Index

Symbols

--ameta AMDirT-convert command line option --aspera AMDirT-convert command line option --bibliography AMDirT-convert command line option --columns AMDirT-validate command line option --curl AMDirT-convert command line option --doi AMDirT-validate command line option --eager AMDirT-convert command line option --fetchngs AMDirT-convert command line option --library_output AMDirT-autofill command line option --librarymetadata AMDirT-convert command line option --line_dup AMDirT-validate command line option --mag AMDirT-convert command line option --markdown AMDirT-merge command line option AMDirT-validate command line option --multi_values AMDirT-validate command line option --online_archive AMDirT-validate command line option --outdir AMDirT-merge command line option --output AMDirT-convert command line option --remote AMDirT-validate command line option --sample_output AMDirT-autofill command line option --schema_check AMDirT-validate command line option

--table_name AMDirT-autofill command line option AMDirT-merge command line option --table_type AMDirT-merge command line option --tables AMDirT-convert command line option AMDirT-viewer command line option --taxprofiler AMDirT-convert command line option --verbose AMDirT command line option --version AMDirT command line option -a AMDirT-validate command line option -c AMDirT-validate command line option -d AMDirT-validate command line option -i AMDirT-validate command line option -l AMDirT-autofill command line option -m AMDirT-merge command line option AMDirT-validate command line option -n AMDirT-autofill command line option AMDirT-merge command line option -o AMDirT-convert command line option AMDirT-merge command line option -s AMDirT-autofill command line option AMDirT-validate command line option -t AMDirT-convert command line option AMDirT-merge command line option AMDirT-viewer command line option

_

__get_json__() (AMDirT.core.ena.ENABrowserAPI method) (AMDirT.core.ena.ENAPortalAPI method) __init__() (AMDirT.core.ena.ENABrowserAPI method) (AMDirT.core.ena.ENAPortalAPI method) (AMDirT.validate.application.AMDirValidator method)

__repr__() (AMDirT.core.ena.ENABrowserAPI method) (AMDirT.core.ena.ENAPortalAPI method) (AMDirT.validate.application.AMDirValidator method) __weakref__ (AMDirT.core.ena.ENABrowserAPI attribute) (AMDirT.core.ena.ENAPortalAPI attribute) (AMDirT.validate.application.AMDirValidator attribute)

A

ACCESSION AMDirT-autofill command line option AMDirT command line option --verbose --version AMDirT-autofill command line option --library_output --sample_output --table_name -l -n -s ACCESSION AMDirT-convert command line option --ameta --aspera --bibliography --curl --eager --fetchngs --librarymetadata --mag --output --tables --taxprofiler -o -t SAMPLES TABLE_NAME AMDirT-merge command line option --markdown --outdir --table_name --table_type -m -n -o -t DATASET

AMDirT-validate command line option --columns --doi --line_dup --markdown --multi_values --online_archive --remote --schema_check -a -c -d -i -m -s DATASET SCHEMA AMDirT-viewer command line option --tables -t AMDirValidator (class in AMDirT.validate.application)

B

base_url (AMDirT.core.ena.ENAPortalAPI attribute)

C

check_columns() (AMDirT.validate.application.AMDirValidator method) check_duplicate_rows() (AMDirT.validate.application.AMDirValidator method)

check_multi_values() (AMDirT.validate.application.AMDirValidator method) check_sample_accession() (AMDirT.validate.application.AMDirValidator method) cleanup_errors() (AMDirT.validate.application.AMDirValidator method)

D

DATASET AMDirT-merge command line option AMDirT-validate command line option dataset (AMDirT.validate.application.AMDirValidator attribute)

dataset_json (AMDirT.validate.application.AMDirValidator attribute) dataset_name (AMDirT.validate.application.AMDirValidator attribute) dataset_to_json() (AMDirT.validate.application.AMDirValidator method) doc() (AMDirT.core.ena.ENABrowserAPI method) (AMDirT.core.ena.ENAPortalAPI method)

E

ENABrowserAPI (class in AMDirT.core.ena)

ENAPortalAPI (class in AMDirT.core.ena) errors (AMDirT.validate.application.AMDirValidator attribute)

L

list_fields() (AMDirT.core.ena.ENAPortalAPI method)

list_results() (AMDirT.core.ena.ENAPortalAPI method)

M

merge_new_df() (in module AMDirT.merge)

Q

query() (AMDirT.core.ena.ENAPortalAPI method)

R

read_dataset() (AMDirT.validate.application.AMDirValidator method) read_schema() (AMDirT.validate.application.AMDirValidator method)

run_app() (in module AMDirT.viewer) run_autofill() (in module AMDirT.autofill) run_convert() (in module AMDirT.convert)

S

SAMPLES AMDirT-convert command line option SCHEMA AMDirT-validate command line option

schema (AMDirT.validate.application.AMDirValidator attribute) schema_name (AMDirT.validate.application.AMDirValidator attribute) status() (AMDirT.core.ena.ENABrowserAPI method) (AMDirT.core.ena.ENAPortalAPI method)

T

TABLE_NAME AMDirT-convert command line option

to_markdown() (AMDirT.validate.application.AMDirValidator method) to_rich() (AMDirT.validate.application.AMDirValidator method)

V

validate_schema() (AMDirT.validate.application.AMDirValidator method)