I am attempting to perform a BLAST search using BioRuby on a Windows XP machine with Ruby 1.9.3 and BioRuby 1.4.3_0001. I have installed the necessary dependencies, e.g., cairo, but the output is as follows:
C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_require.rb:45:in `r
equire': cannot load such file -- cairo.so (LoadError)
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:45:in `require'
from C:/Ruby193/lib/ruby/gems/1.9.1/gems/cairo-1.12.6-x86-mingw32/lib/ca
iro.rb:46:in `rescue in <top (required)>'
from C:/Ruby193/lib/ruby/gems/1.9.1/gems/cairo-1.12.6-x86-mingw32/lib/ca
iro.rb:42:in `<top (required)>'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:110:in `require'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:110:in `rescue in require'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:35:in `require'
from C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-graphics-1.4/lib/bio-graphi
cs.rb:11:in `<top (required)>'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:110:in `require'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:110:in `rescue in require'
from C:/Ruby193/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_requir
e.rb:35:in `require'
from bio283.rb:2:in `<main>'
The sample code I am using is as follows:
require 'bio'
require 'bio-graphics'
remote_blast_factory = Bio::Blast.remote('blastp', 'swissprot',
'-e 0.0001', 'genomenet')
seq = Bio::Sequence::AA.new('MFRTKRSALVRRLWRSRAPGGEDEEEGAGGGGGGGELRGE')
# run the actual BLAST by querying the factory
report = remote_blast_factory.query(seq)
# Then, to parse the report, see Bio::Blast::Report
report.each do |hit|
puts hit.evalue # E-value
puts hit.sw # Smith-Waterman score (*)
puts hit.identity # % identity
puts hit.overlap # length of overlapping region
puts hit.query_id # identifier of query sequence
puts hit.query_def # definition(comment line) of query sequence
puts hit.query_len # length of query sequence
puts hit.query_seq # sequence of homologous region
puts hit.target_id # identifier of hit sequence
puts hit.target_def # definition(comment line) of hit sequence
puts hit.target_len # length of hit sequence
puts hit.target_seq # hit of homologous region of hit sequence
puts hit.query_start # start position of homologous
# region in query sequence
puts hit.query_end # end position of homologous region
# in query sequence
puts hit.target_start # start position of homologous region
# in hit(target) sequence
puts hit.target_end # end position of homologous region
# in hit(target) sequence
puts hit.lap_at # array of above four numbers
end
Could someone explain why the problem is occurring? I noticed the file name 'cairo.so' in the output. Could that relate to a linux/unix op. sys?
Thanks,
Caitlin
One of the libraries you installed depends on cairo. You have to install it. The .so extension is a Ruby library written in C, used in Unix. In Windows, you need a corresponding .dll file installed.
Related
I'm trying to write a simple test for a ruby script that uses gets and I'm experiencing some weird behavior.
When I run the test with rspec it passes fine, but as soon as I run rspec with any flags, like rspec -f json or rspec -O rand the test will fail and give me No such file or directory # rb_sysopen - -O, where -O is whatever the flag that was run.
Stranger still is that if I run rspec and specify the test file like rspec spec/gets_spec.rb, I get a completely different error:
Failure/Error: expect { require_relative '../gets' }.to output("Hello, Lena!\n").to_stdout
expected block to output "Hello, Lena!\n" to stdout, but output "Hello, Describe \"gets.rb\" do!\n"
Diff:
## -1,2 +1,2 ##
-Hello, Lena!
+Hello, Describe "gets.rb" do!
# ./spec/gets_spec.rb:14:in `block (2 levels) in <top (required)>'
I'm having trouble figuring out the right way to write my test so that this doesn't happen but I'm not sure what part of my code needs to change.
I'm using ruby 2.6.3
I learned about testing input from this question
The script, gets.rb, looks like
puts "Hello, #{gets.chomp.capitalize}!"
My test looks like
describe "gets.rb" do
before do
$stdin = StringIO.new("lena")
end
after do
$stdin = STDIN
end
it "should output 'Hello, name!'" , points: 1 do
allow($stdin).to receive(:gets).and_return("lena")
expect { require_relative "../gets" }.to output("Hello, Lena!\n").to_stdout
end
end
Here's the full failure message:
Failures:
1) gets.rb should output 'Hello, name!'
