fishtank 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: add18ae1c07c493e96189169c4778ed32957d607
+  data.tar.gz: db48f20638c8a6b1e7c862b600ac5eebd1817dd8
+SHA512:
+  metadata.gz: e4d6e8a31882916057a05e1124e58202149a559e7610066b5f1402ae4552cf41aa0fc97a8d48dd22cb8cdf76d3ae1ebfe286319ada875abd902bea6816d5e008
+  data.tar.gz: 7bc4637813b2449f45d0019563251da03e34dcc56705f405cc42a03f23cc796e56d72d85d07a38e650c316f2915371b6969750722d5a05ff5c626f2c376288e2

data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.4.2
+before_install: gem install bundler -v 1.16.0

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in fishtank.gemspec
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    fishtank (0.1.0)
+      phenoscaperb
+      rasem
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    awesome_print (1.8.0)
+    byebug (9.1.0)
+    diff-lcs (1.3)
+    faraday (0.12.0.1)
+      multipart-post (>= 1.2, < 3)
+    faraday_middleware (0.11.0.1)
+      faraday (>= 0.7.4, < 1.0)
+    mini_portile2 (2.3.0)
+    multi_json (1.12.2)
+    multipart-post (2.0.0)
+    nokogiri (1.8.1)
+      mini_portile2 (~> 2.3.0)
+    phenoscaperb (0.1.0)
+      faraday (~> 0.12.0.1)
+      faraday_middleware (~> 0.11.0.1)
+      multi_json (~> 1.12, >= 1.12.1)
+      nokogiri (~> 1.8, >= 1.8.1)
+      thor (~> 0.20.0)
+      xml-to-hash (~> 1.0, >= 1.0.3)
+    rake (10.5.0)
+    rasem (0.7.1)
+    rspec (3.7.0)
+      rspec-core (~> 3.7.0)
+      rspec-expectations (~> 3.7.0)
+      rspec-mocks (~> 3.7.0)
+    rspec-core (3.7.0)
+      rspec-support (~> 3.7.0)
+    rspec-expectations (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-mocks (3.7.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.7.0)
+    rspec-support (3.7.0)
+    thor (0.20.0)
+    xml-to-hash (1.0.3)
+      nokogiri (~> 1, >= 1.6)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  awesome_print
+  bundler (~> 1.16)
+  byebug
+  fishtank!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.16.0

data/LICENSE

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+MIT License
+
+Copyright (c) 2017 Phenoscape
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2017 Matt Yoder
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+
+# Fishtank
+
+This library uses the [phenoscaperb](https://github.com/phenoscape/phenoscaperb) gem to query the [Phenoscape API](http://kb.phenoscape.org/apidocs/) for basic statistics on a taxon, entity, and quality basis.  It then renders the results as an SVG visualization.
+
+![viz](/doc/viz.png)
+
+# Basic use
+
+```
+gem install fishtank
+```
+
+```
+require 'fishtank'
+
+fish = 'VTO_0037519'
+lizard = 'VTO_9007513' 
+pan = 'VTO_0011989'
+homininae = 'VTO_0011988'
+
+# Create a new tank
+tank = FishTank::Tank.new
+
+# Make some Taxa
+t = FishTank::Taxon::Arm.new(taxon_id: homininae)
+f = FishTank::Taxon::Fish.new(taxon_id: fish)
+v = FishTank::Taxon::Tetrapod.new(taxon_id: lizard)
+
+# Add the Taxa to the tank
+tank.add(t)
+tank.add(f)
+tank.add(v)
+
+# Render the tank
+FishTank::Draw.tank(tank: tank, attributes: FishTank::QUALITIES)
+```
+
+Then in the terminal (file is SVG, `.html` is convenience)
+
+```
+ruby your_file.rb > index.html
+open index.html
+```
+
+# About, thanks.
+
+Concieved and implemented at the  [2017 Phenoscape KB-DataFest](https://github.com/phenoscape/KB-DataFest-2017). Special thanks to Wasila Dahdul for her help with the taxon models and Scott Chamberlain for phenoscaperb.
+
+# License
+
+MIT
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "fishtank"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/fishtank.gemspec

