ruby_astm 1.4.3 → 1.4.4
Sign up to get free protection for your applications and to get access to all the features.
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 1edecd39318ba2231234a0bd46de36f2eded3843
|
4
|
+
data.tar.gz: c0da0a6d63ec31c478b083ecbf11c5772f709ab9
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 2b4ad9ac1b9db8eedcddf90db7fb09a2b8868388f8268591b7273900e66f4baeebf447dc93ec4772398fd87928b5edf2f591d20d895daa12a5db16e7ace0d678
|
7
|
+
data.tar.gz: 72c2afa43a44ae1d6c20ea21e26e8d9ea3cd357495c291a08694fdc1d0f65289b23b5c0e5ec5b296bf9731ddc667bd6fb9aac8c849a0ed90c467cbf6b6fc9f0d
|
data/lib/ruby_astm.rb
CHANGED
@@ -17,5 +17,6 @@ require_relative "ruby_astm/HL7/hl7_header"
|
|
17
17
|
require_relative "ruby_astm/HL7/hl7_patient"
|
18
18
|
require_relative "ruby_astm/HL7/hl7_order"
|
19
19
|
require_relative "ruby_astm/HL7/hl7_observation"
|
20
|
+
require_relative "ruby_astm/custom/siemens_abg_electrolyte_module"
|
20
21
|
require_relative "ruby_astm/custom/siemens_abg_electrolyte_server"
|
21
22
|
|
@@ -9,27 +9,6 @@ require "rest-firebase"
|
|
9
9
|
class AstmServer
|
10
10
|
|
11
11
|
include LabInterface
|
12
|
-
|
13
|
-
|
14
|
-
def self.log(message)
|
15
|
-
puts "" + message
|
16
|
-
$redis.zadd("ruby_astm_log",Time.now.to_i,message)
|
17
|
-
end
|
18
|
-
|
19
|
-
def self.root_path
|
20
|
-
File.dirname __dir__
|
21
|
-
end
|
22
|
-
|
23
|
-
def self.default_mappings
|
24
|
-
File.join AstmServer.root_path,"mappings.json"
|
25
|
-
end
|
26
|
-
|
27
|
-
$ENQ = "[5]"
|
28
|
-
$start_text = "[2]"
|
29
|
-
$end_text = "[3]"
|
30
|
-
$record_end = "[13]"
|
31
|
-
$frame_end = "[10]"
|
32
|
-
|
33
12
|
|
34
13
|
## DEFAULT SERIAL PORT : /dev/ttyS0
|
35
14
|
## DEFAULT USB PORT : /dev/ttyUSB0
|
@@ -38,7 +17,7 @@ class AstmServer
|
|
38
17
|
#def initialize(server_ip=nil,server_port=nil,mpg=nil,respond_to_queries=false,serial_port='/dev/ttyS0',usb_port='/dev/ttyUSB0',serial_baud=9600,serial_parity=8,usb_baud=19200,usb_parity=8)
|
39
18
|
def initialize(ethernet_connections,serial_connections,mpg=nil,respond_to_queries=nil)
|
40
19
|
$redis = Redis.new
|
41
|
-
|
20
|
+
self.class.log("Initializing AstmServer")
|
42
21
|
self.ethernet_connections = ethernet_connections
|
43
22
|
self.serial_connections = serial_connections
|
44
23
|
self.server_ip = server_ip || "127.0.0.1"
|
@@ -50,7 +29,7 @@ class AstmServer
|
|
50
29
|
self.usb_port = usb_port
|
51
30
|
self.usb_baud = usb_baud
|
52
31
|
self.usb_parity = usb_parity
|
53
|
-
$mappings = JSON.parse(IO.read(mpg ||
|
32
|
+
$mappings = JSON.parse(IO.read(mpg || self.class.default_mappings))
|
54
33
|
end
|
55
34
|
|
56
35
|
def start_server
|
@@ -59,7 +38,7 @@ class AstmServer
|
|
59
38
|
raise "please provide a valid ethernet configuration with ip address" unless econn[:server_ip]
|
60
39
|
raise "please provide a valid ethernet configuration with port" unless econn[:server_port]
|
61
40
|
EventMachine::start_server econn[:server_ip], econn[:server_port], LabInterface
|
62
|
-
|
41
|
+
self.class.log("Running ETHERNET with configuration #{econn}")
|
63
42
|
end
|
64
43
|
self.serial_connections.each do |sconn|
|
65
44
|
raise "please provide a valid serial configuration with port address" unless sconn[:port_address]
|
@@ -0,0 +1,322 @@
|
|
1
|
+
module SiemensAbgElectrolyteModule
|
2
|
+
|
3
|
+
include LabInterface
|
4
|
+
|
5
|
+
def self.included base
|
6
|