Failure/Error: expect { require_relative '../gets' }.to output("Hello, Lena!\n").to_stdout
Errno::ENOENT:
No such file or directory # rb_sysopen - -O
#./gets.rb:1:in `gets'
# ./gets.rb:1:in `gets'
# ./gets.rb:1:in `<top (required)>'
# ./spec/gets_spec.rb:14:in `require_relative'
# ./spec/gets_spec.rb:14:in `block (3 levels) in <top (required)>'
# ./spec/gets_spec.rb:14:in `block (2 levels) in <top (required)>'
You can try to use a little different approach:
describe "gets.rb" do
it "should output 'Hello, name!'" do
allow_any_instance_of(Object).to receive(:gets).and_return("lena")
expect { require_relative "../gets.rb" }.to output("Hello, Lena!\n").to_stdout
end
end
allow_any_instance_of I took from https://makandracards.com/makandra/41096-stubbing-terminal-user-input-in-rspec
Reading user input in console applications is usually done using Kernel#gets.
The page suggests to use Object.any_instance.stub(gets: 'user input') but it's deprecated syntax already and I've updated it.
here's my code:
> !#usr/bin/ruby
require 'fileutils'
Dir.chdir "/home/john/Documents"
if (Dir.exist?("Photoshoot") === false) then
Dir.mkdir "Photoshoot"
puts "Directory: 'Photoshoot' created"
end
Dir.chdir "/run/user/1000/gvfs"
camdirs = Dir.glob('*')
numcams = camdirs.length
camnum = 0
campath = []
while camnum < numcams do
campath.push("/run/user/1000/gvfs/#{camdirs[camnum]}/DCIM")
puts campath[camnum]
camnum += 1
end
campath.each do |path|
Dir.chdir (path)
foldnum = 0
foldir = Dir.glob('*')
puts foldir
Dir.entries("#{path}/#{foldir[foldnum]}").each do |filename|
filetype = File.extname(filename)
if filetype == ".JPG"
FileUtils.mv("#{path}/#{foldir[foldnum]}/#{filename}", "/home/john/Documents/Photoshoot")
end
foldnum += 1
end
end
puts "#{numcams} cameras detected"
I'm just trying to go into some cameras I have connected and extract all the images into a file but its giving me this error. One of the things that's messing me up is that the images are stored in sub-folders under DCIM. When I just use .entries it gives me the folders the images are in as well as the images.
/usr/lib/ruby/2.3.0/fileutils.rb:1387:in `copy': unknown file type: /run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C021%5D/DCIM//IMG_0092.JPG (RuntimeError)
from /usr/lib/ruby/2.3.0/fileutils.rb:472:in `block in copy_entry'
from /usr/lib/ruby/2.3.0/fileutils.rb:1498:in `wrap_traverse'
from /usr/lib/ruby/2.3.0/fileutils.rb:469:in `copy_entry'
from /usr/lib/ruby/2.3.0/fileutils.rb:530:in `rescue in block in mv'
from /usr/lib/ruby/2.3.0/fileutils.rb:527:in `block in mv'
from /usr/lib/ruby/2.3.0/fileutils.rb:1571:in `block in fu_each_src_dest'
from /usr/lib/ruby/2.3.0/fileutils.rb:1585:in `fu_each_src_dest0'
from /usr/lib/ruby/2.3.0/fileutils.rb:1569:in `fu_each_src_dest'
from /usr/lib/ruby/2.3.0/fileutils.rb:517:in `mv'
from /home/john/Desktop/TestExtract.rb:34:in `block (2 levels) in <main>'
from /home/john/Desktop/TestExtract.rb:31:in `each'
from /home/john/Desktop/TestExtract.rb:31:in `block in <main>'
from /home/john/Desktop/TestExtract.rb:26:in `each'
from /home/john/Desktop/TestExtract.rb:26:in `<main>'
/run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C022%5D/DCIM
/run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C021%5D/DCIM
/run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C020%5D/DCIM
104___03
105___04
106___05
102___01
[Finished in 0.1s with exit code 1]
[shell_cmd: ruby "/home/john/Desktop/TestExtract.rb"]
[dir: /home/john/Desktop]
[path: /home/john/bin:/home/john/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin]
Any advice? I can't figure out what's wrong.
