Module: LabInterface

Included in:
AstmServer, SiemensAbgElectrolyteModule
Defined in:
lib/ruby_astm/lab_interface.rb

Defined Under Namespace

Modules: ClassMethods

Constant Summary collapse

ACK = 
"\x06"
ENQ = 
"\x05"
STX = 
"\x02"
LF = 
"\x10"
CR = 
"\x13"
ETX = 
"\x03"
EOT = 
"\x04"

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#data_buffer ⇒ Object

buffer of incoming data.



43
44
45
 
# File 'lib/ruby_astm/lab_interface.rb', line 43

def data_buffer
  @data_buffer
end

#data_bytes ⇒ Object

just an array of byte arrays, cleared on calling process text



35
36
37
 
# File 'lib/ruby_astm/lab_interface.rb', line 35

def data_bytes
  @data_bytes
end

#ethernet_connections ⇒ Object

Returns the value of attribute ethernet_connections.



18
19
20
 
# File 'lib/ruby_astm/lab_interface.rb', line 18

def ethernet_connections
  @ethernet_connections
end

#ethernet_server ⇒ Object

Returns the value of attribute ethernet_server.



20
21
22
 
# File 'lib/ruby_astm/lab_interface.rb', line 20

def ethernet_server
  @ethernet_server
end

#headers ⇒ Object

Returns the value of attribute headers.



38
39
40
 
# File 'lib/ruby_astm/lab_interface.rb', line 38

def headers
  @headers
end

#mapping ⇒ Object

Returns the value of attribute mapping.



39
40
41
 
# File 'lib/ruby_astm/lab_interface.rb', line 39

def mapping
  @mapping
end

#mid_frame_end_detected ⇒ Object

Returns the value of attribute mid_frame_end_detected.



29
30
31
 
# File 'lib/ruby_astm/lab_interface.rb', line 29

def mid_frame_end_detected
  @mid_frame_end_detected
end

#respond_to_queries ⇒ Object

Returns the value of attribute respond_to_queries.



40
41
42
 
# File 'lib/ruby_astm/lab_interface.rb', line 40

def respond_to_queries
  @respond_to_queries
end

#serial_baud ⇒ Object

Returns the value of attribute serial_baud.



24
25
26
 
# File 'lib/ruby_astm/lab_interface.rb', line 24

def serial_baud
  @serial_baud
end

#serial_connections ⇒ Object

Returns the value of attribute serial_connections.



19
20
21
 
# File 'lib/ruby_astm/lab_interface.rb', line 19

def serial_connections
  @serial_connections
end

#serial_parity ⇒ Object

Returns the value of attribute serial_parity.



25
26
27
 
# File 'lib/ruby_astm/lab_interface.rb', line 25

def serial_parity
  @serial_parity
end

#serial_port ⇒ Object

Returns the value of attribute serial_port.



23
24
25
 
# File 'lib/ruby_astm/lab_interface.rb', line 23

def serial_port
  @serial_port
end

#server_ip ⇒ Object

Returns the value of attribute server_ip.



21
22
23
 
# File 'lib/ruby_astm/lab_interface.rb', line 21

def server_ip
  @server_ip
end

#server_port ⇒ Object

Returns the value of attribute server_port.



22
23
24
 
# File 'lib/ruby_astm/lab_interface.rb', line 22

def server_port
  @server_port
end

#test_data_bytes ⇒ Object

gather bytes to store for us to test.



32
33
34
 
# File 'lib/ruby_astm/lab_interface.rb', line 32

def test_data_bytes
  @test_data_bytes
end

#usb_baud ⇒ Object

Returns the value of attribute usb_baud.



27
28
29
 
# File 'lib/ruby_astm/lab_interface.rb', line 27

def usb_baud
  @usb_baud
end

#usb_parity ⇒ Object

Returns the value of attribute usb_parity.



28
29
30
 
# File 'lib/ruby_astm/lab_interface.rb', line 28

def usb_parity
  @usb_parity
end

#usb_port ⇒ Object

Returns the value of attribute usb_port.