+
base.extend ClassMethods
|
7
|
+
end
|
8
|
+
|
9
|
+
|
10
|
+
SIEMENS_ELECTROLYTE_END = [10,10,10,10]
|
11
|
+
ELECTROLYTE_START = [45, 45, 45, 32]
|
12
|
+
attr_accessor :current_text_segment
|
13
|
+
|
14
|
+
def get_po2
|
15
|
+
m = []
|
16
|
+
self.current_text_segment.scan(/pO2\s+(?<k>(\d+)(\.\d)*)(\^|v)?\s+mmHg/) do |l|
|
17
|
+
n = Regexp.last_match
|
18
|
+
m << n[:k].to_s
|
19
|
+
end
|
20
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
21
|
+
return m[0] if m.size == 1
|
22
|
+
return nil
|
23
|
+
end
|
24
|
+
|
25
|
+
def get_pco2
|
26
|
+
m = []
|
27
|
+
self.current_text_segment.scan(/pCO2\s+(?<k>(\d+)(\.\d)*)(\^|v)?\s+mmHg/) do |l|
|
28
|
+
n = Regexp.last_match
|
29
|
+
m << n[:k].to_s
|
30
|
+
end
|
31
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
32
|
+
return m[0] if m.size == 1
|
33
|
+
return nil
|
34
|
+
end
|
35
|
+
|
36
|
+
def get_ph
|
37
|
+
m = []
|
38
|
+
self.current_text_segment.scan(/pH\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+$/) do |l|
|
39
|
+
n = Regexp.last_match
|
40
|
+
m << n[:k].to_s
|
41
|
+
end
|
42
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
43
|
+
return m[0] if m.size == 1
|
44
|
+
return nil
|
45
|
+
end
|
46
|
+
|
47
|
+
def get_na
|
48
|
+
m = []
|
49
|
+
self.current_text_segment.scan(/Na\+\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+mmol\/L/) do |l|
|
50
|
+
n = Regexp.last_match
|
51
|
+
m << n[:k].to_s
|
52
|
+
end
|
53
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
54
|
+
return m[0] if m.size == 1
|
55
|
+
return nil
|
56
|
+
end
|
57
|
+
|
58
|
+
def get_k
|
59
|
+
m = []
|
60
|
+
self.current_text_segment.scan(/K\+\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+mmol\/L/) do |l|
|
61
|
+
n = Regexp.last_match
|
62
|
+
m << n[:k].to_s
|
63
|
+
end
|
64
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
65
|
+
return m[0] if m.size == 1
|
66
|
+
return nil
|
67
|
+
end
|
68
|
+
|
69
|
+
def get_cl
|
70
|
+
m = []
|
71
|
+
self.current_text_segment.scan(/Cl\-\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+mmol\/L/) do |l|
|
72
|
+
n = Regexp.last_match
|
73
|
+
m << n[:k].to_s
|
74
|
+
end
|
75
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
76
|
+
return m[0] if m.size == 1
|
77
|
+
return nil
|
78
|
+
end
|
79
|
+
|
80
|
+
def get_patient_id
|
81
|
+
m = []
|
82
|
+
self.current_text_segment.scan(/Patient\s+ID\s+(?<k>\d+)$/) do |l|
|
83
|
+
n = Regexp.last_match
|
84
|
+
m << n[:k].to_s
|
85
|
+
end
|
86
|
+
raise "more than one result #{m.to_s}" if (m.size > 1)
|
87
|
+
return m[0] if m.size == 1
|
88
|
+
return nil
|
89
|
+
end
|
90
|
+
|
91
|
+
## we override the lab interface methods
|
92
|
+
## and we don't pollute the lab interface itself.
|
93
|
+
## as this is a custom analyzer.
|
94
|
+
## @param[Array] :
|
95
|
+
## [[bytes],[bytes]....]
|
96
|
+
def process_electrolytes(data_bytes)
|
97
|
+
#puts "came to process electrolytes_plain_text"
|
98
|
+
byte_arr = data_bytes.flatten
|
99
|
+
#puts "the end part of the arr is"
|
100
|
+
return if byte_arr[-4..-1] != SIEMENS_ELECTROLYTE_END
|
101
|
+
self.data_bytes = []
|
102
|
+
concat = ""
|
103
|
+
byte_arr.each do |byte|
|
104
|
+
x = [byte].pack('c*').force_encoding('UTF-8')
|
105
|
+
if x == "\r"
|
106
|
+
concat+="\n"
|
107
|
+
elsif x == "\n"
|
108
|
+
#puts "new line found --- "
|
109
|
+
concat+=x
|
110
|
+
#puts "last thing in concat."