The reason the path to your files looks strange is because your camera storage has been mounted using FUSE. If you look very closely, you'll see that it is looking for:
/run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C021%5D/DCIM//IMG_0092.JPG
You have two forward slashes before the final filename. Try correcting this on line 34 of your app.
If the problem still manifests then it is possible that the user running the operation in Ruby does not have permission to that filesystem or the manner in which the paths are constructed by FUSE is not compatible with Ruby FileUtils.
You can try to run:
cat /run/user/1000/gvfs/gphoto2:host=%5Busb%3A002%2C021%5D/DCIM/IMG_0092.JPG
as the same user that is running the Ruby process to ensure you have read permission to the filesystem.
I have a directory with 100+ zip files and I need to read the files inside the zip files to do some data processing, without unzipping the archive.
Is there a Ruby library to read the contents of files in zip archives, without unzipping the file?
Using rubyzip gives an error:
require 'zip'
Zip::File.open('my_zip.zip') do |zip_file|
# Handle entries one by one
zip_file.each do |entry|
# Extract to file/directory/symlink
puts "Extracting #{entry.name}"
entry.extract('here')
# Read into memory
content = entry.get_input_stream.read
end
end
Gives this error:
test.rb:12:in `block (2 levels) in <main>': undefined method `read' for Zip::NullInputStream:Module (NoMethodError)
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/entry_set.rb:42:in `call'
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/entry_set.rb:42:in `block in each'
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/entry_set.rb:41:in `each'
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/entry_set.rb:41:in `each'
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/central_directory.rb:182:in `each'
from test.rb:6:in `block in <main>'
from .gem/ruby/gems/rubyzip-1.1.6/lib/zip/file.rb:99:in `open'
from test.rb:4:in `<main>'
The Zip::NullInputStream is returned if the entry is a directory and not a file, could that be the case?
Here's a more robust variation of the code:
#!/usr/bin/env ruby
require 'rubygems'
require 'zip'
Zip::File.open('my_zip.zip') do |zip_file|
# Handle entries one by one
zip_file.each do |entry|
if entry.directory?
puts "#{entry.name} is a folder!"
elsif entry.symlink?
puts "#{entry.name} is a symlink!"
elsif entry.file?
puts "#{entry.name} is a regular file!"
# Read into memory
entry.get_input_stream { |io| content = io.read }
# Output
puts content
else
puts "#{entry.name} is something unknown, oops!"
end
end
end
I came across the same issue and checking for if entry.file?, before entry.get_input_stream.read, resolved the issue.
require 'zip'
Zip::File.open('my_zip.zip') do |zip_file|
# Handle entries one by one
zip_file.each do |entry|
# Extract to file/directory/symlink
puts "Extracting #{entry.name}"
entry.extract('here')
# Read into memory
if entry.file?
content = entry.get_input_stream.read
end
end
end
I am working through some Ruby problem sets. I'm using Ubuntu 14.04, rbenv 0.4.0-98-g13a474c, rspec 3.1.4, and ruby 2.0.0p353. I'm running into the following errors for every test I run and I'm hoping someone might be able to guide me in the right direction to a solution.
I have run rspec tests successfully in the past but I can't seem to figure out the issue with my current setup.
Here is the message I receive for every test I run:
6) age is an integer
Failure/Error: Unable to find matching line from backtrace
ArgumentError:
wrong number of arguments (0 for 1)
# /usr/lib/ruby/vendor_ruby/rspec/mocks.rb:10:in `setup'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/mocking_adapters/rspec.rb:19:in `setup_mocks_for_rspec'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example.rb:366:in `run_before_example'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example.rb:150:in `block in run'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example.rb:328:in `with_around_example_hooks'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example.rb:148:in `run'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example_group.rb:500:in `block in run_examples'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example_group.rb:496:in `map'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example_group.rb:496:in `run_examples'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/example_group.rb:463:in `run'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:111:in `block (2 levels) in run_specs'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:111:in `map'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:111:in `block in run_specs'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/reporter.rb:53:in `report'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:107:in `run_specs'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:85:in `run'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:69:in `run'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/lib/rspec/core/runner.rb:37:in `invoke'