26
27
28
 
# File 'lib/ruby_astm/lab_interface.rb', line 26

def usb_port
  @usb_port
end

Class Method Details

.included(base) ⇒ Object 



5
6
7
 
# File 'lib/ruby_astm/lab_interface.rb', line 5

def self.included base
  base.extend ClassMethods
end

Instance Method Details

#checksum(input) ⇒ Object 



101
102
103
104
105
106
107
108
109
110
111
112
 
# File 'lib/ruby_astm/lab_interface.rb', line 101

def checksum(input)
  strString = input
  checksum = strString.sum
  b = checksum.to_s(16)
  strCksm = b[-2..-1]
  if strCksm.length < 2 
    for i in strString.length..1
       strCksm = "0" + strCksm
    end
  end
  strCksm.upcase
end

#generate_response ⇒ Object 



114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
 
# File 'lib/ruby_astm/lab_interface.rb', line 114

def generate_response
  header_responses = self.headers[-1].build_one_response
  header_responses.each_with_index {|response,key|
    message_checksum = checksum(response + terminator + ETX)
    final_resp = STX + response + terminator + ETX + message_checksum + "\r" 
    final_resp_arr = final_resp.bytes.to_a
    final_resp_arr << 10
    if (self.headers[-1].response_sent == false)
      puts "sending the  data as follows----------------------------------------------"
      puts "response sent is:"
      puts self.headers[-1].response_sent
      puts final_resp_arr.to_s
      puts final_resp_arr.pack('c*').gsub(/\r/,'\n')
      send_data(final_resp_arr.pack('c*')) 
      self.headers[-1].response_sent = true if (key == (header_responses.size - 1))
    else
      puts "sending EOT"
      send_data(EOT)
    end
  }
end

#is_mid_frame_end?(bytes_array) ⇒ Boolean

Returns:

  • (Boolean) 


136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
 
# File 'lib/ruby_astm/lab_interface.rb', line 136

def is_mid_frame_end?(bytes_array)

  ## if you get 13,10,2 anywhere, ignore that and the subsequent digit.
  bytes_indices_to_delete = []
  unless bytes_array.blank?
    bytes_array.each_with_index{|val,key|
      if bytes_array.size >= (key + 2)
        if bytes_array[key..(key+2)] == [13,10,2]
          bytes_indices_to_delete.push(key - 3)
          bytes_indices_to_delete.push(key - 2)
          bytes_indices_to_delete.push(key - 1)
          bytes_indices_to_delete.push(key)
          bytes_indices_to_delete.push(key + 1)
          bytes_indices_to_delete.push(key + 2)
        end
      end
    }
  end
  bytes_indices_to_delete
end

#pre_process_bytes(byte_arr, concat) ⇒ Object 



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
 
# File 'lib/ruby_astm/lab_interface.rb', line 157

def pre_process_bytes(byte_arr,concat)

    puts byte_arr.to_s
    indices_to_delete = is_mid_frame_end?(byte_arr)
    #puts "indices to delete"
    #puts indices_to_delete.to_s

    if self.mid_frame_end_detected == true
      #puts "deletected mid fram is true, so deleting first byte before delete"
      #puts byte_arr.to_s
      byte_arr = byte_arr[1..-1]
      #puts "after deleteing"
      #puts byte_arr.to_s
      self.mid_frame_end_detected = false
    end

    unless indices_to_delete.blank?
      if byte_arr[(indices_to_delete[-1] + 1)]
        #puts "before deleting frame number "
        #puts byte_arr.to_s
        byte_arr.delete_at((indices_to_delete[-1] + 1))
        #puts "after deleting"
        #puts byte_arr.to_s
      else
        self.mid_frame_end_detected = true
      end
    end
    #puts "byte arr before reject"
    byte_arr = byte_arr.reject.with_index{|c,i|  indices_to_delete.include? i}
    

    byte_arr.each do |byte|
      x = [byte].pack('c*').force_encoding('UTF-8')
      if x == "\r"
        concat+="\n"
      elsif x == "\n"
        #puts "new line found --- "
        concat+=x
        #puts "last thing in concat."
        #puts concat[-1].to_s
      else
        concat+=x
      end
    end

    concat



end

#process_electrolytes(data_bytes) ⇒ Object

@param :

[bytes],.…


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
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
 
# File 'lib/ruby_astm/lab_interface.rb', line 214

def process_electrolytes(data_bytes)
  #puts "came to process electrolytes_plain_text"
  byte_arr = data_bytes.flatten
  #puts "the end part of the arr is"
  return if byte_arr[-4..-1] != SIEMENS_ELECTROLYTE_END
  self.data_bytes = []
  concat = ""
  byte_arr.each do |byte|
      x = [byte].pack('c*').force_encoding('UTF-8')
      if x == "\r"
        concat+="\n"
      elsif x == "\n"
        #puts "new line found --- "
        concat+=x
        #puts "last thing in concat."
        #puts concat[-1].to_s
      else
        concat+=x
      end
  end
  ## nwo write concat to file
  ## File.open("electrolytes_plain_text.txt", 'a+') { |file| file.write(concat) }
  ## Header
  ## Patient
  ## Order
  ## Result
  ## Terminator

