I have had some difficulties in using extended classes in rails, in particular extending the Matrix class - and I have also asked some questions related to this:
Am I extending this inbuilt ruby class correctly
Using custom functions in rails app
Where do I put this matrix class in my rails app
In general the answers have been around autoloading in rails 3. However, when I extend 'Math' new functions work, when I extend 'Matrix' new functions don't work - even if I treat them in the same way
I've tried many iterations and change module names, requires, autoloads but here are my latest key files:
application.rb:
require File.expand_path('../boot', __FILE__)
require 'rails/all'
require 'matrix'
# If you have a Gemfile, require the gems listed there, including any gems
# you've limited to :test, :development, or :production.
Bundler.require(:default, Rails.env) if defined?(Bundler)
module SimpleFixed
class Application < Rails::Application
# Settings in config/environments/* take precedence over those specified here.
# Application configuration should go into files in config/initializers
# -- all .rb files in that directory are automatically loaded.
# Custom directories with classes and modules you want to be autoloadable.
# **I have tried all these autoload variants**
# config.autoload_paths += %W(#{config.root}/extras)
# config.autoload_paths += %W(#{config.root}/lib)
# config.autoload_paths += Dir["#{config.root}/lib/**/"]
# config.autoload_paths << "#{Rails.root}/lib"
config.autoload_paths << "#{::Rails.root.to_s}/lib" # <-- set path
require "extend_matrix" # <-- forcibly load your matrix extension
*other standard code here*
lib/extend_math.rb
module Math
class << self
def cube_it(num)
num**3
end
def add_five(num)
num+5
end
end
end
lib/extend_matrix.rb
module Extend_matrix **An error is raised if I call this Matrix**
class Matrix
def symmetric?
return false if not square?
(0 ... row_size).each do |i|
(0 .. i).each do |j|
return false if self[i,j] != self[j,i]
end
end
true
end
def cholesky_factor
raise ArgumentError, "must provide symmetric matrix" unless symmetric?
l = Array.new(row_size) {Array.new(row_size, 0)}
(0 ... row_size).each do |k|
(0 ... row_size).each do |i|
if i == k
sum = (0 .. k-1).inject(0.0) {|sum, j| sum + l[k][j] ** 2}
val = Math.sqrt(self[k,k] - sum)
l[k][k] = val
elsif i > k
sum = (0 .. k-1).inject(0.0) {|sum, j| sum + l[i][j] * l[k][j]}
val = (self[k,i] - sum) / l[k][k]
l[i][k] = val
end
end
end
Matrix[*l]
end
end
end
my view page:
<%= Math.add_five(6) %> **works*
<%= Matrix[[25,15,-5],[15,18,0],[-5,0,11]].cholesky_factor %> **doesn't work**
Could it be because Math is a Module in ruby but Matrix is a class? If so, how do I correct for this?
If you have a look at the implementation of Matrix, you will see the reason. For me, it is located in .../ruby192/lib/ruby/1.9.1/matrix.rb. The definition is (omitted all methods):
class Matrix
include Enumerable
include ExceptionForMatrix
...
end
That means that Matrix is not contained in a module. Your source for your additions should begin:
class Matrix
def symmetric?
...
end
def cholesky_factor
...
end
end
So your addition to a class or module has to match the current definition. Matrix is known as Matrix in the Ruby constants, and not as Extend_matrix::Matrix which is what you have defined.
Related
I'm using https://github.com/kenn/active_flag and https://github.com/chanzuckerberg/sorbet-rails
This is what its rbi looks like:
module ActiveFlag
extend ActiveSupport::Concern
end
class ActiveFlag::Definition
def column; end
def human(key, options = nil); end
def humans; end
def initialize(column, keys, klass); end
def keys; end
def maps; end
def pairs; end
def set_all!(key); end
def to_array(integer); end
def to_i(arg); end
def to_value(instance, integer); end
def unset_all!(key); end
end
class ActiveFlag::Railtie < Rails::Railtie
end
class ActiveFlag::Value < Set
def method_missing(symbol, *args, &block); end
def raw; end
def set!(key, options = nil); end
def set(key); end
def set?(key); end
def to_human; end
def to_s; end
def unset!(key, options = nil); end
def unset(key); end
def unset?(key); end
def with(instance, definition); end
end
module ActiveFlag::ClassMethods
def flag(column, keys); end
end
class ActiveRecord::Base
extend ActiveFlag::ClassMethods
end
The last bit (extending AR::Base) I added, the rest srb rbi gems generated automatically.
