his_emr_api_lab 1.1.22 → 1.1.23
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- checksums.yaml +4 -4
- data/MIT-LICENSE +20 -0
- data/README.md +71 -0
- data/Rakefile +32 -0
- data/app/controllers/lab/application_controller.rb +6 -0
- data/app/controllers/lab/labels_controller.rb +17 -0
- data/app/controllers/lab/orders_controller.rb +38 -0
- data/app/controllers/lab/reasons_for_test_controller.rb +9 -0
- data/app/controllers/lab/results_controller.rb +19 -0
- data/app/controllers/lab/specimen_types_controller.rb +15 -0
- data/app/controllers/lab/test_result_indicators_controller.rb +9 -0
- data/app/controllers/lab/test_types_controller.rb +15 -0
- data/app/controllers/lab/tests_controller.rb +26 -0
- data/app/jobs/lab/application_job.rb +4 -0
- data/app/jobs/lab/push_order_job.rb +12 -0
- data/app/jobs/lab/update_patient_orders_job.rb +32 -0
- data/app/jobs/lab/void_order_job.rb +17 -0
- data/app/mailers/lab/application_mailer.rb +6 -0
- data/app/models/lab/application_record.rb +5 -0
- data/app/models/lab/lab_accession_number_counter.rb +13 -0
- data/app/models/lab/lab_encounter.rb +7 -0
- data/app/models/lab/lab_order.rb +58 -0
- data/app/models/lab/lab_result.rb +31 -0
- data/app/models/lab/lab_test.rb +19 -0
- data/app/models/lab/lims_failed_import.rb +4 -0
- data/app/models/lab/lims_order_mapping.rb +10 -0
- data/app/serializers/lab/lab_order_serializer.rb +55 -0
- data/app/serializers/lab/result_serializer.rb +36 -0
- data/app/serializers/lab/test_serializer.rb +29 -0
- data/app/services/lab/accession_number_service.rb +77 -0
- data/app/services/lab/concepts_service.rb +82 -0
- data/app/services/lab/labelling_service/order_label.rb +106 -0
- data/app/services/lab/lims/api/blackhole_api.rb +21 -0
- data/app/services/lab/lims/api/couchdb_api.rb +53 -0
- data/app/services/lab/lims/api/mysql_api.rb +316 -0
- data/app/services/lab/lims/api/rest_api.rb +416 -0
- data/app/services/lab/lims/api/ws_api.rb +121 -0
- data/app/services/lab/lims/api_factory.rb +19 -0
- data/app/services/lab/lims/config.rb +100 -0
- data/app/services/lab/lims/exceptions.rb +11 -0
- data/app/services/lab/lims/migrator.rb +216 -0
- data/app/services/lab/lims/order_dto.rb +105 -0
- data/app/services/lab/lims/order_serializer.rb +244 -0
- data/app/services/lab/lims/pull_worker.rb +289 -0
- data/app/services/lab/lims/push_worker.rb +149 -0
- data/app/services/lab/lims/utils.rb +91 -0
- data/app/services/lab/lims/worker.rb +86 -0
- data/app/services/lab/metadata.rb +24 -0
- data/app/services/lab/orders_search_service.rb +66 -0
- data/app/services/lab/orders_service.rb +212 -0
- data/app/services/lab/results_service.rb +149 -0
- data/app/services/lab/tests_service.rb +93 -0
- data/config/routes.rb +17 -0
- data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +12 -0
- data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +15 -0
- data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +15 -0
- data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +5 -0
- data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +19 -0
- data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +20 -0
- data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +7 -0
- data/lib/auto12epl.rb +201 -0
- data/lib/couch_bum/couch_bum.rb +92 -0
- data/lib/generators/lab/install/USAGE +9 -0
- data/lib/generators/lab/install/install_generator.rb +19 -0
- data/lib/generators/lab/install/templates/rswag-ui-lab.rb +5 -0
- data/lib/generators/lab/install/templates/start_worker.rb +32 -0
- data/lib/generators/lab/install/templates/swagger.yaml +714 -0
- data/lib/his_emr_api_lab.rb +5 -0
- data/lib/lab/engine.rb +15 -0
- data/lib/lab/version.rb +5 -0
- data/lib/logger_multiplexor.rb +38 -0
- data/lib/tasks/lab_tasks.rake +25 -0
- data/lib/tasks/loaders/data/reasons-for-test.csv +7 -0
- data/lib/tasks/loaders/data/test-measures.csv +225 -0
- data/lib/tasks/loaders/data/tests.csv +161 -0
- data/lib/tasks/loaders/loader_mixin.rb +53 -0
- data/lib/tasks/loaders/metadata_loader.rb +26 -0
- data/lib/tasks/loaders/reasons_for_test_loader.rb +23 -0
- data/lib/tasks/loaders/specimens_loader.rb +65 -0
- data/lib/tasks/loaders/test_result_indicators_loader.rb +54 -0
- metadata +81 -2
data/lib/auto12epl.rb
ADDED
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#!/usr/bin/ruby
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# Jeremy Espino MD MS
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# 28-JAN-2016
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class Float
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# function to round down a float to an integer value
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def round_down n=0
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n < 1 ? self.to_i.to_f : (self - 0.5 / 10**n).round(n)
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end
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end
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# Generates EPL code that conforms to the Auto12-A standard for specimen labeling
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class Auto12Epl
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attr_accessor :element_font
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attr_accessor :barcode_human_font
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DPI = 203
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LABEL_WIDTH_IN = 2.0
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LABEL_HEIGHT_IN = 0.5
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# font constants
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FONT_X_DOTS = [8, 10, 12, 14, 32]
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FONT_Y_DOTS = [12, 16, 20, 24, 24]
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FONT_PAD_DOTS = 2
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# element heights
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HEIGHT_MARGIN = 0.031
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HEIGHT_ELEMENT = 0.1
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HEIGHT_ELEMENT_SPACE = 0.01
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HEIGHT_PID = 0.1
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HEIGHT_BARCODE = 0.200
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HEIGHT_BARCODE_HUMAN = 0.050
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# element widths
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WIDTH_ELEMENT = 1.94
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WIDTH_BARCODE = 1.395
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WIDTH_BARCODE_HUMAN = 1.688
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# margins
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L_MARGIN = 0.031
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L_MARGIN_BARCODE = 0.25
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# stat locations
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L_MARGIN_BARCODE_W_STAT = 0.200
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L_MARGIN_W_STAT = 0.150