  ## GET PO2
  concat.scan(/pCO2\s+(?<pco>(\d+)(\.\d)*)(\^|v)?\s+mmHg/) do |k|
    n = Regexp.last_match
    puts n[:pco].to_s
  end

  ## GET PCO2
  concat.scan(/pO2\s+(?<po>(\d+)(\.\d)*)(\^|v)?\s+mmHg/) do |k|
    n = Regexp.last_match
    puts n[:po].to_s
  end

  ## GET PH

  ## GET NA+

  ## GET K+

  ## GET CL-

  ## GET PATIENT_ID

  ## GET DATE AND TIME

  start_measure = false
  
  concat.split(/\n/).each do |line|
    if line =~ /348\-D718/
      header = Header.new({:line => line})
      self.headers ||= []
      self.headers << header
    elsif line =~ /\-{32}/
    elsif line =~ /Patient\s+ID/
    elsif line =~ /Measured/
    elsif line =~ /outside ref/
    else
    end
  end

end

#process_text(text) ⇒ Object 



412
413
414
415
416
417
418
419
420
 
# File 'lib/ruby_astm/lab_interface.rb', line 412

def process_text(text)
    puts "text is:"
    puts text
    text.split("\n").each do |l|
      puts "doing line:#{l}" 
    line = Line.new({:text => l})
      process_type(line)
    end
end

#process_text_file(full_file_path) ⇒ Object

can process a file which contains ASTM output. this method is added so that you can load previously generated ASTM output into your database it also simplifies testing.



84
85
86
87
88
89
90
91
 
# File 'lib/ruby_astm/lab_interface.rb', line 84

def process_text_file(full_file_path)
  #full_file_path ||= File.join root,'../test','resources','sysmex_550_sample.txt'
  IO.read(full_file_path).each_line do |line|
    line.split('\\r').each do |txt| 
      process_text(txt)
    end
  end
end

#process_type(line) ⇒ Object 



422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
 
# File 'lib/ruby_astm/lab_interface.rb', line 422

def process_type(line)
    case line.type
    when "Hl7_Header"
      hl7_header = Hl7Header.new({:line => line})
      self.headers ||= []
      self.headers << hl7_header
    when "Hl7_Observation"
      unless self.headers.blank?
        unless self.headers[-1].patients.blank?
          unless self.headers[-1].patients[-1].orders[-1].blank?
            hl7_observation = Hl7Observation.new({:line => line})
            self.headers[-1].patients[-1].orders[-1].results[hl7_observation.name] ||= hl7_observation
          end
        end
      end
    when "Hl7_Patient"
      hl7_patient = Hl7Patient.new({:line => line})
      self.headers[-1].patients << hl7_patient
    when "Hl7_Order"
      unless self.headers[-1].patients.blank?
        hl7_order = Hl7Order.new({:line => line, :patient_id => self.headers[-1].patients[-1].patient_id})
        self.headers[-1].patients[-1].orders << hl7_order
      end
    when "Header"
      puts "got header"
      header = Header.new({:line => line})
      self.headers ||= []
      self.headers << header
    when "Query"
      puts "got query"
      query = Query.new({:line => line})
      unless self.headers.blank?
        self.headers[-1].queries << query
      end
    when "Patient"
      puts "got patient."
      patient = Patient.new({:line => line})
      unless self.headers.blank?
        self.headers[-1].patients << patient
      end
    when "Order"
      order = Order.new({:line => line})
      unless self.headers.blank?
        unless self.headers[-1].patients.blank?
          self.headers[-1].patients[-1].orders << order
        end
      end
    when "Result"
      result = Result.new({:line => line})
      unless self.headers.blank?
        unless self.headers[-1].patients.blank?
          unless self.headers[-1].patients[-1].orders[-1].blank?
            self.headers[-1].patients[-1].orders[-1].results[result.name] ||= result
          end
        end
      end
    when "Terminator"
      ## it didn't terminate so there was no commit being called.
      unless self.headers.blank?
        puts "got terminator."
        self.headers[-1].commit
      end
    end
end

#receive_data(data) ⇒ Object 



283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
 
# File 'lib/ruby_astm/lab_interface.rb', line 283

def receive_data(data)
    

  begin


    self.data_buffer ||= ''

    #puts "incoming data bytes."