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+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "fishtank/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "fishtank"
+  spec.version       = Fishtank::VERSION
+  spec.authors       = ["Matt Yoder"]
+  spec.email         = ["diapriid@gmail.com"]
+
+  spec.summary       = %q{A visualization experiment for the Phenoscape KB.}
+  spec.description   = %q{An experiment to map various attributes of the Phenoscape KB to cartoon figures, using SVG.}
+  spec.homepage      = "https://github.com/phenoscape/fishtank"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'phenoscaperb'
+  spec.add_dependency 'rasem'
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "awesome_print"
+  spec.add_development_dependency "byebug"
+
+end

data/lib/fishtank.rb

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+
+
+
+require 'phenoscaperb'
+require 'awesome_print'
+require 'byebug'
+
+require "fishtank/version"
+
+require 'fishtank/draw'
+require 'fishtank/simple_nexml'
+require 'fishtank/tank'
+require 'fishtank/taxon'
+require 'fishtank/taxon/fish'
+require 'fishtank/taxon/tetrapod'
+require 'fishtank/taxon/arm'
+
+
+module FishTank
+
+  BASE = 'http://purl.obolibrary.org/obo/'
+
+  # TODO: move to file
+  QUALITIES = [ 
+    'PATO_0000052',  # shape
+    'PATO_0000117',  # size
+    'PATO_0000014',  # color
+    'PATO_0000070',  # count/amount
+    'PATO_0000140'   # position
+  ] 
+
+  def self.attributes
+    QUALITIES + [:otus, :rows, :cells]
+  end
+
+end

data/lib/fishtank/draw.rb

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+require 'rasem'
+
+module FishTank
+
+  module Draw
+
+    @offset_x = 0
+    @offset_y = 0
+
+    @img = Rasem::SVGImage.new(width: 2000, height: 2000, 'font-size'.to_sym => '8') 
+
+    # Draw the tank
+    def self.tank(tank: nil, attributes: [:cells] ) 
+      raise 'tank please' if tank.nil?
+
+      tank.taxa.each do |t|
+        attributes.each do |a|
+          render_taxon(t, a)
+
+          @img.text(@offset_x, @offset_y + t.pic_height + 2) do 
+            raw a
+          end 
+
+          @offset_x += t.pic_width + 10
+        end
+
+        @img.text(0, @offset_y + t.pic_height + 15) do
+          raw t.label 
+        end 
+
+        @offset_x = 0
+        @offset_y += t.pic_height + 40 
+      end  
+
+      puts @img.to_s
+    end
+
+    def self.render_taxon(taxon, attribute)
+      taxon.description.each do |entity, v|
+        s = { 
+          fill: svg_color(taxon, entity, attribute), 
+          stroke: svg_color(taxon, entity, :otus), # for now we hard code stroke 
+          'stroke-width'.to_sym => '0.5'
+        }
+
+        draw_part( v[0] + @offset_x, v[1] + @offset_y, v[2], v[3], style: s )
+        if taxon.symmetry.keys.include?(entity)
+          z = taxon.symmetry[entity]  
+          draw_part( z[0] + @offset_x, z[1] + @offset_y, z[2], z[3], style: s )
+        end
+
+      end
+    end
+
+    def self.draw_part(x, y, width, height, style: {})
+      @img.rectangle x, y, width, height, style: style
+    end
+
+    def self.svg_color(taxon, entity, attribute)
+      v = (taxon.stats[entity][:crunched][attribute] * 255).to_i
+      "rgb(#{v}, 0, 0)"
+    end
+  end
+
+end
+
+
+

