tasci_merger 0.3.1 → 0.3.2
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- checksums.yaml +4 -4
- data/lib/man_merger.rb +228 -231
- data/tasci_merger.gemspec +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: a7097b481a5ccd05ccbb429433cc122fcfedc655
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4
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data.tar.gz: 981ca465620a29860db631b0678d6c69e9e37810
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5
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: e301450ff95d0764fee633acf430fb63f08bd5c953a265c5203cc1fc9e6e4bffa88597ec88939d467d5bd148185eb16d02ca532d4f6ac1cd146b2fe88e0603c4
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7
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data.tar.gz: 9c260f76bc1610525f46aa9884eb7c91f211d34f5d2e7d3120de5ff4870b28b5449d643755959ccaeb3850a49c77dad1fb3574466ff452699360bbf56bc3f332
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data/lib/man_merger.rb
CHANGED
@@ -3,297 +3,294 @@ require 'csv'
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3
3
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## CHANGELOG
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# 2173 Master file: change sp16,17,18 to *_rev
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end
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class ManMerger
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LIST_DIR = "/usr/local/htdocs/access/lib/data/etl/klerman_merge_man_files/file_lists/"
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8
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T_DRIVE_DIRS = ["/home/pwm4/Windows/tdrive/IPM/Modafinil_FD_42.85h/", "/home/pwm4/Windows/tdrive/IPM/NSBRI_65d_Entrainment/"]
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9
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+
#T_DRIVE_DIR = "/home/pwm4/Windows/tdrive/IPM/Modafinil_FD_42.85h/"
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10
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EPOCH_LENGTH = 30
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def merge_files
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subject_list = load_subject_list
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subject_list.each do |subject_code, file_list|
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merged_file = CSV.open("/usr/local/htdocs/access/lib/data/etl/klerman_merge_man_files/merged_files/#{subject_code}_merged.csv", "wb")
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merged_file << %w(SUBJECT_CODE LABTIME SLEEP_STAGE SLEEP_PERIOD SEM_FLAG)
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17
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MY_LOG.info "---- #{subject_code}"
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previous_first_labtime = nil
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previous_last_labtime = nil
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subject_year = get_subject_year(file_list)
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file_list.each do |file_hash|
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matched_files = Dir.glob("#{T_DRIVE_DIRS[0]}#{subject_code}/PSG/SCORED/**/#{file_hash[:pattern]}.man", File::FNM_CASEFOLD)
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matched_files = Dir.glob("#{T_DRIVE_DIRS[1]}#{subject_code}/Sleep/#{file_hash[:pattern]}.man", File::FNM_CASEFOLD) if matched_files.length != 1
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26
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+
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## Validate File List
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28
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if matched_files.length != 1
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29
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raise StandardError, "None or more than one matched file. #{file_hash[:pattern]} #{matched_files} #{matched_files.length} #{subject_code}"
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else
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man_file_path = matched_files[0]
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end
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-
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-
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-
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man_file = File.open(man_file_path)
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LOADER_LOGGER.info "--- Loading #{man_file_path}"
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file_info = {}
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-
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-
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## Ignore Corrupted Files
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#next if tasci_file_path == "/home/pwm4/Windows/tdrive/IPM/AFOSR9_Slp_Restrict//24B7GXT3/PSG/TASCI_SEM/24b7gxt3_082907_wp19ap1_PID_24B7GXT3_082907_WP19AP1_RID_0_SEM.TASCI"
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-
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-
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-
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# Date from file name
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matched_date = /_(\d\d)(\d\d)(\d\d)_/.match(man_file_path)
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44
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file_info[:fn_date] = (matched_date ? Time.zone.local((matched_date[3].to_i > 30 ? matched_date[3].to_i + 1900 : matched_date[3].to_i + 2000), matched_date[1].to_i, matched_date[2].to_i) : nil)
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48
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-
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-
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# read file
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lines = man_file.readlines("\r")
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# delete possible empty last line
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49
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lines.pop if lines.last.blank?