|
111
|
+
#puts concat[-1].to_s
|
112
|
+
else
|
113
|
+
concat+=x
|
114
|
+
end
|
115
|
+
end
|
116
|
+
|
117
|
+
self.headers ||= [Header.new]
|
118
|
+
concat.split("--------------------------------").each do |record|
|
119
|
+
|
120
|
+
self.current_text_segment = record
|
121
|
+
if patient_id = get_patient_id
|
122
|
+
self.headers[-1].patients ||= []
|
123
|
+
p = Patient.new
|
124
|
+
p.patient_id = patient_id
|
125
|
+
p.orders ||= []
|
126
|
+
o = Order.new
|
127
|
+
o.results ||= {}
|
128
|
+
if sodium = get_na
|
129
|
+
r = Result.new
|
130
|
+
r.name = "SNATRIUM"
|
131
|
+
r.report_name = "Serum Electrolytes"
|
132
|
+
r.value = sodium
|
133
|
+
r.units = "mmol/L"
|
134
|
+
r.timestamp = Time.now.to_i
|
135
|
+
o.results["SNATRIUM"] = r
|
136
|
+
end
|
137
|
+
|
138
|
+
if potassium = get_k
|
139
|
+
r = Result.new
|
140
|
+
r.name = "SPOTASSIUM"
|
141
|
+
r.report_name = "Serum Electrolytes"
|
142
|
+
r.value = potassium
|
143
|
+
r.units = "mmol/L"
|
144
|
+
r.timestamp = Time.now.to_i
|
145
|
+
o.results["SPOTASSIUM"] = r
|
146
|
+
end
|
147
|
+
|
148
|
+
if chloride = get_cl
|
149
|
+
r = Result.new
|
150
|
+
r.name = "SCHLORIDE"
|
151
|
+
r.report_name = "Serum Electrolytes"
|
152
|
+
r.value = chloride
|
153
|
+
r.units = "mmol/L"
|
154
|
+
r.timestamp = Time.now.to_i
|
155
|
+
o.results["SCHLORIDE"] = r
|
156
|
+
end
|
157
|
+
|
158
|
+
if ph = get_ph
|
159
|
+
r = Result.new
|
160
|
+
r.name = "pH"
|
161
|
+
r.report_name = "Serum Electrolytes"
|
162
|
+
r.value = ph
|
163
|
+
r.units = "mmol/L"
|
164
|
+
r.timestamp = Time.now.to_i
|
165
|
+
o.results["pH"] = r
|
166
|
+
end
|
167
|
+
|
168
|
+
if po2 = get_po2
|
169
|
+
r = Result.new
|
170
|
+
r.name = "po2"
|
171
|
+
r.report_name = "Serum Electrolytes"
|
172
|
+
r.value = po2
|
173
|
+
r.units = "mmHg"
|
174
|
+
r.timestamp = Time.now.to_i
|
175
|
+
o.results["po2"] = r
|
176
|
+
end
|
177
|
+
|
178
|
+
if pco2 = get_pco2
|
179
|
+
r = Result.new
|
180
|
+
r.name = "pco2"
|
181
|
+
r.report_name = "Serum Electrolytes"
|
182
|
+
r.value = pco2
|
183
|
+
r.units = "mmHg"
|
184
|
+
r.timestamp = Time.now.to_i
|
185
|
+
o.results["pco2"] = r
|
186
|
+
end
|
187
|
+
|
188
|
+
p.orders << o
|
189
|
+
self.headers[-1].patients << p
|
190
|
+
end
|
191
|
+
end
|
192
|
+
|
193
|
+
end
|
194
|
+
|
195
|
+
def process_text_file(full_file_path)
|
196
|
+
k = IO.read(full_file_path)
|
197
|
+
process_electrolytes(k.bytes)
|
198
|
+
end
|
199
|
+
|
200
|
+
|
201
|
+
def receive_data(data)
|
202
|
+
|
203
|
+
|
204
|
+
begin
|
205
|
+
|
206
|
+
|
207
|
+
self.data_buffer ||= ''
|
208
|
+
|
209
|
+
concat = ""
|
210
|
+
|
211
|
+
byte_arr = data.bytes.to_a
|
212
|
+
|
213
|
+
self.test_data_bytes ||= []
|
214
|
+
|
215
|
+
self.data_bytes ||= []
|
216
|
+
|
217
|
+
self.test_data_bytes.push(byte_arr)
|
218
|
+
|
219
|
+
self.data_bytes.push(byte_arr)
|
220
|
+
|
221
|
+
|
222
|
+
concat = pre_process_bytes(byte_arr,concat)
|
223
|
+
|
224
|
+
#puts "concat is:"
|
225
|
+
|
226
|
+
#puts concat.to_s
|
227
|
+
|
228
|
+
self.data_buffer << concat
|
229
|
+
|
230
|
+
## if the last byte is EOT, then call process text.
|
231
|
+
## inside that split by line and process one at a time.
|
232
|
+
##process_text(concat)
|
233
|
+
#puts "data bytes -1: #{self.data_bytes[-1]}"
|
234
|
+
#puts "data bytes 0: #{self.data_bytes[0]}"
|
235
|
+
#if self.data_bytes[0] == ELECTROLYTE_START
|
236
|
+
self.process_electrolytes(self.data_bytes)
|
237
|
+
#end
|
238
|
+
=begin
|
239
|
+
if data.bytes.to_a[-1] == 4
|
240
|
+
puts "GOT EOT --- PROCESSING BUFFER, AND CLEARING."