data/lib/fishtank/fishtank.rb

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+
+require 'rasem'
+require 'phenoscaperb'
+require 'awesome_print'
+
+require_relative 'simple_nexml.rb'
+
+require 'byebug'
+
+class FishTank
+  BASE = 'http://purl.obolibrary.org/obo/'
+
+  # TODO: move to file
+  QUALITIES = [ 
+   'PATO_0000052',  # shape
+   'PATO_0000117',  # size
+   'PATO_0000014',  # color
+   'PATO_0000070',  # count/amount
+   'PATO_0000140'   # position
+  ] 
+
+  METADATA = {
+    'UBERON_0001703' =>  [0, 10, 10, 10],  # 'neurocranium'
+    'UBERON_0000970' =>  [3, 12, 3, 3],    # 'eye'
+    'UBERON_0001708' =>  [1, 17, 5, 2],    # 'jaw skeleton'
+    'UBERON_0002090' =>  [10, 10, 30, 10], # 'post-cranial axial skeleton'
+    'UBERON_0003097' =>  [12, 0, 10, 10],  # 'dorsal fin'
+    'UBERON_0000151' =>  [5, 20, 10, 10],  # 'pectoral fin'
+    'UBERON_0000152' =>  [17, 20, 10, 10], # 'pelvic fin'
+    'UBERON_4000164' =>  [30, 5, 10, 20],  # 'caudal fin'
+  }
+
+  # the svg image object
+  attr_accessor :img
+
+  attr_accessor :parent_taxon
+
+  # All observed descendants of the parent_taxon
+  attr_accessor :children
+
+  attr_accessor :taxon_stats
+
+  def initialize(taxon: nil)
+    raise 'the tank is empty, sad, and lonely, give it a fish, like "taxon: 123"' if taxon.nil?
+    @img = Rasem::SVGImage.new(width: 100, height: 100) 
+    @parent_taxon = taxon 
+    @taxon_stats = {}
+    @all_otus = []
+  end
+
+  def render
+  end
+
+  def render_fish(taxon)
+    get_metadata(taxon) 
+
+    METADATA.each do |entity, v|
+      draw_fish_part(
+        v[0], v[1], v[2], v[3], 
+        style: { 
+          fill: svg_color(taxon, entity, :cells), 
+          stroke: svg_color(taxon, entity, :rows), 
+          'stroke-width'.to_sym => '0.5'
+        }
+      )
+    end
+    puts img.to_s
+  end
+
+  def svg_color(taxon, entity, attribute)
+    "rgb(#{(taxon_stats[taxon][entity][:crunched][attribute] * 255).to_i}, 0, 0)"
+  end
+
+  def draw_fish_part(x, y, width, height, style: {})
+    img.rectangle x, y, width, height, style: style
+  end
+
+  # @return [XML]
+  def get_nexml(taxon, entity)
+    Phenoscape::Ontotrace.ontotrace(taxon: iri_for(taxon), entity: some_iri(entity), ret: 'noko')
+  end
+
+  def get_metadata(taxon)
+    @taxon_stats[taxon] ||= {}
+    METADATA.each do |k, v|
+      @taxon_stats[taxon][k] ||= {}
+      @taxon_stats[taxon][k][:raw] ||= {}
+
+      xml = get_nexml(taxon, k) 
+      o = SimpleNexml.new(doc: xml, taxon: taxon)
+      @taxon_stats[taxon][k][:raw] = o.stats[:count]
+    end
+
+    crunch_stats(taxon)
+  end
+
+  def crunch_stats(taxon)
+    totals = { otus: 0, rows: 0, cells: 0}
+
+    taxon_stats[taxon].keys.each do |entity|
+      taxon_stats[taxon][entity][:raw].each do |k, count|
+        totals[k] += count 
+      end 
+    end
+
+    METADATA.each do |entity, v|
+      taxon_stats[taxon][entity][:crunched] ||= {}
+      totals.keys.each do |t|
+        taxon_stats[taxon][entity][:crunched][t] = taxon_stats[taxon][entity][:raw][t].to_f / totals[t].to_f
+      end
+    end
+  end
+
+  def get_all_metadata
+    get_metadata(parent_taxon)
+  end
+
+  def some_iri(entity)
+    iri_for('BFO_0000050') + ' some ' +  iri_for(entity) 
+  end
+
+  def iri_for(id)
+    '<' + BASE + id + '>'
+  end
+
+end
+
+
+
+# f.get_all_metadata
+
+# curl -X GET "http://kb.phenoscape.org/api/taxon/annotations?entity=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001703&quality=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000052&in_taxon=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVTO_0037519&parts=true&historical_homologs=false&serial_homologs=false&limit=20&offset=0&total=true" -H  "accept: application/json"