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-
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53
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-
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55
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# get file first and last times
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matched_time = /(\d\d):(\d\d):(\d\d):(\d\d\d)/.match(lines.first)
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53
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file_info[:first_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
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54
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matched_time = /(\d\d):(\d\d):(\d\d):(\d\d\d)/.match(lines.last)
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55
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file_info[:last_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
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57
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# validate first/last times
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58
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if file_hash[:start_time] != file_info[:first_time]
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59
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MY_LOG.error "---- FIRST TIME MISMATCH ---\n#{man_file_path}\n#{file_hash[:start_time]} #{file_info[:first_time]}\n\n"
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60
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end
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61
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if file_hash[:last_line_time] != file_info[:last_time]
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MY_LOG.error "---- LAST TIME MISMATCH ----\n#{man_file_path}\n#{file_hash[:last_line_time]} #{file_info[:last_time]}\n\n"
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63
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end
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64
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if file_hash[:last_line_number] != lines.length
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65
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MY_LOG.error "---- LINE COUNT MISMATCH ----\n#{man_file_path}\n#{file_hash[:last_line_number]} #{lines.length}\n\n"
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end
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-
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##
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# VALIDATION
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file_hash[:start_labtime] = Labtime.from_decimal(file_hash[:start_labtime], subject_year)
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71
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file_hash[:last_line_labtime] = Labtime.from_decimal(file_hash[:last_line_labtime], subject_year)
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73
72
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74
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-
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75
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-
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73
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+
start_realtime = file_hash[:start_labtime].to_time
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last_line_realtime = file_hash[:last_line_labtime].to_time
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75
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77
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-
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78
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-
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76
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first_realtime = file_hash[:start_labtime].time_zone.local(start_realtime.year, start_realtime.month, start_realtime.day, file_info[:first_time][:hour], file_info[:first_time][:min], file_info[:first_time][:sec])
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77
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last_realtime = file_hash[:last_line_labtime].time_zone.local(last_line_realtime.year, last_line_realtime.month, last_line_realtime.day, file_info[:last_time][:hour], file_info[:last_time][:min], file_info[:last_time][:sec])
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80
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-
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81
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-
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82
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-
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79
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+
file_info[:first_labtime] = Labtime.parse(first_realtime)
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80
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+
file_info[:last_labtime] = Labtime.parse(last_realtime)
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81
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+
predicted_last_labtime = Labtime.parse(file_info[:first_labtime].to_time + ((lines.length - 1) * 30).seconds)
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-
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85
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-
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86
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-
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87
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-
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88
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-
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83
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+
sep = false
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84
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if (file_hash[:start_labtime].time_in_seconds - file_info[:first_labtime].time_in_seconds).abs > 2
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85
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MY_LOG.error "---- FIRST LABTIME MISMATCH ----\n#{man_file_path}\n#{file_hash[:start_labtime].time_in_seconds - file_info[:first_labtime].time_in_seconds} | #{file_hash[:start_labtime].to_time}\n#{file_hash[:start_labtime]} | #{file_info[:first_labtime]}\n"
|
86
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sep = true
|
87
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+
end
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-
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91
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-
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-
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93
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-
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94
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-
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95
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-
end
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96
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if (file_info[:last_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds).abs > 0
|
97
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-
MY_LOG.error "---- PRED LABTIME MISMATCH ----\n#{man_file_path}\n#{(file_info[:last_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds)} | #{predicted_last_labtime.to_time}\nl: #{file_info[:last_labtime]} | #{predicted_last_labtime}\n"
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98
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-
sep = true
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99
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-
end
|
89
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+
# These checks fail if DST TRANSITION HAPPENS
|
90
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if last_line_realtime.dst? == start_realtime.dst?