|
241
|
+
process_text(self.data_buffer)
|
242
|
+
#root_path = File.dirname __dir
|
243
|
+
#puts "root path #{root_path}"
|
244
|
+
#IO.write((File.join root_path,'test','resources','roche_multi_frame_bytes.txt'),self.test_data_bytes.to_s)
|
245
|
+
#puts self.test_data_bytes.flatten.to_s
|
246
|
+
self.data_buffer = ''
|
247
|
+
unless self.headers.blank?
|
248
|
+
if self.headers[-1].queries.blank?
|
249
|
+
#puts "no queries in header so sending ack after getting EOT and processing the buffer"
|
250
|
+
send_data(ACK)
|
251
|
+
else
|
252
|
+
#puts "sending ENQ"
|
253
|
+
send_data(ENQ)
|
254
|
+
end
|
255
|
+
else
|
256
|
+
puts "sending catch all --------------- ACK --------------"
|
257
|
+
send_data(ACK)
|
258
|
+
end
|
259
|
+
elsif data.bytes.to_a[0] == 6
|
260
|
+
puts "GOT ACK --- GENERATING RESPONSE"
|
261
|
+
unless self.headers.blank?
|
262
|
+
header_responses = self.headers[-1].build_one_response({machine_name: self.headers[-1].machine_name})
|
263
|
+
## if no queries then, we have to send ack.
|
264
|
+
if header_responses.blank?
|
265
|
+
#puts "sending ACK since there are no queries in the header"
|
266
|
+
send_data(ACK)
|
267
|
+
end
|
268
|
+
header_responses.each_with_index {|response,key|
|
269
|
+
message_checksum = checksum(response + terminator + ETX)
|
270
|
+
final_resp = STX + response + terminator + ETX + message_checksum + "\r"
|
271
|
+
final_resp_arr = final_resp.bytes.to_a
|
272
|
+
final_resp_arr << 10
|
273
|
+
if (self.headers[-1].response_sent == false)
|
274
|
+
#puts "sending the data as follows----------------------------------------------"
|
275
|
+
#puts "response sent is:"
|
276
|
+
#puts self.headers[-1].response_sent
|
277
|
+
#puts final_resp_arr.pack('c*').gsub(/\r/,'\n')
|
278
|
+
send_data(final_resp_arr.pack('c*'))
|
279
|
+
self.headers[-1].response_sent = true if (key == (header_responses.size - 1))
|
280
|
+
else
|
281
|
+
#puts "sending EOT"
|
282
|
+
send_data(EOT)
|
283
|
+
end
|
284
|
+
}
|
285
|
+
else
|
286
|
+
#puts "NO HEADERS PRESENT --- "
|
287
|
+
end
|
288
|
+
elsif data.bytes.to_a[0] == 255
|
289
|
+
puts " ----------- got 255 data -----------, not sending anything back. "
|
290
|
+
else
|
291
|
+
#unless self.data_buffer.blank?
|
292
|
+
# puts self.data_buffer.gsub(/\r/,'\n').to_s
|
293
|
+
#end
|
294
|
+
## send the header
|
295
|
+
#puts "--------- SENT ACK -----------"
|
296
|
+
## strip non utf 8 characters from it.
|
297
|
+
self.data_buffer.encode!('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '')
|
298
|
+
if self.data_buffer =~ /MSH\|/
|
299
|
+
#puts " -------------- HEADERS ARE BLANK WITH HL7, sending ack. ------------ "
|
300
|
+
process_text(self.data_buffer)
|
301
|
+
self.data_buffer = ''
|
302
|
+
if self.headers.size > 0
|
303
|
+
self.headers[-1].commit
|
304
|
+
send_data(self.headers[-1].generate_ack_success_response)
|
305
|
+
end
|
306
|
+
else
|
307
|
+
#puts " -------------- HEADERS ARE BLANK NOT HL7, sending ack. ------------ "
|
308
|
+
send_data(ACK)
|
309
|
+
end
|
310
|
+
end
|
311
|
+
=end
|
312
|
+
rescue => e
|
313
|
+
|
314
|
+
#self.headers = []
|
315
|
+
AstmServer.log("data was: " + self.data_buffer + "error is:" + e.backtrace.to_s)
|
316
|
+
#send_data(EOT)
|
317
|
+
end
|
318
|
+
|
319
|
+
end
|
320
|
+
|
321
|
+
|
322
|
+
end
|
@@ -1,315 +1,46 @@
|
|
1
|
-
class SiemensAbgElectrolyteServer
|
2
|
-
|
3
|
-
|
4
|
-
|
5
|
-
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
self.