data/lib/fishtank/simple_nexml.rb

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+# TODO: this doesn't belong in this repo
+
+require 'nokogiri'
+
+# Parse NeXML document and return some data
+class SimpleNexml
+
+  attr_accessor :doc
+  attr_accessor :taxon
+  attr_accessor :entity
+
+  def initialize(doc: nil, taxon: nil, entity: nil)
+    @doc = doc
+  end
+
+  def stats
+    return {
+      count: {
+        otus: otus.count,
+        rows: rows.count,
+        cells: cells.count
+      }
+    }
+  end
+
+  def otus
+    doc.css("otus")
+  end
+
+  def cells
+    doc.css("cell")
+  end
+
+  def rows
+    doc.css("row")
+  end
+
+  # @return [Array]
+  #   all chars referenced in rows
+  def referenced_chars
+    cells.inject({}) {|hsh, c| hsh.merge!(c.to_h['char'] => nil)}.keys
+  end
+
+  # @return [Array]
+  #   all states referenced in rows
+  def referenced_states
+    cells.inject({}) {|hsh, c| hsh.merge!(c.to_h['state'] => nil)}.keys
+  end
+
+  # @return [Array]
+  #   all chars referenced in rows
+  def referenced_otus
+    rows.css("row").inject({}) {|hsh, c| hsh.merge!(c.to_h['otu'] => nil)}.keys
+  end
+
+end
+
+

data/lib/fishtank/tank.rb

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+
+module FishTank
+
+  class Tank
+    attr_accessor :taxa
+
+    def initialize
+      @taxa = []
+    end
+
+    def add(taxon)
+      @taxa.push(taxon)
+    end
+  end
+
+end
+

data/lib/fishtank/taxon.rb

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+module FishTank
+  class Taxon
+
+    # METADATA = {}
+
+    attr_accessor :label 
+    attr_accessor :stats
+
+    def initialize(taxon_id: nil)
+      @label = taxon_id 
+      @stats = {}
+      get_metadata
+      crunch_stats
+    end
+
+    # @return [XML]
+    def get_nexml(entity)
+      Phenoscape::Ontotrace.ontotrace(taxon: iri_for(label), entity: some_iri(entity), ret: 'noko')
+    end
+
+    # @return [Integer]
+    def get_phenotype_total(entity, quality)
+      Phenoscape::Taxa.annotations(
+        in_taxon: base_for(label), 
+        entity: base_for(entity), 
+        quality: base_for(quality),
+        total: true,
+        parts: true
+      )['total']
+    end
+
+    def get_metadata
+      @stats ||= {}
+      description.each do |k, v|
+        @stats[k] ||= {}
+        @stats[k][:raw] ||= {}
+
+        xml = get_nexml(k) 
+        o = SimpleNexml.new(doc: xml, taxon: label)
+        @stats[k][:raw] = o.stats[:count]
+
+        FishTank::QUALITIES.each do |q|
+          @stats[k][:raw][q] = get_phenotype_total(k, q)
+        end
+      end
+      true 
+    end
+
+    def crunch_stats
+      totals = {} 
+
+      stats.keys.each do |entity|
+        stats[entity][:raw].each do |k, count|
+          totals[k] ||= 0
+          totals[k] += count 
+        end 
+      end
+
+      description.each do |entity, v|
+        stats[entity][:crunched] ||= {}
+        totals.keys.each do |t|
+          v = totals[t] == 0 ? 0.to_f : stats[entity][:raw][t].to_f / totals[t].to_f
+          stats[entity][:crunched][t] = v 
+        end
+      end
+      true
+    end
+
+    def some_iri(entity)
+      iri_for('BFO_0000050') + ' some ' +  iri_for(entity) 
+    end
+
+    def iri_for(id)
+      '<' + base_for(id) + '>'
+    end
+
+    def base_for(id)
+      BASE + id
+    end
+
+    def attributes
+    end
+
+    def symmetry
+      return {}
+    end
+
+    # @return [Integer]
+    def pic_width
+      60 
+    end
+
+    # @return [Integer]
+    def pic_height
+      100
+    end
+
+  end
+
+end
+
+

