wc_kb.__main__

---

Command line programs for managing knowledge bases for whole-cell models

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2018-04-20

Copyright:

2018, Karr Lab

License:

MIT

3.2.1. Module Contents

3.2.1.1. Classes

BaseController	Base controller for command line application
ValidateController	Validate knowledge base and display errors
DifferenceController	Display difference between two knowledge bases
NormalizeController	Normalize knowledge base
ConvertController	Convert knowledge base among Excel (.xlsx), comma separated (.csv), JavaScript Object Notation (.json),
CreateTemplateController	Create file with knowledge base template (i.e. create file with row and column labels)
UpdateVersionMetadataController	Update version metadata of a knowledge base (URL, branch, revision, wc_kb version)
App	Command line application

3.2.1.2. Functions

main()

class wc_kb.__main__.BaseController

Bases: cement.Controller

Base controller for command line application

class Meta

label = 'base'

description = 'Command line programs for managing knowledge bases for whole-cell models'

help = 'Command line programs for managing knowledge bases for whole-cell models'

arguments = [(['-v', '--version'],)]

_default()

class wc_kb.__main__.ValidateController

Bases: cement.Controller

Validate knowledge base and display errors

class Meta

label = 'validate'

description = 'Validate knowledge base and display errors'

help = 'Validate knowledge base and display errors'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['core_path'],), (['seq_path'],), (['--taxon'],)]

_default()

class wc_kb.__main__.DifferenceController

Bases: cement.Controller

Display difference between two knowledge bases

class Meta

label = 'difference'

description = 'Get difference between two knowledge bases'

help = 'Get difference between two knowledge bases'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['core_path_1'],), (['seq_path_1'],), (['core_path_2'],), (['seq_path_2'],), (['--taxon'],),...

_default()

static remove_metadata(kb)

Remove metadata from Knowledge base

Parameters:

kb (wc_utils.workbook.Workbook) – knowledge base

class wc_kb.__main__.NormalizeController

Bases: cement.Controller

Normalize knowledge base

class Meta

label = 'normalize'

description = 'Normalize knowledge base'

help = 'Normalize knowledge base'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['source_core'],), (['source_seq'],), (['--dest-core'],), (['--dest-seq'],), (['--taxon'],),...

_default()

class wc_kb.__main__.ConvertController

Bases: cement.Controller

Convert knowledge base among Excel (.xlsx), comma separated (.csv), JavaScript Object Notation (.json), tab separated (.tsv), and Yet Another Markup Language (.yaml, .yml) formats

class Meta

label = 'convert'

description = 'Convert knowledge base among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'

help = 'Convert knowledge base among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['source_core'],), (['source_seq'],), (['dest_core'],), (['dest_seq'],), (['--taxon'],),...

_default()

class wc_kb.__main__.CreateTemplateController

Bases: cement.Controller

Create file with knowledge base template (i.e. create file with row and column labels)

class Meta

label = 'create-template'

description = 'Create file with knowledge base template: blank file(s) with row and column labels'

help = 'Create file with knowledge base template: blank file(s) with row and column labels'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['path_core'],), (['path_seq'],), (['--ignore-repo-metadata'],), (['--taxon'],), (['--unprotected'],)]

_default()

class wc_kb.__main__.UpdateVersionMetadataController

Bases: cement.Controller

Update version metadata of a knowledge base (URL, branch, revision, wc_kb version)

class Meta

label = 'update-version-metadata'

description = 'Update version metadata of a knowledge base (URL, branch, revision, wc_kb version)'

help = 'Update version metadata of a knowledge base (URL, branch, revision, wc_kb version)'

stacked_on = 'base'

stacked_type = 'nested'

arguments = [(['path_core'],), (['path_seq'],), (['--taxon'],), (['--ignore-repo-metadata'],), (['--unprotected'],)]

_default()

class wc_kb.__main__.App

Bases: cement.App

Command line application

class Meta

label = 'wc-kb'

base_controller = 'base'

handlers

wc_kb.__main__.main()