|
91
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if (file_hash[:last_line_labtime].time_in_seconds - file_info[:last_labtime].time_in_seconds).abs > 2
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92
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MY_LOG.error "---- LAST LABTIME MISMATCH ----\n#{man_file_path}\n#{file_hash[:last_line_labtime].time_in_seconds - file_info[:last_labtime].time_in_seconds} | #{file_hash[:last_line_labtime].to_time}\n#{file_hash[:last_line_labtime]} | #{file_info[:last_labtime]}\n"
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93
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sep = true
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100
94
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end
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101
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-
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102
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-
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103
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-
MY_LOG.error "---- !PRED LABTIME MISMATCH ----\n#{man_file_path}\n#{(file_hash[:last_line_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds)} | #{predicted_last_labtime.to_time}\nl: #{file_info[:last_line_labtime]} | #{predicted_last_labtime}\n"
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95
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if (file_info[:last_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds).abs > 0
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96
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MY_LOG.error "---- PRED LABTIME MISMATCH ----\n#{man_file_path}\n#{(file_info[:last_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds)} | #{predicted_last_labtime.to_time}\nl: #{file_info[:last_labtime]} | #{predicted_last_labtime}\n"
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97
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sep = true
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98
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end
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+
end
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100
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107
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-
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108
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-
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109
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-
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101
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if (file_hash[:last_line_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds).abs > 2
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MY_LOG.error "---- !PRED LABTIME MISMATCH ----\n#{man_file_path}\n#{(file_hash[:last_line_labtime].time_in_seconds - predicted_last_labtime.time_in_seconds)} | #{predicted_last_labtime.to_time}\nl: #{file_info[:last_line_labtime]} | #{predicted_last_labtime}\n"
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sep = true
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+
end
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105
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111
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-
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112
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-
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106
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+
unless previous_first_labtime.nil? or previous_last_labtime.nil?
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107
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MY_LOG.error "Start time is before previous end labtime for #{man_file_path}" if file_info[:first_labtime] < previous_last_labtime
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108
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+
end
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109
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+
|
110
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raise StandardError, "AHHHHH" if file_info[:first_labtime].sec != first_realtime.sec
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111
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+
raise StandardError, "AHHHHH" if file_info[:last_labtime].sec != last_realtime.sec
|
113
112
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114
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-
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113
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+
MY_LOG.info "-----------------------------------\n\n" if sep
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115
114
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116
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-
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117
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-
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115
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+
last_labtime = nil
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116
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+
ibob_flag = 0
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118
117
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119
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-
|
120
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-
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118
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+
lines.each_with_index do |line, line_number|
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119
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#merged_file << %w(SUBJECT_CODE LABTIME SLEEP_STAGE SLEEP_PERIOD SEM_FLAG)
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121
120
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=begin
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122
121
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sleep man file:
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123
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-
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124
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-
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125
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-
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126
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-
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127
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-
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128
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-
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129
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-
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130
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-
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131
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-
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122
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+
0 undef/unscored
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123
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1 stage 1