data/lib/fishtank/taxon/arm.rb

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+module FishTank
+
+  # Generic Arm/limb 
+  class Taxon::Arm < FishTank::Taxon
+
+    def description
+      return {
+        'UBERON_0000976' =>  [15, 0, 10, 20],   # 'humerus'
+        
+        'UBERON_0001423' =>  [12, 22, 6, 20],   # 'radius'
+        'UBERON_0001424' =>  [22, 22, 6, 20],   # 'ulna'
+       
+        'UBERON_0001435' =>  [10, 44, 20, 15 ], # 'carpal bone'
+        'UBERON_0002374' =>  [8, 61, 24, 15 ],  # 'metacarpal bone'
+
+        'UBERON_0006048' =>  [8,  78, 4, 10 ],  # 'digit 1'
+        'UBERON_0006049' =>  [13, 78, 4, 10 ],  # 'digit 2'
+        'UBERON_0006050' =>  [18, 78, 4, 10 ],  # 'digit 3'
+        'UBERON_0006051' =>  [23, 78, 4, 10 ],  # 'digit 4'
+        'UBERON_0006052' =>  [28, 78, 4, 10 ],  # 'digit 5'
+       }
+    end
+
+  end
+end

data/lib/fishtank/taxon/fish.rb

@@ -0,0 +1,24 @@
+
+module FishTank
+  class Taxon::Fish < FishTank::Taxon
+
+    # Ugh
+    def description
+      return {
+        'UBERON_0001703' =>  [0, 10, 10, 10],  # 'neurocranium'
+        'UBERON_0000970' =>  [3, 12, 3, 3],    # 'eye'
+        'UBERON_0001708' =>  [1, 17, 5, 2],    # 'jaw skeleton'
+        'UBERON_0002090' =>  [10, 10, 30, 10], # 'post-cranial axial skeleton'
+        'UBERON_0003097' =>  [12, 0, 10, 10],  # 'dorsal fin'
+        'UBERON_0000151' =>  [5, 20, 10, 10],  # 'pectoral fin'
+        'UBERON_0000152' =>  [17, 20, 10, 10], # 'pelvic fin'
+        'UBERON_4000164' =>  [30, 5, 10, 20],  # 'caudal fin'
+      }
+    end
+
+    def pic_height
+      50
+    end
+
+  end
+end

data/lib/fishtank/taxon/tetrapod.rb

@@ -0,0 +1,32 @@
+module FishTank
+
+  # Generic Tetrapod
+  class Taxon::Tetrapod < FishTank::Taxon
+
+    # TODO: Update UBERON terms to represent actually meaningful layout, this was cloned from Fish
+    def description
+      return {
+       'UBERON_0001703' =>  [10, 0, 10, 9],    # 'neurocranium'
+       'UBERON_0000970' =>  [8, 3, 4, 4],      # 'eye'
+       'UBERON_0001708' =>  [12, 0, 4, 2],     # 'jaw skeleton' 
+       'UBERON_0014477' =>  [10, 10, 10, 30],  # thoracic skeleton
+       'UBERON_0002102' =>  [0, 16, 10, 6],    # forelimb 
+       'UBERON_0002103' =>  [0, 26, 10, 6],    # hindlimb 
+       'UBERON_0002415' =>  [13, 40, 3, 15],   # tail 
+      }
+    end
+
+    def symmetry
+      return {
+       'UBERON_0000970' => [18, 3, 4, 4],
+       'UBERON_0002102' => [20, 16, 10, 6],
+       'UBERON_0002103' => [20, 26, 10, 6]
+      } 
+    end
+
+    def pic_height
+      75
+    end
+
+  end
+end

data/lib/fishtank/version.rb

@@ -0,0 +1,3 @@
+module Fishtank
+  VERSION = "0.1.0"
+end

metadata

@@ -0,0 +1,166 @@
+--- !ruby/object:Gem::Specification
+name: fishtank
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Matt Yoder
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-12-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: phenoscaperb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rasem
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: An experiment to map various attributes of the Phenoscape KB to cartoon
+  figures, using SVG.
+email:
+- diapriid@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- doc/viz.png
+- fishtank.gemspec
+- lib/fishtank.rb
+- lib/fishtank/draw.rb
+- lib/fishtank/fishtank.rb
+- lib/fishtank/simple_nexml.rb
+- lib/fishtank/tank.rb
+- lib/fishtank/taxon.rb
+- lib/fishtank/taxon/arm.rb
+- lib/fishtank/taxon/fish.rb
+- lib/fishtank/taxon/tetrapod.rb
+- lib/fishtank/version.rb
+homepage: https://github.com/phenoscape/fishtank
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.13
+signing_key: 
+specification_version: 4
+summary: A visualization experiment for the Phenoscape KB.
+test_files: []