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STAT_WIDTH_ELEMENT = 1.78
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STAT_WIDTH_BARCODE = 1.150
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STAT_WIDTH_BARCODE_HUMAN = 1.400
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# constants for generated EPL code
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BARCODE_TYPE = '1A'
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BARCODE_NARROW_WIDTH = '2'
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BARCODE_WIDE_WIDTH = '2'
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BARCODE_ROTATION = '0'
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BARCODE_IS_HUMAN_READABLE = 'N'
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ASCII_HORZ_MULT = 1
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ASCII_VERT_MULT = 1
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def initialize(element_font = 1, barcode_human_font = 1)
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@element_font = element_font
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@barcode_human_font = barcode_human_font
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end
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# Calculate the number of characters that will fit in a given length
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def max_characters(font, length)
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dots_per_char = FONT_X_DOTS.at(font-1) + FONT_PAD_DOTS
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num_char = ( (length * DPI) / dots_per_char).round_down
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num_char.to_int
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end
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# Use basic truncation rule to truncate the name element i.e., if > maxCharacters cutoff and trail with +
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def truncate_name(last_name, first_name, middle_initial, is_stat)
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if is_stat
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name_max_characters = max_characters(@element_font, STAT_WIDTH_ELEMENT)
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else
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name_max_characters = max_characters(@element_font, WIDTH_ELEMENT)
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end
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if concatName(last_name, first_name, middle_initial).length > name_max_characters
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# truncate last?
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if last_name.length > 12
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last_name = last_name[0..11] + '+'
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end
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# truncate first?
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if concatName(last_name, first_name, middle_initial).length > name_max_characters && first_name.length > 7
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first_name = first_name[0..7] + '+'
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end
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end
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concatName(last_name, first_name, middle_initial)
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end
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def concatName(last_name, first_name, middle_initial)
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last_name + ', ' + first_name + (middle_initial == nil ? '' : ' ' + middle_initial)
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end
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# The main function to generate the EPL
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def generate_epl(last_name, first_name, middle_initial, pid, dob, age, gender, col_date_time, col_name, tests, stat, acc_num, schema_track)
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# format text and set margin
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if stat == nil
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name_text = truncate_name(last_name, first_name, middle_initial, false)
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pid_dob_age_gender_text = full_justify(pid, dob + ' ' + age + ' ' + gender, @element_font, WIDTH_ELEMENT)
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l_margin = L_MARGIN
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l_margin_barcode = L_MARGIN_BARCODE
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else
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name_text = truncate_name(last_name, first_name, middle_initial, true)
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pid_dob_age_gender_text = full_justify(pid, dob + ' ' + age + ' ' + gender, @element_font, STAT_WIDTH_ELEMENT)
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stat_element_text = pad_stat_w_space(stat)
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l_margin = L_MARGIN_W_STAT
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l_margin_barcode = L_MARGIN_BARCODE_W_STAT
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end
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barcode_human_text = "#{acc_num} * #{schema_track.gsub(/\-/i, '')}"
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collector_element_text = "Col: #{col_date_time} #{col_name}"
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tests_element_text = tests
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# generate EPL statements
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name_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN), 0, @element_font, false, name_text)
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pid_dob_age_gender_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, pid_dob_age_gender_text)
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barcode_human_element = generate_ascii_element(to_dots(l_margin_barcode), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE), 0, @barcode_human_font, false, barcode_human_text)
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collector_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE + HEIGHT_BARCODE_HUMAN + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, collector_element_text)
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tests_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE + HEIGHT_BARCODE_HUMAN + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, tests_element_text)
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barcode_element = generate_barcode_element(to_dots(l_margin_barcode), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), to_dots(HEIGHT_BARCODE)-4, schema_track)
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stat_element = generate_ascii_element(to_dots(L_MARGIN)+FONT_Y_DOTS.at(@element_font - 1)+FONT_PAD_DOTS, to_dots(HEIGHT_MARGIN), 1, @element_font, true, stat_element_text)