|
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
|
-
end
|
46
|
-
raise "more than one result #{m.to_s}" if (m.size > 1)
|
47
|
-
return m[0] if m.size == 1
|
48
|
-
return nil
|
49
|
-
end
|
50
|
-
|
51
|
-
def get_k
|
52
|
-
m = []
|
53
|
-
self.current_text_segment.scan(/K\+\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+mmol\/L/) do |l|
|
54
|
-
n = Regexp.last_match
|
55
|
-
m << n[:k].to_s
|
56
|
-
end
|
57
|
-
raise "more than one result #{m.to_s}" if (m.size > 1)
|
58
|
-
return m[0] if m.size == 1
|
59
|
-
return nil
|
60
|
-
end
|
61
|
-
|
62
|
-
def get_cl
|
63
|
-
m = []
|
64
|
-
self.current_text_segment.scan(/Cl\-\s+(?<k>(\d+)[\.\d]*)(\^|v)?\s+mmol\/L/) do |l|
|
65
|
-
n = Regexp.last_match
|
66
|
-
m << n[:k].to_s
|
67
|
-
end
|
68
|
-
raise "more than one result #{m.to_s}" if (m.size > 1)
|
69
|
-
return m[0] if m.size == 1
|
70
|
-
return nil
|
71
|
-
end
|
72
|
-
|
73
|
-
def get_patient_id
|
74
|
-
m = []
|
75
|
-
self.current_text_segment.scan(/Patient\s+ID\s+(?<k>\d+)$/) do |l|
|
76
|
-
n = Regexp.last_match
|
77
|
-
m << n[:k].to_s
|
78
|
-
end
|
79
|
-
raise "more than one result #{m.to_s}" if (m.size > 1)
|
80
|
-
return m[0] if m.size == 1
|
81
|
-
return nil
|
82
|
-
end
|
83
|
-
|
84
|
-
## we override the lab interface methods
|
85
|
-
## and we don't pollute the lab interface itself.
|
86
|
-
## as this is a custom analyzer.
|
87
|
-
## @param[Array] :
|
88
|
-
## [[bytes],[bytes]....]
|
89
|
-
def process_electrolytes(data_bytes)
|
90
|
-
#puts "came to process electrolytes_plain_text"
|
91
|
-
byte_arr = data_bytes.flatten
|
92
|
-
#puts "the end part of the arr is"
|
93
|
-
return if byte_arr[-4..-1] != SIEMENS_ELECTROLYTE_END
|
94
|
-
self.data_bytes = []
|
95
|
-
concat = ""
|
96
|
-
byte_arr.each do |byte|
|
97
|
-
x = [byte].pack('c*').force_encoding('UTF-8')
|
98
|
-
if x == "\r"
|
99
|
-
concat+="\n"
|
100
|
-
elsif x == "\n"
|
101
|
-
#puts "new line found --- "
|
102
|
-
concat+=x
|
103
|
-
#puts "last thing in concat."
|
104
|
-
#puts concat[-1].to_s
|
105
|
-
else
|
106
|
-
concat+=x
|
107
|
-
end
|
108
|
-
end
|
109
|
-
|
110
|
-
self.headers ||= [Header.new]
|
111
|
-
concat.split("--------------------------------").each do |record|
|
112
|
-
|
113
|
-
self.current_text_segment = record
|
114
|
-
if patient_id = get_patient_id
|
115
|
-
self.headers[-1].patients ||= []
|
116
|
-
p = Patient.new
|
117
|
-
p.patient_id = patient_id
|
118
|
-
p.orders ||= []
|
119
|
-
o = Order.new
|
120
|
-
o.results ||= {}
|
121
|
-
if sodium = get_na
|
122
|
-
r = Result.new
|
123
|
-
r.name = "SNATRIUM"
|
124
|
-
r.report_name = "Serum Electrolytes"
|
125
|
-
r.value = sodium
|
126
|
-
r.units = "mmol/L"
|
127
|
-
r.timestamp = Time.now.to_i
|
128
|
-
o.results["SNATRIUM"] = r
|
129
|
-
end
|
130
|
-
|
131
|
-
if potassium = get_k
|
132
|
-
r = Result.new
|
133
|
-
r.name = "SPOTASSIUM"
|
134
|
-
r.report_name = "Serum Electrolytes"
|
135
|
-
r.value = potassium
|
136
|
-
r.units = "mmol/L"
|
137
|
-
r.timestamp = Time.now.to_i
|
138
|
-
o.results["SPOTASSIUM"] = r
|
139
|
-
end
|
140
|
-
|
141
|
-
if chloride = get_cl
|
142
|
-
r = Result.new
|
143
|
-
r.name = "SCHLORIDE"
|
144
|
-
r.report_name = "Serum Electrolytes"
|
145
