Module: CMD

Defined in:
lib/rbbt/util/cmd.rb

Constant Summary collapse

TOOLS =
IndiferentHash.setup({})

Class Method Summary collapse

Class Method Details

.bash(cmd) ⇒ Object



69
70
71
# File 'lib/rbbt/util/cmd.rb', line 69

def self.bash(cmd)
  %Q(bash <<EOF\n#{cmd}\nEOF\n)
end

.cmd(tool, cmd = nil, options = {}, &block) ⇒ Object



101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
# File 'lib/rbbt/util/cmd.rb', line 101

def self.cmd(tool, cmd = nil, options = {}, &block)
  options, cmd = cmd, nil if Hash === cmd

  options = Misc.add_defaults options, :stderr => Log::DEBUG
  in_content = options.delete(:in)
  stderr     = options.delete(:stderr)
  pipe       = options.delete(:pipe)
  post       = options.delete(:post)
  log        = options.delete(:log)
  no_fail    = options.delete(:no_fail)
  no_fail    = options.delete(:nofail) if no_fail.nil?
  no_wait    = options.delete(:no_wait)
  xvfb       = options.delete(:xvfb)
  bar        = options.delete(:progress_bar)

  dont_close_in  = options.delete(:dont_close_in)

  log = true if log.nil?
  
  if cmd.nil? && ! Symbol === tool 
    cmd = tool
  else
    tool = get_tool(tool)
    if cmd.nil?
      cmd = tool
    else
      cmd = tool + ' ' + cmd
    end

  end

  case xvfb
  when TrueClass
    cmd = "xvfb-run --server-args='-screen 0 1024x768x24' --auto-servernum #{cmd}"
  when String
    cmd = "xvfb-run --server-args='#{xvfb}' --auto-servernum --server-num=1 #{cmd}"
  when String
  end

  if stderr == true
    stderr = Log::HIGH
  end

  cmd_options = process_cmd_options options
  if cmd =~ /'\{opt\}'/
    cmd.sub!('\'{opt}\'', cmd_options) 
  else
    cmd << " " << cmd_options
  end

  in_content = StringIO.new in_content if String === in_content

  sin, sout, serr, wait_thr = begin
                                Open3.popen3(ENV, cmd)
                              rescue
                                Log.warn $!.message
                                raise ProcessFailed, cmd unless no_fail
                                return
                              end
  pid = wait_thr.pid

  Log.debug{"CMD: [#{pid}] #{cmd}" if log}

  if in_content.respond_to?(:read)
    in_thread = Thread.new(Thread.current) do |parent|
      Thread.current.report_on_exception = false if no_fail
      begin
        begin
          while c = in_content.readpartial(Misc::BLOCK_SIZE)
            sin << c 
          end
        rescue EOFError
        end
        sin.close  unless sin.closed?

        unless dont_close_in
          in_content.close unless in_content.closed? 
          in_content.join if in_content.respond_to? :join 
        end
      rescue
        Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}" unless no_fail
        raise $!
      end
    end
  else
    in_thread = nil
    sin.close
  end

  pids = [pid]

  if pipe

    ConcurrentStream.setup sout, :pids => pids, :autojoin => no_wait, :no_fail => no_fail 

    if (Integer === stderr and log) || bar
      err_thread = Thread.new do
        while line = serr.gets
          bar.process(line) if bar
          sout.log = line
          Log.log "STDERR [#{pid}]: " +  line, stderr if log
        end 
        serr.close
      end
    else
      err_thread = Misc.consume_stream(serr, true)
    end

    sout.threads = [in_thread, err_thread, wait_thr].compact

    sout
  else

    if bar
      err = ""
      err_thread = Thread.new do
        while not serr.eof?
          line = serr.gets 
          bar.process(line) 
          err << line if Integer === stderr and log
        end
        serr.close
      end
    elsif log and Integer === stderr
      err = ""
      err_thread = Thread.new do
        while not serr.eof?
          err << serr.gets 
        end
        serr.close
      end
    else
      Misc.consume_stream(serr, true)
      #serr.close 
      err_thread = nil
      err = ""
    end

    ConcurrentStream.setup sout, :pids => pids, :threads => [in_thread, err_thread].compact, :autojoin => no_wait, :no_fail => no_fail 

    out = StringIO.new sout.read
    sout.close unless sout.closed?