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# combine EPL statements
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if stat == nil
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"\nN\nR216,0\nZT\nS1\n#{name_element}\n#{pid_dob_age_gender_element}\n#{barcode_element}\n#{barcode_human_element}\n#{collector_element}\n#{tests_element}\nP3\n"
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else
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"\nN\nR216,0\nZT\nS1\n#{name_element}\n#{pid_dob_age_gender_element}\n#{barcode_element}\n#{barcode_human_element}\n#{collector_element}\n#{tests_element}\n#{stat_element}\nP3\n"
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end
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end
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# Add spaces before and after the stat text so that black bars appear across the left edge of label
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def pad_stat_w_space(stat)
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num_char = max_characters(@element_font, LABEL_HEIGHT_IN)
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spaces_needed = (num_char - stat.length) / 1
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space = ''
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spaces_needed.times do
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space = space + ' '
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end
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space + stat + space
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end
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# Add spaces between the NPID and the dob/age/gender so that line is fully justified
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def full_justify(pid, dag, font, length)
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max_char = max_characters(font, length)
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spaces_needed = max_char - pid.length - dag.length
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space = ''
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spaces_needed.times do
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space = space + ' '
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end
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pid + space + dag
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end
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# convert inches to number of dots using DPI
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def to_dots(inches)
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(inches * DPI).round
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end
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# generate ascii EPL
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def generate_ascii_element(x, y, rotation, font, is_reverse, text)
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"A#{x.to_s},#{y.to_s},#{rotation.to_s},#{font.to_s},#{ASCII_HORZ_MULT},#{ASCII_VERT_MULT},#{is_reverse ? 'R' : 'N'},\"#{text}\""
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end
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# generate barcode EPL
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def generate_barcode_element(x, y, height, schema_track)
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schema_track = schema_track.gsub("-", "").strip
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"B#{x.to_s},#{y.to_s},#{BARCODE_ROTATION},#{BARCODE_TYPE},#{BARCODE_NARROW_WIDTH},#{BARCODE_WIDE_WIDTH},#{height.to_s},#{BARCODE_IS_HUMAN_READABLE},\"#{schema_track}\""
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end
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end
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if __FILE__ == $0
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auto = Auto12Epl.new
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puts auto.generate_epl("Banda", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", nil, "KCH-16-00001234", "1600001234")
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puts "\n"
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puts auto.generate_epl("Banda", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
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puts "\n"
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puts auto.generate_epl("Bandajustrightlas", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
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puts "\n"
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puts auto.generate_epl("Bandasuperlonglastnamethatwonfit", "Marysuperlonglastnamethatwonfit", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
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puts "\n"
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puts auto.generate_epl("Bandasuperlonglastnamethatwonfit", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
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puts "\n"
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puts auto.generate_epl("Banda", "Marysuperlonglastnamethatwonfit", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
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end
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@@ -0,0 +1,92 @@
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# frozen_string_literal: true
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require 'cgi'
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require 'couchrest'
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##
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# A CouchRest wrapper for the changes API.
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#
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# See: https://github.com/couchrest/couchrest
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class CouchBum
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cattr_accessor :logger
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def initialize(database:, protocol: 'http', host: 'localhost', port: 5984, username: nil, password: nil)
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@connection_string = make_connection_string(protocol, username, password, host, port, database)
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CouchBum.logger ||= Logger.new(STDOUT)
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end
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##
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# Attaches to the Changes API and streams the updates to passed block.
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#
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# This is a blocking call that only stops when there are no more
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# changes to pull or is explicitly terminated by calling +choke+
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# within the passed block.