|
-
r.value = chloride
|
146
|
-
r.units = "mmol/L"
|
147
|
-
r.timestamp = Time.now.to_i
|
148
|
-
o.results["SCHLORIDE"] = r
|
149
|
-
end
|
150
|
-
|
151
|
-
if ph = get_ph
|
152
|
-
r = Result.new
|
153
|
-
r.name = "pH"
|
154
|
-
r.report_name = "Serum Electrolytes"
|
155
|
-
r.value = ph
|
156
|
-
r.units = "mmol/L"
|
157
|
-
r.timestamp = Time.now.to_i
|
158
|
-
o.results["pH"] = r
|
159
|
-
end
|
160
|
-
|
161
|
-
if po2 = get_po2
|
162
|
-
r = Result.new
|
163
|
-
r.name = "po2"
|
164
|
-
r.report_name = "Serum Electrolytes"
|
165
|
-
r.value = po2
|
166
|
-
r.units = "mmHg"
|
167
|
-
r.timestamp = Time.now.to_i
|
168
|
-
o.results["po2"] = r
|
169
|
-
end
|
170
|
-
|
171
|
-
if pco2 = get_pco2
|
172
|
-
r = Result.new
|
173
|
-
r.name = "pco2"
|
174
|
-
r.report_name = "Serum Electrolytes"
|
175
|
-
r.value = pco2
|
176
|
-
r.units = "mmHg"
|
177
|
-
r.timestamp = Time.now.to_i
|
178
|
-
o.results["pco2"] = r
|
179
|
-
end
|
180
|
-
|
181
|
-
p.orders << o
|
182
|
-
self.headers[-1].patients << p
|
183
|
-
end
|
184
|
-
end
|
185
|
-
|
186
|
-
end
|
187
|
-
|
188
|
-
def process_text_file(full_file_path)
|
189
|
-
k = IO.read(full_file_path)
|
190
|
-
process_electrolytes(k.bytes)
|
191
|
-
end
|
192
|
-
|
193
|
-
|
194
|
-
def receive_data(data)
|
195
|
-
|
196
|
-
|
197
|
-
begin
|
198
|
-
|
199
|
-
|
200
|
-
self.data_buffer ||= ''
|
201
|
-
|
202
|
-
concat = ""
|
203
|
-
|
204
|
-
byte_arr = data.bytes.to_a
|
205
|
-
|
206
|
-
self.test_data_bytes ||= []
|
207
|
-
|
208
|
-
self.data_bytes ||= []
|
209
|
-
|
210
|
-
self.test_data_bytes.push(byte_arr)
|
211
|
-
|
212
|
-
self.data_bytes.push(byte_arr)
|
213
|
-
|
214
|
-
|
215
|
-
concat = pre_process_bytes(byte_arr,concat)
|
216
|
-
|
217
|
-
#puts "concat is:"
|
218
|
-
|
219
|
-
#puts concat.to_s
|
220
|
-
|
221
|
-
self.data_buffer << concat
|
222
|
-
|
223
|
-
## if the last byte is EOT, then call process text.
|
224
|
-
## inside that split by line and process one at a time.
|
225
|
-
##process_text(concat)
|
226
|
-
#puts "data bytes -1: #{self.data_bytes[-1]}"
|
227
|
-
#puts "data bytes 0: #{self.data_bytes[0]}"
|
228
|
-
#if self.data_bytes[0] == ELECTROLYTE_START
|
229
|
-
self.process_electrolytes(self.data_bytes)
|
230
|
-
#end
|
231
|
-
=begin
|
232
|
-
if data.bytes.to_a[-1] == 4
|
233
|
-
puts "GOT EOT --- PROCESSING BUFFER, AND CLEARING."
|
234
|
-
process_text(self.data_buffer)
|
235
|
-
#root_path = File.dirname __dir
|
236
|
-
#puts "root path #{root_path}"
|
237
|
-
#IO.write((File.join root_path,'test','resources','roche_multi_frame_bytes.txt'),self.test_data_bytes.to_s)
|
238
|
-
#puts self.test_data_bytes.flatten.to_s
|
239
|
-
self.data_buffer = ''
|
240
|
-
unless self.headers.blank?
|
241
|
-
if self.headers[-1].queries.blank?
|
242
|
-
#puts "no queries in header so sending ack after getting EOT and processing the buffer"
|
243
|
-
send_data(ACK)
|
244
|
-
else
|
245
|
-
#puts "sending ENQ"
|
246
|
-
send_data(ENQ)
|
247
|
-
end
|
248
|
-
else
|
249
|
-
puts "sending catch all --------------- ACK --------------"
|
250
|
-
send_data(ACK)
|
251
|
-
end
|
252
|
-
elsif data.bytes.to_a[0] == 6
|
253
|
-
puts "GOT ACK --- GENERATING RESPONSE"
|
254
|
-
unless self.headers.blank?
