ccls-ccls_engine 3.11.0

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Files changed (269) hide show
  1. data/README.rdoc +182 -0
  2. data/app/models/abstract.rb +181 -0
  3. data/app/models/abstract_search.rb +50 -0
  4. data/app/models/abstract_validations.rb +324 -0
  5. data/app/models/address.rb +70 -0
  6. data/app/models/address_type.rb +15 -0
  7. data/app/models/addressing.rb +147 -0
  8. data/app/models/aliquot.rb +44 -0
  9. data/app/models/aliquot_sample_format.rb +13 -0
  10. data/app/models/analysis.rb +14 -0
  11. data/app/models/bc_request.rb +20 -0
  12. data/app/models/candidate_control.rb +101 -0
  13. data/app/models/context.rb +23 -0
  14. data/app/models/context_data_source.rb +4 -0
  15. data/app/models/county.rb +16 -0
  16. data/app/models/data_source.rb +24 -0
  17. data/app/models/diagnosis.rb +23 -0
  18. data/app/models/document_type.rb +16 -0
  19. data/app/models/document_version.rb +27 -0
  20. data/app/models/enrollment.rb +78 -0
  21. data/app/models/enrollment_validations.rb +167 -0
  22. data/app/models/follow_up.rb +16 -0
  23. data/app/models/follow_up_type.rb +18 -0
  24. data/app/models/gift_card.rb +22 -0
  25. data/app/models/gift_card_search.rb +137 -0
  26. data/app/models/home_exposure_response.rb +24 -0
  27. data/app/models/homex_outcome.rb +75 -0
  28. data/app/models/hospital.rb +22 -0
  29. data/app/models/icf_master_id.rb +30 -0
  30. data/app/models/icf_master_tracker.rb +217 -0
  31. data/app/models/icf_master_tracker_change.rb +9 -0
  32. data/app/models/icf_master_tracker_update.rb +50 -0
  33. data/app/models/ineligible_reason.rb +26 -0
  34. data/app/models/instrument.rb +26 -0
  35. data/app/models/instrument_type.rb +17 -0
  36. data/app/models/instrument_version.rb +28 -0
  37. data/app/models/interview.rb +122 -0
  38. data/app/models/interview_method.rb +17 -0
  39. data/app/models/interview_outcome.rb +16 -0
  40. data/app/models/language.rb +28 -0
  41. data/app/models/live_birth_data_update.rb +142 -0
  42. data/app/models/operational_event.rb +99 -0
  43. data/app/models/operational_event_type.rb +31 -0
  44. data/app/models/organization.rb +28 -0
  45. data/app/models/patient.rb +63 -0
  46. data/app/models/patient_validations.rb +118 -0
  47. data/app/models/person.rb +28 -0
  48. data/app/models/phone_number.rb +105 -0
  49. data/app/models/phone_type.rb +15 -0
  50. data/app/models/project.rb +39 -0
  51. data/app/models/project_outcome.rb +19 -0
  52. data/app/models/race.rb +31 -0
  53. data/app/models/refusal_reason.rb +23 -0
  54. data/app/models/sample.rb +168 -0
  55. data/app/models/sample_kit.rb +14 -0
  56. data/app/models/sample_outcome.rb +16 -0
  57. data/app/models/sample_temperature.rb +14 -0
  58. data/app/models/sample_type.rb +37 -0
  59. data/app/models/search.rb +195 -0
  60. data/app/models/section.rb +18 -0
  61. data/app/models/state.rb +25 -0
  62. data/app/models/study_subject.rb +237 -0
  63. data/app/models/study_subject_abstracts.rb +47 -0
  64. data/app/models/study_subject_addresses.rb +34 -0
  65. data/app/models/study_subject_associations.rb +38 -0
  66. data/app/models/study_subject_duplicates.rb +111 -0
  67. data/app/models/study_subject_enrollments.rb +17 -0
  68. data/app/models/study_subject_homex_outcome.rb +22 -0
  69. data/app/models/study_subject_identifier.rb +153 -0
  70. data/app/models/study_subject_interviews.rb +25 -0
  71. data/app/models/study_subject_languages.rb +21 -0
  72. data/app/models/study_subject_operational_events.rb +66 -0
  73. data/app/models/study_subject_patient.rb +177 -0
  74. data/app/models/study_subject_pii.rb +74 -0
  75. data/app/models/study_subject_races.rb +25 -0
  76. data/app/models/study_subject_search.rb +260 -0
