SubmitCGAP
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Overview
Installing Prerequisites
Installing SubmitCGAP
Using SubmitCGAP
Implementation of submit_cgap
Using rclone instead (experimental)
SubmitCGAP
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C
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D
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E
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F
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K
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L
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M
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R
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T
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W
C
CGAPPermissionError
check_repeatedly() (in module submit_cgap.utils)
check_submit_ingestion() (in module submit_cgap.submission)
compute_file_post_data() (in module submit_cgap.submission)
compute_s3_submission_post_data() (in module submit_cgap.submission)
D
do_any_uploads() (in module submit_cgap.submission)
do_app_arg_defaulting() (in module submit_cgap.submission)
do_uploads() (in module submit_cgap.submission)
E
execute_prearranged_upload() (in module submit_cgap.submission)
extract_metadata_and_upload_credentials() (in module submit_cgap.submission)
F
FakeResponse (class in submit_cgap.utils)
G
GenericKeyManager (class in submit_cgap.base)
get_defaulted_award() (in module submit_cgap.submission)
get_defaulted_consortia() (in module submit_cgap.submission)
get_defaulted_institution() (in module submit_cgap.submission)
get_defaulted_lab() (in module submit_cgap.submission)
get_defaulted_project() (in module submit_cgap.submission)
get_defaulted_submission_centers() (in module submit_cgap.submission)
get_keydict_for_env() (submit_cgap.base.GenericKeyManager method)
get_keydict_for_server() (submit_cgap.base.GenericKeyManager method)
get_metadata_bundles_bucket_from_health_path() (in module submit_cgap.submission)
get_s3_encrypt_key_id() (in module submit_cgap.submission)
get_s3_encrypt_key_id_from_health_page() (in module submit_cgap.submission)
get_section() (in module submit_cgap.submission)
get_user_record() (in module submit_cgap.submission)
I
ingestion_submission_item_url() (in module submit_cgap.submission)
J
json() (submit_cgap.utils.FakeResponse method)
K
keydict_to_keypair() (submit_cgap.base.GenericKeyManager method)
keys_file (submit_cgap.base.GenericKeyManager attribute)
keyword_as_title() (in module submit_cgap.utils)
L
locally_selected_app() (submit_cgap.base.GenericKeyManager method)
M
main() (in module submit_cgap.scripts.make_sample_fastq_file)
(in module submit_cgap.scripts.resume_uploads)
(in module submit_cgap.scripts.submit_metadata_bundle)
(in module submit_cgap.scripts.upload_item_data)
R
raise_for_status() (submit_cgap.utils.FakeResponse method)
resolve_server() (in module submit_cgap.submission)
resume_uploads() (in module submit_cgap.submission)
running_on_windows_native() (in module submit_cgap.submission)
S
S3 (submit_cgap.submission.SubmissionProtocol attribute)
script_catch_errors() (in module submit_cgap.utils)
search_for_file() (in module submit_cgap.submission)
select_app() (submit_cgap.base.GenericKeyManager method)
selected_app (submit_cgap.base.GenericKeyManager attribute)
show() (in module submit_cgap.utils)
show_section() (in module submit_cgap.submission)
show_upload_info() (in module submit_cgap.submission)
show_upload_result() (in module submit_cgap.submission)
SubmissionProtocol (class in submit_cgap.submission)
submit_any_ingestion() (in module submit_cgap.submission)
submit_cgap.base (module)
submit_cgap.exceptions (module)
submit_cgap.scripts.make_sample_fastq_file (module)
submit_cgap.scripts.resume_uploads (module)
submit_cgap.scripts.submit_metadata_bundle (module)
submit_cgap.scripts.upload_item_data (module)
submit_cgap.submission (module)
submit_cgap.tests.test_exceptions (module)
submit_cgap.tests.test_make_sample_fastq_file (module)
submit_cgap.utils (module)
summarize_submission() (in module submit_cgap.submission)
T
test_cgap_permission_error() (in module submit_cgap.tests.test_exceptions)
test_make_sample_fastq_file_script() (in module submit_cgap.tests.test_make_sample_fastq_file)
U
UPLOAD (submit_cgap.submission.SubmissionProtocol attribute)
upload_extra_files() (in module submit_cgap.submission)
upload_file_to_new_uuid() (in module submit_cgap.submission)
upload_file_to_uuid() (in module submit_cgap.submission)
upload_item_data() (in module submit_cgap.submission)
UploadMessageWrapper (class in submit_cgap.submission)
W
wrap_upload_function() (submit_cgap.submission.UploadMessageWrapper method)
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