dry_run() (encode_utils.connection.Connection method)
set_live_run() (encode_utils.connection.Connection method)
set_submission() (encode_utils.connection.Connection method)
size() (encode_utils.aws_storage.S3Object method)
strip_alias_prefix() (in module encode_utils.utils)
SUBMITTED_FILE_PROP_NAME (encode_utils.profiles.Profiles attribute)
T
TIMEOUT (in module encode_utils)
Transfer (class in encode_utils.transfer_to_gcp)
truncate_long_strings_in_objects() (in module encode_utils.utils)
U
UnknownProfile
upload() (encode_utils.aws_storage.S3Upload method)
upload_file() (encode_utils.connection.Connection method)
url_join() (in module encode_utils.utils)
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