  77. data/app/models/study_subject_validations.rb +116 -0
  78. data/app/models/subject_language.rb +11 -0
  79. data/app/models/subject_race.rb +11 -0
  80. data/app/models/subject_relationship.rb +21 -0
  81. data/app/models/subject_type.rb +22 -0
  82. data/app/models/tracing_status.rb +20 -0
  83. data/app/models/transfer.rb +40 -0
  84. data/app/models/unit.rb +14 -0
  85. data/app/models/vital_status.rb +19 -0
  86. data/app/models/zip_code.rb +36 -0
  87. data/config/abstract_fields.yml +1038 -0
  88. data/config/abstract_sections.yml +77 -0
  89. data/config/home_exposure_response_fields.yml +583 -0
  90. data/config/icf_master_tracker_update.yml +56 -0
  91. data/config/live_birth_data_update.yml +56 -0
  92. data/config/shared_use_db.yml +4 -0
  93. data/generators/ccls_engine/USAGE +2 -0
  94. data/generators/ccls_engine/ccls_engine_generator.rb +123 -0
  95. data/generators/ccls_engine/templates/autotest_ccls_engine.rb +3 -0
  96. data/generators/ccls_engine/templates/ccls_engine.rake +12 -0
  97. data/generators/ccls_engine/templates/fixtures/address_types.yml +30 -0
  98. data/generators/ccls_engine/templates/fixtures/context_data_sources.yml +54 -0
  99. data/generators/ccls_engine/templates/fixtures/contexts.yml +19 -0
  100. data/generators/ccls_engine/templates/fixtures/data_sources.yml +40 -0
  101. data/generators/ccls_engine/templates/fixtures/diagnoses.yml +40 -0
  102. data/generators/ccls_engine/templates/fixtures/document_types.yml +65 -0
  103. data/generators/ccls_engine/templates/fixtures/document_versions.csv +155 -0
  104. data/generators/ccls_engine/templates/fixtures/follow_up_types.yml +16 -0
  105. data/generators/ccls_engine/templates/fixtures/hospitals.yml +114 -0
  106. data/generators/ccls_engine/templates/fixtures/ineligible_reasons.yml +35 -0
  107. data/generators/ccls_engine/templates/fixtures/instrument_types.yml +26 -0
  108. data/generators/ccls_engine/templates/fixtures/instrument_versions.yml +22 -0
  109. data/generators/ccls_engine/templates/fixtures/instruments.yml +22 -0
  110. data/generators/ccls_engine/templates/fixtures/interview_methods.yml +30 -0
  111. data/generators/ccls_engine/templates/fixtures/interview_outcomes.yml +31 -0
  112. data/generators/ccls_engine/templates/fixtures/languages.yml +34 -0
  113. data/generators/ccls_engine/templates/fixtures/operational_event_types.yml +141 -0
  114. data/generators/ccls_engine/templates/fixtures/organizations.yml +198 -0
  115. data/generators/ccls_engine/templates/fixtures/people.yml +130 -0
  116. data/generators/ccls_engine/templates/fixtures/phone_types.yml +30 -0
  117. data/generators/ccls_engine/templates/fixtures/project_outcomes.yml +25 -0
  118. data/generators/ccls_engine/templates/fixtures/projects.yml +59 -0
  119. data/generators/ccls_engine/templates/fixtures/races.yml +52 -0
  120. data/generators/ccls_engine/templates/fixtures/refusal_reasons.yml +55 -0
  121. data/generators/ccls_engine/templates/fixtures/sample_outcomes.yml +36 -0
  122. data/generators/ccls_engine/templates/fixtures/sample_temperatures.yml +16 -0
  123. data/generators/ccls_engine/templates/fixtures/sample_types.yml +147 -0
  124. data/generators/ccls_engine/templates/fixtures/sections.yml +31 -0
  125. data/generators/ccls_engine/templates/fixtures/states.yml +363 -0
  126. data/generators/ccls_engine/templates/fixtures/subject_relationships.yml +46 -0
  127. data/generators/ccls_engine/templates/fixtures/subject_types.yml +30 -0
  128. data/generators/ccls_engine/templates/fixtures/tracing_statuses.yml +30 -0
  129. data/generators/ccls_engine/templates/fixtures/units.yml +13 -0
  130. data/generators/ccls_engine/templates/fixtures/vital_statuses.yml +28 -0