    status = wait_thr.value
    if not status.success? and not no_fail
      if !err.empty?
        raise ProcessFailed.new "Command [#{pid}] #{cmd} failed with error status #{status.exitstatus}.\n#{err}"
      else
        raise ProcessFailed.new "Command [#{pid}] #{cmd} failed with error status #{status.exitstatus}"
      end
    else
      Log.log err, stderr if Integer === stderr and log
    end

    out
  end
end

.cmd_log(*args) ⇒ Object



307
308
309
310
# File 'lib/rbbt/util/cmd.rb', line 307

def self.cmd_log(*args)
  cmd_pid(*args)
  nil
end

.cmd_pid(*args) ⇒ Object



259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
# File 'lib/rbbt/util/cmd.rb', line 259

def self.cmd_pid(*args)
  all_args = *args

  bar = all_args.last[:progress_bar] if Hash === all_args.last

  all_args << {} unless Hash === all_args.last

  level = all_args.last[:log] || 0
  level = 0 if TrueClass === level
  level = 10 if FalseClass === level
  level = level.to_i

  all_args.last[:log] = true
  all_args.last[:pipe] = true

  io = cmd(*all_args)
  pid = io.pids.first

  line = "" if bar
  starting = true
  while c = io.getc
    if starting
      if pid
        Log.logn "STDOUT [#{pid}]: ", level
      else
        Log.logn "STDOUT: ", level
      end
      starting = false
    end
    STDERR << c if Log.severity <= level
    line << c if bar
    if c == "\n"
      bar.process(line) if bar
      starting = true
      line = "" if bar
    end
  end 
  begin
    io.join
    bar.remove if bar
  rescue
    bar.remove(true) if bar
    raise $!
  end

  nil
end

.conda(tool, env = nil, channel = 'bioconda') ⇒ Object



13
14
15
16
17
18
19
# File 'lib/rbbt/util/cmd.rb', line 13

def self.conda(tool, env = nil, channel = 'bioconda')
  if env
    CMD.cmd("bash -l -c '(conda activate #{env} && conda install #{tool} -c #{channel})'")      
  else
    CMD.cmd("bash -l -c 'conda install #{tool} -c #{channel}'")      
  end
end

.get_tool(tool) ⇒ Object



21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
# File 'lib/rbbt/util/cmd.rb', line 21

def self.get_tool(tool)
  return tool.to_s unless TOOLS[tool]

  @@init_cmd_tool ||= IndiferentHash.setup({})
  if !@@init_cmd_tool[tool]
    claim, test, block, cmd = TOOLS[tool]
    begin
      if test
        CMD.cmd(test + " ")
      else
        CMD.cmd("#{tool} --help")
      end
    rescue
      if claim
        claim.produce
      else
        block.call
      end
    end
    version_txt = ""
    version = nil
    ["--version", "-version", "--help", ""].each do |f|
      begin
        version_txt += CMD.cmd("#{tool} #{f} 2>&1", :nofail => true).read
        version = Misc.scan_version_text(version_txt, tool)
        break if version
      rescue
        Log.exception $!
      end
    end

    @@init_cmd_tool[tool] = version || true

    return cmd if cmd
  end

  tool.to_s
end

.gzip_pipe(file) ⇒ Object



65
66
67
# File 'lib/rbbt/util/cmd.rb', line 65

def self.gzip_pipe(file)
  Open.gzip?(file) ? "<(gunzip -c '#{file}')" : "'#{file}'"
end

.process_cmd_options(options = {}) ⇒ Object



73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
# File 'lib/rbbt/util/cmd.rb', line 73

def self.process_cmd_options(options = {})
  add_dashes = Misc.process_options options, :add_option_dashes

  string = ""
  options.each do |option, value|
    raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=.]+$/i
    #raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
    value = value.gsub("'","\\'") if value.to_s.include? "'"

    option = "--" << option.to_s if add_dashes and option.to_s[0] != '-'

    case 
    when value.nil? || FalseClass === value 
      next
    when TrueClass === value
      string << "#{option} "
    else
      if option.to_s.chars.to_a.last == "="
        string << "#{option}'#{value}' "
      else
        string << "#{option} '#{value}' "
      end
    end
  end

  string.strip
end

.tool(tool, claim = nil, test = nil, cmd = nil, &block) ⇒ Object



9
10
11
# File 'lib/rbbt/util/cmd.rb', line 9

def self.tool(tool, claim = nil, test = nil, cmd = nil, &block)
  TOOLS[tool] = [claim, test, block, cmd]
end

.versionsObject



60
61
62
63
# File 'lib/rbbt/util/cmd.rb', line 60

def self.versions
  return {} unless defined? @@init_cmd_tool
  @@init_cmd_tool.select{|k,v| v =~ /\d+\./ }
end