# /var/lib/gems/1.9.1/gems/rspec-core-3.1.4/exe/rspec:4:in `<top (required)>'
# /usr/local/bin/rspec:23:in `load'
# /usr/local/bin/rspec:23:in `<main>'
#
# Showing full backtrace because every line was filtered out.
# See docs for RSpec::Configuration#backtrace_exclusion_patterns and
# RSpec::Configuration#backtrace_inclusion_patterns for more information.
Edit: Here is an example of one of the spec files, however, the issue comes up on about 20 spec files. I know my solutions are correct and my peers aren't having the same issues I am:
first_name = "M"
last_name = "R"
age = 23
describe 'first_name' do
it "is defined as a local variable" do
expect(defined?(first_name)).to eq 'local-variable'
end
it "is a String" do
expect(first_name).to be_a String
end
end
describe 'last_name' do
it "is defined as a local variable" do
expect(defined?(last_name)).to eq 'local-variable'
end
it "be a String" do
expect(last_name).to be_a String
end
end
describe 'age' do
it "is defined as a local variable" do
expect(defined?(age)).to eq 'local-variable'
end
it "is an integer" do
expect(age).to be_a Fixnum
end
end
I'm currently on Chapter 7 of Hartl's Tutorial, and every time I run
bundle exec rspec spec/
the following results:
/Users/siciliana/sample_app/spec/spec_helper.rb:31:in `block in <top (required)>': undefined method `infer_base_class_for_anonymous_controllers=' for #<RSpec::Core::Configuration:0x007f7fb3a62b80> (NoMethodError)
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core.rb:79:in `configure'
from /Users/siciliana/sample_app/spec/spec_helper.rb:11:in `<top (required)>'
from /Users/siciliana/sample_app/spec/models/user_spec.rb:12:in `require'
from /Users/siciliana/sample_app/spec/models/user_spec.rb:12:in `<top (required)>'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/configuration.rb:419:in `load'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/configuration.rb:419:in `block in load_spec_files'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/configuration.rb:419:in `map'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/configuration.rb:419:in `load_spec_files'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/command_line.rb:18:in `run'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/runner.rb:80:in `run_in_process'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/runner.rb:69:in `run'
from /usr/local/rvm/gems/ruby-2.0.0-p0/gems/rspec-core-2.6.4/lib/rspec/core/runner.rb:11:in `block in autorun'
Can someone please explain what is happening here to an absolute newbie?
spec_helper.rb :
# This file is copied to spec/ when you run 'rails generate rspec:install'
ENV["RAILS_ENV"] ||= 'test'
require File.expand_path("../../config/environment", __FILE__)
require 'rspec/rails'
require 'rspec/autorun'
#
RSpec.configure do |config|
# ## Mock Framework
#
# If you prefer to use mocha, flexmock or RR, uncomment the appropriate line:
#
# config.mock_with :mocha
# config.mock_with :flexmock
# config.mock_with :rr
# Remove this line if you're not using ActiveRecord or ActiveRecord fixtures
config.fixture_path = "#{::Rails.root}/spec/fixtures"
# If you're not using ActiveRecord, or you'd prefer not to run each of your
# examples within a transaction, remove the following line or assign false
# instead of true.
config.use_transactional_fixtures = true
# If true, the base class of anonymous controllers will be inferred
# automatically. This will be the default behavior in future versions of
# rspec-rails.
config.infer_base_class_for_anonymous_controllers = false
# Run specs in random order to surface order dependencies. If you find an
# order dependency and want to debug it, you can fix the order by providing
# the seed, which is printed after each run.
# --seed 1234
config.order = "random"
end
I was getting the same error (although not following the tutorial).
I believe this setting requires 'rspec/rails'
My solution was to move the line
config.infer_base_class_for_anonymous_controllers = # whatever
From spec_helper.rb to rails_helper.rb.