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124
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+
2 stage 2
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125
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3 stage 3
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126
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4 stage 4
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127
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5 wake
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128
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+
6 REM
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129
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+
7 MVT
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130
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+
8 LOff and LOn
|
132
131
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133
132
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wake man file:
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134
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-
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133
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+
0 undef/un
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135
134
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cored
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136
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-
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137
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-
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138
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-
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139
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-
|
140
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-
|
141
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-
|
142
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-
|
143
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-
|
135
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+
1 stage 1
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136
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+
2 stage 2
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137
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+
3 stage 3
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138
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+
4 stage 4
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139
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+
5 wake
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140
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+
6 REM
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141
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+
7 MVT
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142
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+
8 SEM
|
144
143
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=end
|
145
144
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|
146
145
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|
147
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-
|
148
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-
|
149
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-
|
150
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-
# Sleep Period Coding:
|
151
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-
# 1 Sleep Onset (Lights Off) (IN BED)
|
152
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-
# 2 Sleep Offset (Lights On) (OUT OF BED)
|
153
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-
if file_hash[:type] == :sleep and line_code == 8
|
154
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-
if ibob_flag == 0
|
155
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-
sleep_period = 1
|
156
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-
ibob_flag = 1
|
157
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-
else
|
158
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-
sleep_period = 2
|
159
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-
ibob_flag = 0
|
160
|
-
end
|
161
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-
else
|
162
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-
sleep_period = nil
|
163
|
-
end
|
164
|
-
|
165
|
-
# Sleep Stage Coding:
|
166
|
-
# 1 stage 1
|
167
|
-
# 2 stage 2
|
168
|
-
# 3 stage 3
|
169
|
-
# 4 stage 4
|
170
|
-
# 6 MT
|
171
|
-
# 7 Undef
|
172
|
-
# 5 REM
|
173
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-
# 9 Wake
|
174
|
-
if line_code >= 1 and line_code <= 4
|
175
|
-
line_event = line_code
|
176
|
-
elsif line_code == 0
|
177
|
-
line_event = 7
|
178
|
-
elsif line_code == 5 or line_code == 8
|
179
|
-
line_event = 9
|
180
|
-
elsif line_code == 6
|
181
|
-
line_event = 5
|
182
|
-
elsif line_code == 7
|
183
|
-
line_event = 6
|
184
|
-
else
|
185
|
-
raise StandardError, "Cannot map the following event: #{line_code}"
|
186
|
-
end
|
146
|
+
line_labtime = file_info[:first_labtime].add_seconds(EPOCH_LENGTH * line_number)
|
147
|
+
line_code = /(\d)\s\d\d:\d\d:\d\d:\d\d\d/.match(line)[1].to_i
|
187
148
|
|
188
|
-
|
189
|
-
|
190
|
-
|
191
|
-
|
192
|
-
|
149
|
+
# Sleep Period Coding:
|
150
|
+
# 1 Sleep Onset (Lights Off) (IN BED)
|
151
|
+
# 2 Sleep Offset (Lights On) (OUT OF BED)
|
152
|
+
if file_hash[:type] == :sleep and line_code == 8
|
153
|
+
if ibob_flag == 0
|
154
|
+
sleep_period = 1
|
155
|
+
ibob_flag = 1
|
193
156
|
else
|
194
|
-
|
157
|
+
sleep_period = 2
|
158
|
+
ibob_flag = 0
|
195
159
|
end
|
160
|
+
else
|
161
|
+
sleep_period = nil
|
162
|
+
end
|
196
163
|
|
197
|
-
|
198
|
-
|
199
|
-
|
200
|
-
|
164
|
+
# Sleep Stage Coding:
|
165
|
+
# 1 stage 1
|
166
|
+
# 2 stage 2
|
167
|
+
# 3 stage 3
|
168
|
+
# 4 stage 4
|
169
|
+
# 6 MT
|
170
|
+
# 7 Undef
|
171
|
+
# 5 REM
|
172
|
+
# 9 Wake
|
173
|
+
if line_code >= 1 and line_code <= 4
|
174
|
+
line_event = line_code
|
175
|
+
elsif line_code == 0
|
176
|
+
line_event = 7
|
177
|
+
elsif line_code == 5 or line_code == 8
|
178
|
+
line_event = 9
|
179
|
+
elsif line_code == 6
|
180
|
+
line_event = 5
|
181
|
+
elsif line_code == 7
|
182
|
+
line_event = 6
|
183
|
+
else
|
184
|
+
raise StandardError, "Cannot map the following event: #{line_code}"
|
201
185
|
end
|
202
186
|
|
187
|
+
# SEM Event Coding:
|
188
|
+
# 1 Slow Eye Movement
|
189
|
+
# 0 No Slow Eye Movement
|
190
|
+
if file_hash[:type] == :wake and line_code == 8
|
191
|
+
sem_event = 1
|
192
|
+
else
|
193
|
+
sem_event = 0
|
194
|
+
end
|
203
195
|
|
204
|
-
|
205
|
-
previous_last_labtime = last_labtime
|
196
|
+
last_labtime = line_labtime
|
206
197
|
|
198
|
+
output_line = [subject_code.upcase, line_labtime.to_decimal, line_event, sleep_period, sem_event]
|
199
|
+
merged_file << output_line
|
207
200
|
end
|
208
|
-
|
209
|
-
|
201
|
+
|
202
|
+
|
203
|
+
previous_first_labtime = file_info[:first_labtime]
|
204
|
+
previous_last_labtime = last_labtime
|
210
205
|
|
211
206
|
end
|
207
|
+
merged_file.close
|
208
|
+
MY_LOG.info "---- end #{subject_code}\n\n"
|
209
|
+
|
212
210
|
end
|
211
|
+
end
|
213
212
|
|
214
|
-
|
215
|
-
|
216
|
-
|
217
|
-
|
218
|
-
|
219
|
-
|
220
|
-
|
221
|
-
|
222
|
-
|
223
|
-
|
224
|
-
|
213
|
+
def load_subject_list
|
214
|
+
subject_info = {}
|
215
|
+
Dir.foreach(LIST_DIR) do |file|
|
216
|
+
next if file == '.' or file == '..'