To actually use Active Flag, I then do this in my model:
flag :visible_to, [:employee, :manager, :admin]
visible_to is an integer column. Sorbet Rails has already typed it as such:
sig { returns(Integer) }
def visible_to; end
sig { params(value: Integer).void }
def visible_to=(value); end
sig { returns(T::Boolean) }
def visible_to?; end
I could change this definition, but it's an autogenerated file and I assume the changes will get lost. So the next thing I tried was adding a sig directly above where the method gets used:
sig { returns(ActiveFlag::Value) }
def visible_to; end
flag :visible_to, [:employee, :manager, :admin]
The problem here is that Sorbet fails because the method I've "defined" doesn't return anything. Which I know is fine, because it'll get overriden when flag is called (it uses define_method internally), but I don't know how to communicate this to Sorbet.
Returning value that does not conform to method result type https://srb.help/7005
54 | def visible_to; end
^^^^^^^^^^^^^^^^^^^
Expected ActiveFlag::Value
Method visible_to has return type ActiveFlag::Value
54 | def visible_to; end
^^^^^^^^^^^^^^
Got NilClass originating from:
54 | def visible_to; e
So my question is. What's the best way to tell Sorbet that this method will return an ActiveFlag::Value once it gets defined, ideally without making a manual change to an autogenerated file?
btw. I tried to see how types for enum in Rails are handled... it doesn't look like that's been done on sorbet-typed yet. Possibly for the same reason.
When you want to override a generated rbi file you can create a second rbi file for the same class in your workspace and move the methods in there. Sorbet will handle merging multiple definitions files for you. We keep these files in a separate sorbet/custom directory next to the generated files; others keep the rbi files next to the rb files in their application directory.
As to enums, Sorbet does not natively support enum literal types so that's likely why.
You could implement a custom plugin for sorbet-rails to generate methods added by active_flag and remove the sigs generated wrongly. Here is the documentation for it:
https://github.com/chanzuckerberg/sorbet-rails/blob/master/README.md#extending-model-generation-task-with-custom-plugins
In my rails app in lib/matrix.rb I have entered the following code to extend the inbuilt Matrix class:
module Matrix
require 'matrix'
class Matrix
def symmetric?
return false if not square?
(0 ... row_size).each do |i|
(0 .. i).each do |j|
return false if self[i,j] != self[j,i]
end
end
true
end
def cholesky_factor
raise ArgumentError, "must provide symmetric matrix" unless symmetric?
l = Array.new(row_size) {Array.new(row_size, 0)}
(0 ... row_size).each do |k|
(0 ... row_size).each do |i|
if i == k
sum = (0 .. k-1).inject(0.0) {|sum, j| sum + l[k][j] ** 2}
val = Math.sqrt(self[k,k] - sum)
l[k][k] = val
elsif i > k
sum = (0 .. k-1).inject(0.0) {|sum, j| sum + l[i][j] * l[k][j]}
val = (self[k,i] - sum) / l[k][k]
l[i][k] = val
end
end
end
Matrix[*l]
end
end
end
Is this the correct way to add methods to an existing class within the rails app? Should I have the require matrix line there?
EDIT 1: Additional info provided
I have now removed the require 'matrix' line.
If I type the following test code in a view page, it only works if I delete my lib/matrix.rb file:
<% require 'matrix' %>
<%
m = Matrix[
[0,0],
[1,1]
]
%>
<%= m.column(0) %>
Otherwise it gives the error:
undefined method `[]' for Matrix:Module
It appears that I am eliminating the default methods of the built in Matrix class when I try to extend the class. Is there a way around this error?
no you should not have to require 'matrix' here. Whoever uses your code(rails app in your case), should use require 'matrix'
To extend a core class in Rails, you simply open it, add your methods, and close it. For example, to extend the Matrix class:
class Matrix
def my_method
"New method"
end
end
You should not need to require 'matrix' in your code either. As long as the file holding your extension is in one of the autoload paths, you should have direct access to the new methods.