|
255
|
-
header_responses = self.headers[-1].build_one_response({machine_name: self.headers[-1].machine_name})
|
256
|
-
## if no queries then, we have to send ack.
|
257
|
-
if header_responses.blank?
|
258
|
-
#puts "sending ACK since there are no queries in the header"
|
259
|
-
send_data(ACK)
|
260
|
-
end
|
261
|
-
header_responses.each_with_index {|response,key|
|
262
|
-
message_checksum = checksum(response + terminator + ETX)
|
263
|
-
final_resp = STX + response + terminator + ETX + message_checksum + "\r"
|
264
|
-
final_resp_arr = final_resp.bytes.to_a
|
265
|
-
final_resp_arr << 10
|
266
|
-
if (self.headers[-1].response_sent == false)
|
267
|
-
#puts "sending the data as follows----------------------------------------------"
|
268
|
-
#puts "response sent is:"
|
269
|
-
#puts self.headers[-1].response_sent
|
270
|
-
#puts final_resp_arr.pack('c*').gsub(/\r/,'\n')
|
271
|
-
send_data(final_resp_arr.pack('c*'))
|
272
|
-
self.headers[-1].response_sent = true if (key == (header_responses.size - 1))
|
273
|
-
else
|
274
|
-
#puts "sending EOT"
|
275
|
-
send_data(EOT)
|
276
|
-
end
|
277
|
-
}
|
278
|
-
else
|
279
|
-
#puts "NO HEADERS PRESENT --- "
|
280
|
-
end
|
281
|
-
elsif data.bytes.to_a[0] == 255
|
282
|
-
puts " ----------- got 255 data -----------, not sending anything back. "
|
283
|
-
else
|
284
|
-
#unless self.data_buffer.blank?
|
285
|
-
# puts self.data_buffer.gsub(/\r/,'\n').to_s
|
286
|
-
#end
|
287
|
-
## send the header
|
288
|
-
#puts "--------- SENT ACK -----------"
|
289
|
-
## strip non utf 8 characters from it.
|
290
|
-
self.data_buffer.encode!('UTF-8', 'binary', invalid: :replace, undef: :replace, replace: '')
|
291
|
-
if self.data_buffer =~ /MSH\|/
|
292
|
-
#puts " -------------- HEADERS ARE BLANK WITH HL7, sending ack. ------------ "
|
293
|
-
process_text(self.data_buffer)
|
294
|
-
self.data_buffer = ''
|
295
|
-
if self.headers.size > 0
|
296
|
-
self.headers[-1].commit
|
297
|
-
send_data(self.headers[-1].generate_ack_success_response)
|
298
|
-
end
|
299
|
-
else
|
300
|
-
#puts " -------------- HEADERS ARE BLANK NOT HL7, sending ack. ------------ "
|
301
|
-
send_data(ACK)
|
302
|
-
end
|
303
|
-
end
|
304
|
-
=end
|
305
|
-
rescue => e
|
306
|
-
|
307
|
-
#self.headers = []
|
308
|
-
AstmServer.log("data was: " + self.data_buffer + "error is:" + e.backtrace.to_s)
|
309
|
-
#send_data(EOT)