|
217
|
+
#MY_LOG.info "#{file}"
|
218
|
+
csv_file = CSV.open("#{LIST_DIR}#{file}", {headers: true})
|
219
|
+
|
220
|
+
# Match and Validate File Name
|
221
|
+
matched_sc = /(.*)SLEEP\.csv/i.match(File.basename(csv_file.path))
|
222
|
+
if matched_sc
|
223
|
+
subject_code = matched_sc[1].upcase
|
224
|
+
else
|
225
|
+
next
|
226
|
+
end
|
227
|
+
|
228
|
+
subject_info[subject_code] = []
|
229
|
+
csv_file.each do |row|
|
230
|
+
file_info = {}
|
231
|
+
pattern = /(.*)\.man/i.match(row[0])
|
232
|
+
|
233
|
+
matched_time = /(\d\d):(\d\d):(\d\d):(\d\d\d)/.match(row[1])
|
234
|
+
if matched_time
|
235
|
+
file_info[:start_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
|
225
236
|
else
|
237
|
+
MY_LOG.error "No Valid Start Time Found: #{row}"
|
226
238
|
next
|
227
239
|
end
|
228
240
|
|
229
|
-
|
230
|
-
|
231
|
-
file_info = {}
|
232
|
-
|
233
|
-
|
234
|
-
|
235
|
-
|
236
|
-
file_info[:start_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
|
237
|
-
else
|
238
|
-
MY_LOG.error "No Valid Start Time Found: #{row}"
|
239
|
-
next
|
240
|
-
end
|
241
|
-
|
242
|
-
matched_time = /(\d\d):(\d\d):(\d\d):(\d\d\d)/.match(row[4])
|
243
|
-
if matched_time
|
244
|
-
file_info[:last_line_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
|
245
|
-
else
|
246
|
-
MY_LOG.error "No Valid End Time Found: #{row}"
|
247
|
-
next
|
248
|
-
end
|
241
|
+
matched_time = /(\d\d):(\d\d):(\d\d):(\d\d\d)/.match(row[4])
|
242
|
+
if matched_time
|
243
|
+
file_info[:last_line_time] = {hour: matched_time[1].to_i, min: matched_time[2].to_i, sec: matched_time[3].to_i}
|
244
|
+
else
|
245
|
+
MY_LOG.error "No Valid End Time Found: #{row}"
|
246
|
+
next
|
247
|
+
end
|
249
248
|
|
250
|
-
|
251
|
-
|
252
|
-
|
249
|
+
file_info[:start_labtime] = row[2].to_f
|
250
|
+
file_info[:last_line_number] = row[3].to_i
|
251
|
+
file_info[:last_line_labtime] = row[5].to_f
|
253
252
|
|
254
|
-
|
255
|
-
|
256
|
-
|
253
|
+
if pattern
|
254
|
+
file_info[:pattern] = pattern[1]
|
255
|
+
subject_info[subject_code] << file_info
|
257
256
|
|
258
|
-
|
259
|
-
|
260
|
-
|
257
|
+
# Determine if sleep or wake file
|
258
|
+
raise StandardError, "CAN'T DETERMINE SP/WP (none match): #{pattern[1]}" unless (/_sp?\d/i.match(pattern[1]) or /_wp?\d/i.match(pattern[1]))
|
259
|
+
raise StandardError, "CAN'T DETERMINE SP/WP (both match): #{pattern[1]}" if (/_sp?\d/i.match(pattern[1]) and /_wp?\d/i.match(pattern[1]))
|
261
260
|
|
262
|
-
|
263
|
-
|
264
|
-
|
265
|
-
|
266
|
-
else
|
267
|
-
raise StandardError, "Didn't match any SP/WP..."