    concat = ""
    
 
    byte_arr = data.bytes.to_a
    
    self.test_data_bytes ||= []
    
    self.data_bytes ||= []

    self.test_data_bytes.push(byte_arr)

    self.data_bytes.push(byte_arr)

  
    concat = pre_process_bytes(byte_arr,concat)
 
    puts "concat is:"
    
    puts concat.to_s
    
    self.data_buffer << concat

    ## if the last byte is EOT, then call process text.
    ## inside that split by line and process one at a time.
    ##process_text(concat)   
    #puts "data bytes -1: #{self.data_bytes[-1]}"
    #puts "data bytes 0: #{self.data_bytes[0]}"   
    #if self.data_bytes[0] == ELECTROLYTE_START
    #self.process_electrolytes(self.data_bytes) 
    #end

    if data.bytes.to_a[-1] == 4
      puts "GOT EOT --- PROCESSING BUFFER, AND CLEARING."
      process_text(self.data_buffer)
      #root_path = File.dirname __dir
      #puts "root path #{root_path}"
      #IO.write((File.join root_path,'test','resources','roche_multi_frame_bytes.txt'),self.test_data_bytes.to_s)
      #puts self.test_data_bytes.flatten.to_s
      self.data_buffer = ''
      unless self.headers.blank?
        if self.headers[-1].queries.blank?
          #puts "no queries in header so sending ack after getting EOT and processing the buffer"
          send_data(ACK)
        else
          #puts "sending ENQ"
          send_data(ENQ)
        end
      else
        puts "sending catch all --------------- ACK --------------"
        send_data(ACK)
      end
    elsif data.bytes.to_a[0] == 6
      puts "GOT ACK --- GENERATING RESPONSE"
      unless self.headers.blank?
        header_responses = self.headers[-1].build_one_response({machine_name: self.headers[-1].machine_name})
        ## if no queries then, we have to send ack.
        if header_responses.blank?
          #puts "sending ACK since there are no queries in the header"
          send_data(ACK)
        end
        header_responses.each_with_index {|response,key|
          message_checksum = checksum(response + terminator + ETX)
          final_resp = STX + response + terminator + ETX + message_checksum + "\r" 
          final_resp_arr = final_resp.bytes.to_a
          final_resp_arr << 10
          if (self.headers[-1].response_sent == false)
            #puts "sending the  data as follows----------------------------------------------"
            #puts "response sent is:"
            #puts self.headers[-1].response_sent
            #puts final_resp_arr.pack('c*').gsub(/\r/,'\n')
            send_data(final_resp_arr.pack('c*')) 
            self.headers[-1].response_sent = true if (key == (header_responses.size - 1))
          else
            #puts "sending EOT"
            send_data(EOT)
          end
        }
      else
        #puts "NO HEADERS PRESENT --- "
      end
    elsif data.bytes.to_a[0] == 255
      puts  " ----------- got 255 data -----------, not sending anything back. "
    else
      #unless self.data_buffer.blank?
      #  puts self.data_buffer.gsub(/\r/,'\n').to_s
      #end
      ## send the header 
      #puts "--------- SENT ACK -----------"
      ## strip non utf 8 characters from it.
      self.data_buffer.encode!('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '')
      if self.data_buffer =~ /MSH\|/
        #puts " -------------- HEADERS ARE BLANK WITH HL7, sending ack. ------------ "
        process_text(self.data_buffer)
        self.data_buffer = ''
        if self.headers.size > 0
          self.headers[-1].commit
          send_data(self.headers[-1].generate_ack_success_response)
        end
      else
        #puts " -------------- HEADERS ARE BLANK NOT HL7, sending ack. ------------ "
        send_data(ACK)
      end
    end

  rescue => e
    
    #self.headers = []
    AstmServer.log("data was: " + self.data_buffer + "error is:" + e.backtrace.to_s)
    #send_data(EOT)
  end

end

#root ⇒ Object

returns the root directory of the gem.



77
78
79
 
# File 'lib/ruby_astm/lab_interface.rb', line 77

def root
    File.dirname __dir__
end

#send_enq ⇒ Object 



406
407
408
409
410
 
# File 'lib/ruby_astm/lab_interface.rb', line 406

def send_enq
  #puts "enq as bytes is:"
  #puts ENQ.unpack('c*')
  send_data(ENQ)
end

#terminator ⇒ Object 



96
97
98
 
# File 'lib/ruby_astm/lab_interface.rb', line 96

def terminator
  "L|1|N\r"
end

#unbind ⇒ Object

1.STX + response + LF + ETX 2.response 3.STX + response + “L|1|Nr” + ETX 4.response + “L|1|Nr”



493
494
495
 
# File 'lib/ruby_astm/lab_interface.rb', line 493

def unbind
   puts "-- someone disconnected from the echo server!"
end

#write_bytes_to_file(bytes) ⇒ Object 



208
209
210
 
# File 'lib/ruby_astm/lab_interface.rb', line 208

def write_bytes_to_file(bytes)

end