Submit-CGAP
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Overview
Awscli/Rclone Submission (experimental)
Basic Setup
Installing SubmitCGAP
Getting Started
submit_cgap package
Submit-CGAP
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Index
A
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C
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D
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E
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F
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G
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I
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J
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K
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M
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R
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S
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T
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W
A
alternate_keydicts_filename() (submit_cgap.base.KeyManager class method)
alternate_keydicts_filename_from_environ() (submit_cgap.base.KeyManager class method)
C
CGAPEnvKeyMissing
CGAPKeyMissing
CGAPPermissionError
CGAPServerKeyMissing
D
default_env_for_testing() (in module submit_cgap.tests.test_base)
DEFAULT_KEYDICTS_FILENAME (submit_cgap.base.KeyManager attribute)
do_any_uploads() (in module submit_cgap.submission)
do_uploads() (in module submit_cgap.submission)
E
execute_prearranged_upload() (in module submit_cgap.submission)
F
FakeResponse (class in submit_cgap.utils)
G
get_cgap_keydicts() (in module submit_cgap.auth)
get_defaulted_institution() (in module submit_cgap.submission)
get_defaulted_project() (in module submit_cgap.submission)
get_keydict_for_env() (in module submit_cgap.auth)
get_keydict_for_server() (in module submit_cgap.auth)
get_keypair_for_env() (in module submit_cgap.auth)
get_keypair_for_server() (in module submit_cgap.auth)
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() (in module submit_cgap.auth)
keydicts_filename() (submit_cgap.base.KeyManager class method)
KeyManager (class in submit_cgap.base)
keypair_to_keydict() (in module submit_cgap.auth)
keyword_as_title() (in module submit_cgap.utils)
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
script_catch_errors() (in module submit_cgap.utils)
search_for_file() (in module submit_cgap.submission)
show() (in module submit_cgap.utils)
show_section() (in module submit_cgap.submission)
show_upload_info() (in module submit_cgap.submission)
submit_any_ingestion() (in module submit_cgap.submission)
submit_cgap (module)
submit_cgap.auth (module)
submit_cgap.base (module)
submit_cgap.exceptions (module)
submit_cgap.scripts (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 (module)
submit_cgap.tests.test_base (module)
submit_cgap.tests.test_exceptions (module)
submit_cgap.tests.test_make_sample_fastq_file (module)
submit_cgap.utils (module)
T
test_cgap_env_key_missing() (in module submit_cgap.tests.test_exceptions)
test_cgap_key_missing() (in module submit_cgap.tests.test_exceptions)
test_cgap_permission_error() (in module submit_cgap.tests.test_exceptions)
test_cgap_server_key_missing() (in module submit_cgap.tests.test_exceptions)
test_defaults() (in module submit_cgap.tests.test_base)
test_keymanager() (in module submit_cgap.tests.test_base)
test_make_sample_fastq_file_script() (in module submit_cgap.tests.test_make_sample_fastq_file)
U
upload_extra_files() (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)
UsingCGAPKeysFile() (in module submit_cgap.base)
W
wrap_upload_function() (submit_cgap.submission.UploadMessageWrapper method)
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