Tap Workflows

8/14/2019 Tap Workflows

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Tap Workflows

a b1

b c1

c2

c

?

x

x1

x2

y

y1 z


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Tap (Task Application)

Framework for command line apps

Configurations, Documentation, Distribution

Workflows: sequence, fork, merge, syncmerge, switch


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Workflows

a --: b --: c

Think of a, b, c as methods(literally they are)


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Sequence

a --: b --: c

result_a = a(input)result_b = b(result_a)result_c = c(result_b)


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Fork

--a[b, c]

result_a = a(input)result_b = b(result_a)result_c = c(result_a)


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Merge

--c{a,b}

result_a = a(input)result_b = b(input)result_c = c(result_a, result_b)


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Variations

a --:i b

a(input).each do |result_a| # ib(result_a)end

a --:s b

b(*a(input)) # s


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Variations

a --:i b --:a c

results_b = []a(input).each do |result_a| # i

results_b


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Tap Workflows

Build workflows from command line

Get behavior like in a script


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Think about |

Pipe is just a sequence

Serves us well... but its just a sequence

% git diff | mate


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Example

Digest: splits a protein sequence

Fragment: numerical transform on substrings

Format Mfg: formats results as .mgf


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Desired Workflow

(protein) - - [peptides...]

(peptide) - - [data, headers]

(data, headers) - - string

digest --:i fragment --:s mgf


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Fragment


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Fragment


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Fragment


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Demo

% tap run -- fragment --help% rap fragment --help

% rap fragment PEPTIDE% rap fragment PEPTIDE --: dump% rap digest PROTEIN --: dump% rap digest PROTEIN --:i fragment --: dump

% rap digest PROTEIN --:i fragment --:a dump% rap digest PROTEIN --:i fragment --:s format_mgf--:a dump


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Demo% rap digest PROTEIN --:i fragment --format_mgf -- format_mgf --mz-precision 2 --dump --no-audit --no-yaml --1[2,3]s --4{2,3}a

- [digest, PROTEIN]- [fragment]- [format_mgf]

- [format_mgf, --mz-precision, 2]- [dump, --no-audit, --no-yaml]- 0:1i- 1[2,3]s

- 4{2,3}a


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Why is this good?

Tasks are distributable as gems

Encapsulation/Reuse

Structured enough for novel interfaces


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Tap-Server

Alpha alpha alpha

Tasks and Workflows in the browser

Immediate, easy interface for new users(customers, friends)

Simple Distributable Controllers


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Demo

% tap server

http://localhost:8080/http://localhost:8080/schema

% tap run

http://localhost:8080/capture/tutorial

% rap load --: tap-http:submit
http://localhost:8080/schemahttp://localhost:8080/http://localhost:8080/schemahttp://localhost:8080/schemahttp://localhost:8080/http://localhost:8080/


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Demo Summary

All happens in tap-server

Install a gem, get local controllers... tutorials,gui, etc.

Potential for interaction with web data

Potential to use browser as task interface


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Goodies...

Rap - rakish syntax for declaring tasks

Lazydoc - pull comments into object space

Configurable - class-based configs mapping tocommand line

Rap.task :sample, :one, :key => value do |task, args|

task.key # => valueargs.one # => 1 (% rap sample 1)

end


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Gotchas

Discovering tasks

Task documentation must have ::manifesttap.yml - used in pwd to manually specifywhich gems to include; package with gemto allow autodiscovery of gem tasks

Rap tasks dont package, pass results, orappear in tap-server. Local tasks only.


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tap.rubyforge.org

Tap Workflows

Documents