|
310
|
-
end
|
311
|
-
|
312
|
-
end
|
313
|
-
|
1
|
+
class SiemensAbgElectrolyteServer
|
2
|
+
|
3
|
+
include SiemensAbgElectrolyteModule
|
4
|
+
|
5
|
+
## DEFAULT SERIAL PORT : /dev/ttyS0
|
6
|
+
## DEFAULT USB PORT : /dev/ttyUSB0
|
7
|
+
## @param[Array] ethernet_connections : each element is expected to be a hash, with keys for :server_ip, :server_port.
|
8
|
+
## @param[Array] serial_connections : each element is expected to be a hash with port_address, baud_rate, and parity
|
9
|
+
#def initialize(server_ip=nil,server_port=nil,mpg=nil,respond_to_queries=false,serial_port='/dev/ttyS0',usb_port='/dev/ttyUSB0',serial_baud=9600,serial_parity=8,usb_baud=19200,usb_parity=8)
|
10
|
+
def initialize(ethernet_connections,serial_connections,mpg=nil,respond_to_queries=nil)
|
11
|
+
$redis = Redis.new
|
12
|
+
self.class.log("Initializing AstmServer")
|
13
|
+
self.ethernet_connections = ethernet_connections
|
14
|
+
self.serial_connections = serial_connections
|
15
|
+
self.server_ip = server_ip || "127.0.0.1"
|
16
|
+
self.server_port = server_port || 3000
|
17
|
+
self.respond_to_queries = respond_to_queries
|
18
|
+
self.serial_port = serial_port
|
19
|
+
self.serial_baud = serial_baud
|
20
|
+
self.serial_parity = serial_parity
|
21
|
+
self.usb_port = usb_port
|
22
|
+
self.usb_baud = usb_baud
|
23
|
+
self.usb_parity = usb_parity
|
24
|
+
$mappings = JSON.parse(IO.read(mpg || self.class.default_mappings))
|
25
|
+
end
|
26
|
+
|
27
|
+
def start_server
|
28
|
+
EventMachine.run {
|
29
|
+
self.ethernet_connections.each do |econn|
|
30
|
+
raise "please provide a valid ethernet configuration with ip address" unless econn[:server_ip]
|
31
|
+
raise "please provide a valid ethernet configuration with port" unless econn[:server_port]
|
32
|
+
EventMachine::start_server econn[:server_ip], econn[:server_port], SiemensAbgElectrolyteModule
|
33
|
+
self.class.log("Running ETHERNET with configuration #{econn}")
|
34
|
+
end
|
35
|
+
self.serial_connections.each do |sconn|
|
36
|
+
raise "please provide a valid serial configuration with port address" unless sconn[:port_address]
|
37
|
+
raise "please provide a valid serial configuration with baud rate" unless sconn[:baud_rate]
|
38
|
+
raise "please provide a valid serial configuration with parity" unless sconn[:parity]
|
39
|
+
EventMachine.open_serial(sconn[:port_address], sconn[:baud_rate], sconn[:parity],SiemensAbgElectrolyteModule)
|
40
|
+
puts "RUNNING SERIAL port with configuration : #{sconn}"
|
41
|
+
end
|
42
|
+
|
43
|
+
}
|
44
|
+
end
|
314
45
|
|
315
46
|
end
|
@@ -2,6 +2,10 @@ require "active_support/all"
|
|
2
2
|
|
3
3
|
module LabInterface
|
4
4
|
|
5
|
+
def self.included base
|
6
|
+
base.extend ClassMethods
|
7
|
+
end
|
8
|
+
|
5
9
|
ACK = "\x06"
|
6
10
|
ENQ = "\x05"
|
7
11
|
STX = "\x02"
|
@@ -13,7 +17,6 @@ module LabInterface
|
|
13
17
|
|
14
18
|
attr_accessor :ethernet_connections
|
15
19
|
attr_accessor :serial_connections
|
16
|
-
|
17
20
|
attr_accessor :ethernet_server
|
18
21
|
attr_accessor :server_ip
|
19
22
|
attr_accessor :server_port
|
@@ -38,7 +41,37 @@ module LabInterface
|
|
38
41
|
|
39
42
|
## buffer of incoming data.
|
40
43
|
attr_accessor :data_buffer
|
44
|
+
|
45
|
+
$ENQ = "[5]"
|
46
|
+
$start_text = "[2]"
|
47
|
+
$end_text = "[3]"
|
48
|
+
$record_end = "[13]"
|
49
|
+
$frame_end = "[10]"
|
50
|
+
|
41
51
|
|
52
|
+
#######################################################
|
53
|
+
##
|
54
|
+
##
|
55
|
+
##
|
56
|
+
## CLASS METHODS
|
57
|
+
##
|
58
|
+
##
|
59
|
+
##
|
60
|
+
#######################################################
|
61
|
+
module ClassMethods
|
62
|
+
def log(message)
|
63
|
+
puts "" + message
|
64
|
+
$redis.zadd("ruby_astm_log",Time.now.to_i,message)
|
65
|
+
end
|
66
|
+
|
67
|
+
def root_path
|
68
|
+
File.dirname __dir__
|
69
|
+
end
|
70
|
+
|
71
|
+
def default_mappings
|
72
|
+
File.join root_path,"mappings.json"
|
73
|
+
end
|
74
|
+
end
|
42
75
|
|
43
76
|
## returns the root directory of the gem.
|
44
77
|
def root
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ruby_astm
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.4.
|
4
|
+
version: 1.4.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Bhargav Raut
|
@@ -155,6 +155,7 @@ files:
|
|
155
155
|
- lib/ruby_astm/HL7/hl7_order.rb
|
156
156
|
- lib/ruby_astm/HL7/hl7_patient.rb
|
157
157
|
- lib/ruby_astm/astm_server.rb
|
158
|
+
- lib/ruby_astm/custom/siemens_abg_electrolyte_module.rb
|
158
159
|
- lib/ruby_astm/custom/siemens_abg_electrolyte_server.rb
|
159
160
|
- lib/ruby_astm/frame.rb
|
160
161
|
- lib/ruby_astm/header.rb
|