If you need to add a directory to your Rails autoload path, simply update /config/application.rb with the following line:
config.autoload_paths += %W(#{config.root}/app/extras) # Autoload /app/extras/*.rb
I have a ruby script that extracts information from a file (genbank) and I would like to load this data into the database. I have created the model and the schema and a connection script:
require 'active_record'
def establish_connection(db_location= "protein.db.sqlite3")
ActiveRecord::Base.establish_connection(
:adapter => "sqlite3",
:database => db_location,
:pool => 5,
:timeout => 5000
)
end
This is my script that outputs the data:
require 'rubygems'
require 'bio'
require 'snp_db_models'
establish_connection
snp_positions_file = File.open("snp_position.txt")
outfile = File.open("output.txt", "w")
genome_sequence = Bio::FlatFile.open(Bio::EMBL, "ref.embl").next_entry
snp_positions = Array.new
snp_positions_file.gets # header line
while line = snp_positions_file.gets
snp_details = line.chomp.split("\t")
snp_seq = snp_details[1]
snp_positions << snp_details[1].to_i
end
mean_snp_per_base = snp_positions.size/genome_sequence.sequence_length.to_f
puts "Mean snps per base: #{mean_snp_per_base}"
#outfile = File.open("/Volumes/DataRAID/Projects/GAS/fastq_files/bowtie_results/snp_annotation/genes_with_higher_snps.tsv", "w")
outfile.puts("CDS start\tCDS end\tStrand\tGene\tLocus_tag\tnote\tsnp_ID\ttranslation_seq\tProduct\tNo_of_snps_per_gene\tsnp_rate_vs_mean")
genome_sequence.features do |feature|
if feature.feature !~ /gene/i && feature.feature !~ /source/i
start_pos = feature.locations.locations.first.from
end_pos = feature.locations.locations.first.to
number_of_snps_in_gene = (snp_positions & (start_pos..end_pos).to_a).size # intersect finds number of times snp occurs within cds location
mean_snp_per_base_in_gene = number_of_snps_in_gene.to_f/(end_pos - start_pos)
outfile.print "#{start_pos}\t"
outfile.print "#{end_pos}\t"
if feature.locations.locations.first.strand == 1
outfile.print "forward\t"
else
outfile.print "reverse\t"
end
qualifiers = feature.to_hash
["gene", "locus_tag", "note", "snp_id", "translation", "product"].each do |qualifier|
if qualifiers.has_key?(qualifier) # if there is gene and product in the file
# puts "#{qualifier}: #{qualifiers[qualifier]}"
outfile.print "#{qualifiers[qualifier].join(",")}\t"
else
outfile.print " \t"
end
end
outfile.print "#{number_of_snps_in_gene}\t"
outfile.print "%.2f" % (mean_snp_per_base_in_gene/mean_snp_per_base)
outfile.puts
end
end
outfile.close
How can I load the data in outfile.txt into the database. Do I have to do something like marshall dump?
Thanks in advance
Mark
Your can write a rake task to do this. Save it in lib/tasks and give it a .rake extension.
desc "rake task to load data into db"
task :load_data_db => :environment do
...
end
Since the rails environment is loaded, you can access your Model directly as you would in any Rails model/controller. Of course, it'll connect to the database depending on the environment variable defined when you execute your rake task.
In a mere script, your models are unknown.
You have to define a minimum to use them as if in a Rails App. Simply declare them:
class Foo << ActiveRecord:Base
end
Otherwise, in a Rails context, use rake tasks which are aware of the Rails app details.
I've been working on a rails project where I am needed to serialize permissions for user roles and store in the database. As far as that goes I'm all good. Now my problem comes when I want to modify the serialized data from a rails generated form.
I acted on instinct and tried with the expected behavior.
That would be to use something like this:
f.check_box :permissions_customer_club_events_read
But as no getters or setters exist for the serialized data, this doesn't work (obviously :p). Now I wonder how I would go about tackling this problem and the only thing that comes to mind is dynamically generating getter and setter methods from my serialized hash.
Example:
def permissions_customer_club_events_read=(val)
permissions[:customer][:club][:events][:read] = val
end
def permissions_customer_club_events_read
permissions[:customer][:club][:events][:read]
end
Anyone understand what I'm getting at?