|
268
|
-
end
|
261
|
+
if /_sp?\d/i.match(pattern[1])
|
262
|
+
file_info[:type] = :sleep
|
263
|
+
elsif /_wp?\d/i.match(pattern[1])
|
264
|
+
file_info[:type] = :wake
|
269
265
|
else
|
270
|
-
|
271
|
-
next
|
266
|
+
raise StandardError, "Didn't match any SP/WP..."
|
272
267
|
end
|
268
|
+
else
|
269
|
+
MY_LOG.info "No Valid File Name Found: #{row}"
|
270
|
+
next
|
273
271
|
end
|
274
|
-
#MY_LOG.info subject_info[subject_code]
|
275
272
|
end
|
276
|
-
#MY_LOG.info subject_info
|
277
|
-
subject_info
|
278
|
-
end
|
279
|
-
|
280
|
-
def get_subject_year(file_list)
|
281
|
-
years = file_list.map do |h|
|
282
|
-
matched_date = /_(\d\d)(\d\d)(\d\d)_/.match(h[:pattern])
|
283
|
-
matched_date ? matched_date[3] : nil
|
284
|
-
end
|
285
|
-
years.delete_if {|x| x.nil? }
|
286
|
-
years = years.uniq
|
287
|
-
|
288
|
-
raise StandardError, "More than one unique year found in files: #{years}" if years.length > 1
|
289
|
-
year = years.first.to_i
|
290
|
-
year > 30 ? year + 1900 : year + 2000
|
273
|
+
#MY_LOG.info subject_info[subject_code]
|
291
274
|
end
|
275
|
+
#MY_LOG.info subject_info.inspect
|
276
|
+
subject_info
|
292
277
|
end
|
293
278
|
|
279
|
+
def get_subject_year(file_list)
|
280
|
+
years = file_list.map do |h|
|
281
|
+
matched_date = /_(\d\d)(\d\d)(\d\d)_/.match(h[:pattern])
|
282
|
+
matched_date ? matched_date[3] : nil
|
283
|
+
end
|
284
|
+
years.delete_if {|x| x.nil? }
|
285
|
+
years = years.uniq
|
294
286
|
|
287
|
+
raise StandardError, "More than one unique year found in files: #{years}" if years.length > 1
|
288
|
+
year = years.first.to_i
|
289
|
+
year > 30 ? year + 1900 : year + 2000
|
290
|
+
end
|
295
291
|
end
|
296
292
|
|
293
|
+
|
297
294
|
=begin
|
298
295
|
path: /home/pwm4/Windows/tdrive/IPM/Modafinil_FD_42.85h/
|
299
296
|
path: /usr/local/htdocs/access/lib/data/etl/klerman_merge_man_files/file_list
|
data/tasci_merger.gemspec
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
s.name = 'tasci_merger'
|
3
|
-
s.version = '0.3.
|
4
|
-
s.date = '2018-
|
3
|
+
s.version = '0.3.2'
|
4
|
+
s.date = '2018-07-12'
|
5
5
|
s.summary = "Merger utility for TASCI scored sleep files."
|
6
6
|
s.description = "Merger utility for TASCI scored sleep files, built for the Division of Sleep and Circadian Disorders at BWH."
|
7
7
|
s.authors = ["Piotr Mankowski", "Chenxi Gao"]
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: tasci_merger
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.3.
|
4
|
+
version: 0.3.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Piotr Mankowski
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2018-
|
12
|
+
date: 2018-07-12 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: activesupport
|