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def binge_changes(since: 0, limit: nil, include_docs: nil, &block)
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catch(:choke) do
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logger.debug("Binging #{limit} changes from '#{since}'")
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|
+
params = stringify_params(limit: limit, include_docs: include_docs)
|
29
|
+
params = "since=#{since}&#{params}" unless since.blank?
|
30
|
+
|
31
|
+
changes = couch_rest(:get, "_changes?#{params}")
|
32
|
+
context = BingeContext.new(changes)
|
33
|
+
changes['results'].each do |change|
|
34
|
+
context.current_seq = change['seq']
|
35
|
+
context.instance_exec(change, &block)
|
36
|
+
end
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
def couch_rest(method, route, *args, **kwargs)
|
41
|
+
url = expand_route(route)
|
42
|
+
CouchRest.send(method, url, *args, **kwargs)
|
43
|
+
rescue CouchRest::Exception => e
|
44
|
+
logger.error("Failed to communicate with CouchDB: Status: #{e.http_code} - #{e.http_body}")
|
45
|
+
raise e
|
46
|
+
end
|
47
|
+
|
48
|
+
private
|
49
|
+
|
50
|
+
# Context under which the callback passed to binge_changes is executed.
|
51
|
+
class BingeContext
|
52
|
+
attr_accessor :current_seq
|
53
|
+
|
54
|
+
def initialize(changes)
|
55
|
+
@changes = changes
|
56
|
+
end
|
57
|
+
|
58
|
+
def choke
|
59
|
+
throw :choke
|
60
|
+
end
|
61
|
+
|
62
|
+
def last_seq
|
63
|
+
@changes['last_seq']
|
64
|
+
end
|
65
|
+
|
66
|
+
def pending
|
67
|
+
@changes['pending']
|
68
|
+
end
|
69
|
+
end
|
70
|
+
|
71
|
+
def make_connection_string(protocol, username, password, host, port, database)
|
72
|
+
auth = username ? "#{CGI.escape(username)}:#{CGI.escape(password)}@" : ''
|
73
|
+
|
74
|
+
"#{protocol}://#{auth}#{host}:#{port}/#{database}"
|
75
|
+
end
|
76
|
+
|
77
|
+
def expand_route(route)
|
78
|
+
route = route.gsub(%r{^/+}, '')
|
79
|
+
|
80
|
+
"#{@connection_string}/#{route}"
|
81
|
+
end
|
82
|
+
|
83
|
+
def stringify_params(params)
|
84
|
+
params.reduce('') do |str_params, entry|
|
85
|
+
name, value = entry
|
86
|
+
next params unless value
|
87
|
+
|
88
|
+
param = "#{name}=#{value}"
|
89
|
+
str_params.empty? ? param : "#{str_params}&#{param}"
|
90
|
+
end
|
91
|
+
end
|
92
|
+
end
|
@@ -0,0 +1,19 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module Lab
|
4
|
+
class InstallGenerator < Rails::Generators::Base
|
5
|
+
source_root File.expand_path('templates', __dir__)
|
6
|
+
|
7
|
+
def copy_openapi_docs
|
8
|
+
copy_file('swagger.yaml', 'swagger/lab/v1/swagger.yaml')
|
9
|
+
end
|
10
|
+
|
11
|
+
def copy_rswag_initializer
|
12
|
+
copy_file('rswag-ui-lab.rb', 'config/initializers/rswag-ui-lab.rb')
|
13
|
+
end
|
14
|
+
|
15
|
+
def copy_worker
|
16
|
+
copy_file('start_worker.rb', 'bin/lab/start_worker.rb')
|
17
|
+
end
|
18
|
+
end
|
19
|
+
end
|
@@ -0,0 +1,32 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
require 'logger_multiplexor'
|
4
|
+
|
5
|
+
Rails.logger = LoggerMultiplexor.new(Rails.root.join('log/lims-push.log'), $stdout)
|
6
|
+
api = Lab::Lims::Api.new
|
7
|
+
worker = Lab::Lims::Worker.new(api)
|
8
|
+
|
9
|
+
def with_lock(lock_file)
|
10
|
+
File.open("log/#{lock_file}", File::RDWR | File::CREAT, 0o644) do |file|
|
11
|
+
unless file.flock(File::LOCK_EX | File::LOCK_NB)
|
12
|
+
Rails.logger.warn("Failed to start new process due to lock: #{lock_file}")
|
13
|
+
exit 2
|
14
|
+
end
|
15
|
+
|
16
|
+
file.rewind
|
17
|
+
file.puts("Process ##{Process.pid} started at #{Time.now}")
|
18
|
+
|
19
|
+
yield
|
20
|
+
end
|
21
|
+
end
|
22
|
+
|
23
|
+
case ARGV[0]&.downcase
|
24
|
+
when 'push'
|
25
|
+
with_lock('lims-push.lock') { worker.push_orders }
|
26
|
+
when 'pull'
|
27
|
+
with_lock('lims-pull.lock') { worker.pull_orders }
|
28
|
+
else
|
29
|
+
warn 'Error: No or invalid action specified: Valid actions are push and pull'
|
30
|
+
warn 'USAGE: rails runner start_worker.rb push'
|
31
|
+
exit 1
|
32
|
+
end
|