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 --dates amdirt-convert command line option --doi amdirt-validate command line option --eager amdirt-convert command line option --fetchngs amdirt-convert command line option --libraries 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 --local_json_schema 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 amdirt-download command line option --output_ena_table amdirt-autofill command line option --release amdirt-download command line option --remote amdirt-validate command line option --sample_output amdirt-autofill command line option --schema_check amdirt-validate command line option

--sratoolkit amdirt-convert command line option --table amdirt-download command line option --table_name amdirt-autofill command line option amdirt-merge command line option --table_type amdirt-download command line option 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 amdirt-validate 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-download command line option amdirt-merge command line option -r amdirt-download command line option -s amdirt-autofill command line option amdirt-validate command line option -t amdirt-autofill command line option amdirt-convert command line option amdirt-download command line option amdirt-merge command line option amdirt-viewer command line option -y amdirt-download 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 --output_ena_table --sample_output --table_name -l -n -s -t ACCESSION amdirt-convert command line option --ameta --aspera --bibliography --curl --dates --eager --fetchngs --libraries --librarymetadata --mag --output --sratoolkit --tables --taxprofiler -o -t SAMPLES TABLE_NAME amdirt-download command line option --output --release --table --table_type -o -r -t -y

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 --local_json_schema --markdown --multi_values --online_archive --remote --schema_check -a -c -d -i -l -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)