  131. data/generators/ccls_engine/templates/functional/roles_controller_test.rb +142 -0
  132. data/generators/ccls_engine/templates/functional/sessions_controller_test.rb +19 -0
  133. data/generators/ccls_engine/templates/functional/users_controller_test.rb +94 -0
  134. data/generators/ccls_engine/templates/images/sort_down.png +0 -0
  135. data/generators/ccls_engine/templates/images/sort_up.png +0 -0
  136. data/generators/ccls_engine/templates/initializer.rb +28 -0
  137. data/generators/ccls_engine/templates/javascripts/ccls_engine.js +24 -0
  138. data/generators/ccls_engine/templates/javascripts/jquery-ui.js +763 -0
  139. data/generators/ccls_engine/templates/javascripts/jquery.js +154 -0
  140. data/generators/ccls_engine/templates/javascripts/jrails.js +1 -0
  141. data/generators/ccls_engine/templates/migrations/create_user_invitations.rb +18 -0
  142. data/generators/ccls_engine/templates/migrations/create_users.rb +33 -0
  143. data/generators/ccls_engine/templates/migrations/drop_user_invitations.rb +18 -0
  144. data/generators/ccls_engine/templates/stylesheets/ccls_engine.css +180 -0
  145. data/generators/ccls_engine/templates/stylesheets/user.css +35 -0
  146. data/generators/ccls_engine/templates/stylesheets/users.css +23 -0
  147. data/generators/ccls_engine/templates/unit/core_extension_test.rb +18 -0
  148. data/generators/ccls_engine/templates/unit/role_test.rb +30 -0
  149. data/generators/ccls_engine/templates/unit/user_test.rb +321 -0
  150. data/lib/ccls-ccls_engine.rb +1 -0
  151. data/lib/ccls_engine.rb +135 -0
  152. data/lib/ccls_engine/action_view_extension.rb +3 -0
  153. data/lib/ccls_engine/action_view_extension/base.rb +53 -0
  154. data/lib/ccls_engine/action_view_extension/form_builder.rb +39 -0
  155. data/lib/ccls_engine/active_record_extension.rb +2 -0
  156. data/lib/ccls_engine/active_record_extension/base.rb +70 -0
  157. data/lib/ccls_engine/active_record_shared.rb +8 -0
  158. data/lib/ccls_engine/assertions.rb +69 -0
  159. data/lib/ccls_engine/autotest.rb +54 -0
  160. data/lib/ccls_engine/ccls_user.rb +117 -0
  161. data/lib/ccls_engine/core_extension.rb +14 -0
  162. data/lib/ccls_engine/date_and_time_formats.rb +30 -0
  163. data/lib/ccls_engine/factories.rb +880 -0
  164. data/lib/ccls_engine/factory_test_helper.rb +276 -0
  165. data/lib/ccls_engine/helper.rb +112 -0
  166. data/lib/ccls_engine/icf_master_tracker_update_test_helper.rb +121 -0
  167. data/lib/ccls_engine/live_birth_data_update_test_helper.rb +110 -0
  168. data/lib/ccls_engine/package_test_helper.rb +49 -0
  169. data/lib/ccls_engine/shared_database.rb +20 -0
  170. data/lib/ccls_engine/tasks.rb +1 -0
  171. data/lib/ccls_engine/test_tasks.rb +52 -0
  172. data/lib/ccls_engine/translation_table.rb +86 -0
  173. data/lib/shared_migration.rb +5 -0
  174. data/lib/surveyor/survey_extensions.rb +125 -0
  175. data/lib/tasks/application.rake +286 -0
  176. data/lib/tasks/calnet_authenticated.rake +6 -0
  177. data/lib/tasks/common_lib.rake +7 -0
  178. data/lib/tasks/database.rake +288 -0
  179. data/lib/tasks/documentation.rake +71 -0
  180. data/lib/tasks/homex_import.rake +723 -0
  181. data/lib/tasks/odms_import.rake +1116 -0
  182. data/lib/tasks/simply_authorized.rake +6 -0
  183. data/lib/tasks/ucb_ccls_engine_tasks.rake +4 -0
  184. data/lib/tasks/use_db.rake +4 -0
  185. data/rails/init.rb +4 -0
  186. data/test/unit/ccls/abstract_search_test.rb +150 -0
  187. data/test/unit/ccls/abstract_test.rb +674 -0
  188. data/test/unit/ccls/address_test.rb +155 -0
  189. data/test/unit/ccls/address_type_test.rb +25 -0
  190. data/test/unit/ccls/addressing_test.rb +466 -0
  191. data/test/unit/ccls/aliquot_sample_format_test.rb +20 -0
  192. data/test/unit/ccls/aliquot_test.rb +156 -0