Here is my Model:
class User::Affiliation::Role < ActiveRecord::Base
require 'yajl'
class YajlCoder
def dump data
Yajl.dump data
end
def load data
return unless data
Yajl.load data
end
end
serialize :permissions, YajlCoder.new
after_initialize :init
def init
## Sets base permission structure ##
self.permissions ||= YAML.load_file("#{Rails.root}/config/permissions.yml")
end
end
I suggest you have a look at something like attr_bucket. Ostensibly, this can be used to solve some inheritance annoyances, but it will also solve your problem for you. Here is the essence.
It looks like you know what all your permissions are, but you want to serialize all of them into the same database field. But within your actual rails app, you want to treat all your permissions as if they were totally separate fields. This is exactly what a solution like attr_bucket will let you do. Let's take your example, you would do something like this:
class User::Affiliation::Role < ActiveRecord::Base
attr_bucket :permissions => [:permissions_customer_club_events_read, :permissions_customer_club_events_write, :permission_do_crazy_things]
after_initialize :init
def init
## Sets base permission structure ##
self.permissions ||= YAML.load_file("#{Rails.root}/config/permissions.yml")
end
end
Now you will be able to use permissions_customer_club_events_read, permissions_customer_club_events_write, permission_do_crazy_things as if they were separate database fields (this includes using them in forms etc.), but when you actually save your objects all those fields would get 'bucketed' together and serialized into the :permissions field.
The only caveat is the serialization mechanism, I believe attr_bucket will serialize everything using YAML, whereas you were using JSON. If this doesn't matter then you're golden, otherwise you might need to patch attr_bucket to use json instead of YAML which should be pretty straight forward.
Sorry if I did not understand the question ;)
You could have a customdata module, included in your model, and use method_missing:
module CustomData
def self.included(base)
base.instance_eval do
after_save :save_data
end
def method_missing(method, *args, &block)
if method.to_s =~ /^data_/
data[method] ? data[method] : nil
else
super
end
end
def data
#data ||= begin
#get and return your data
end
end
private
def save_data
end
end
With this method, you would have to use f.check_box :data_permissions_customer_club_events_read
It's not really complete, but I hope you get the idea ;)
attr_bucket seems like a good solution too.
This worked out for me in the end, this is how I solved it.
serialize :permissions, YajlCoder.new
after_initialize :init
def init
self.permissions ||= YAML.load_file("#{Rails.root}/config/permissions.yml")['customer']
build_attributes_from self.permissions, :permissions
end
private
def build_attributes_from store, prefix, path=[]
store.each do |k,v|
if v.class == Hash
build_attributes_from v, prefix, ( path + [k] )
else
create_attr_accessors_from prefix, ( path + [k] )
end
end
end
def create_attr_accessors_from prefix, path=[]
method_name = prefix.to_s + "_" + path.join('_')
class << self
self
end.send :define_method, method_name do
self.permissions.dig(:path => path)
end
class << self
self
end.send :define_method, "#{method_name}=" do |value|
self.permissions.dig(:path => path, :value => value)
end
end
And some monkey patching for hashes...
class Hash
def dig(args={})
path = args[:path].to_enum || []
value = args[:value] || nil
if value == nil
path.inject(self) do |location, key|
location.respond_to?(:keys) ? location[key] : nil
end
else
path.inject(self) do |location, key|
location[key] = ( location[key].class == Hash ) ? location[key] : value
end
end
end
end
Now getter and setter methods are generated for all of the serialized fields.
How can you tell if a generate or destroy command has been used to invoke a custom generator?
In Rails 2 you could do this:
if options[:command] == :destroy
...
end
I want to print out some helpful information, but only when rails generate has been called, not when rails destroy is called:
if is_generating
puts "You're generated something!"
end
Thanks.
check the generator class's behavior. It seems you should get either :invoke for generate or :revoke for destroy. For example, I added this:
class PatternGenerator < Rails::Generators::NamedBase
def echo_behavior
p "generate? #{generating?}"
p "destroying? #{destroying?}"
end
protected
def generating?
:invoke == behavior
end
def destroying?
:revoke == behavior
end
end
Running this, I get:
younker % rails g pattern foo
"generate? true"
"destroying? false"
younker % rails destroy pattern foo
"generate? false"
"destroying? true"
Seems to work and makes sense, so that's my final answer.