  193. data/test/unit/ccls/analysis_test.rb +31 -0
  194. data/test/unit/ccls/bc_request_test.rb +43 -0
  195. data/test/unit/ccls/candidate_control_test.rb +712 -0
  196. data/test/unit/ccls/context_data_source_test.rb +26 -0
  197. data/test/unit/ccls/context_test.rb +40 -0
  198. data/test/unit/ccls/core_extension_test.rb +17 -0
  199. data/test/unit/ccls/county_test.rb +34 -0
  200. data/test/unit/ccls/data_source_test.rb +41 -0
  201. data/test/unit/ccls/diagnosis_test.rb +51 -0
  202. data/test/unit/ccls/document_type_test.rb +35 -0
  203. data/test/unit/ccls/document_version_test.rb +68 -0
  204. data/test/unit/ccls/enrollment_test.rb +575 -0
  205. data/test/unit/ccls/follow_up_test.rb +23 -0
  206. data/test/unit/ccls/follow_up_type_test.rb +34 -0
  207. data/test/unit/ccls/gift_card_search_test.rb +153 -0
  208. data/test/unit/ccls/gift_card_test.rb +40 -0
  209. data/test/unit/ccls/home_exposure_response_test.rb +83 -0
  210. data/test/unit/ccls/homex_outcome_test.rb +199 -0
  211. data/test/unit/ccls/hospital_test.rb +102 -0
  212. data/test/unit/ccls/icf_master_id_test.rb +30 -0
  213. data/test/unit/ccls/icf_master_tracker_change_test.rb +14 -0
  214. data/test/unit/ccls/icf_master_tracker_test.rb +132 -0
  215. data/test/unit/ccls/icf_master_tracker_update_test.rb +176 -0
  216. data/test/unit/ccls/ineligible_reason_test.rb +48 -0
  217. data/test/unit/ccls/instrument_test.rb +62 -0
  218. data/test/unit/ccls/instrument_type_test.rb +39 -0
  219. data/test/unit/ccls/instrument_version_test.rb +71 -0
  220. data/test/unit/ccls/interview_method_test.rb +44 -0
  221. data/test/unit/ccls/interview_outcome_test.rb +34 -0
  222. data/test/unit/ccls/interview_test.rb +298 -0
  223. data/test/unit/ccls/language_test.rb +47 -0
  224. data/test/unit/ccls/live_birth_data_update_test.rb +358 -0
  225. data/test/unit/ccls/operational_event_test.rb +187 -0
  226. data/test/unit/ccls/operational_event_type_test.rb +51 -0
  227. data/test/unit/ccls/organization_test.rb +64 -0
  228. data/test/unit/ccls/patient_test.rb +538 -0
  229. data/test/unit/ccls/person_test.rb +55 -0
  230. data/test/unit/ccls/phone_number_test.rb +244 -0
  231. data/test/unit/ccls/phone_type_test.rb +32 -0
  232. data/test/unit/ccls/project_outcome_test.rb +34 -0
  233. data/test/unit/ccls/project_test.rb +60 -0
  234. data/test/unit/ccls/race_test.rb +37 -0
  235. data/test/unit/ccls/refusal_reason_test.rb +52 -0
  236. data/test/unit/ccls/role_test.rb +26 -0
  237. data/test/unit/ccls/sample_kit_test.rb +35 -0
  238. data/test/unit/ccls/sample_outcome_test.rb +34 -0
  239. data/test/unit/ccls/sample_temperature_test.rb +25 -0
  240. data/test/unit/ccls/sample_test.rb +363 -0
  241. data/test/unit/ccls/sample_type_test.rb +58 -0
  242. data/test/unit/ccls/section_test.rb +34 -0
  243. data/test/unit/ccls/state_test.rb +31 -0
  244. data/test/unit/ccls/study_subject_abstracts_test.rb +115 -0
  245. data/test/unit/ccls/study_subject_addresses_test.rb +93 -0
  246. data/test/unit/ccls/study_subject_duplicates_test.rb +407 -0
  247. data/test/unit/ccls/study_subject_enrollments_test.rb +65 -0
  248. data/test/unit/ccls/study_subject_homex_outcome_test.rb +64 -0
  249. data/test/unit/ccls/study_subject_identifier_test.rb +439 -0
  250. data/test/unit/ccls/study_subject_interviews_test.rb +26 -0
  251. data/test/unit/ccls/study_subject_languages_test.rb +142 -0
  252. data/test/unit/ccls/study_subject_operational_events_test.rb +53 -0
  253. data/test/unit/ccls/study_subject_patient_test.rb +249 -0
  254. data/test/unit/ccls/study_subject_pii_test.rb +278 -0
  255. data/test/unit/ccls/study_subject_races_test.rb +203 -0
  256. data/test/unit/ccls/study_subject_search_test.rb +704 -0
  257. data/test/unit/ccls/study_subject_test.rb +770 -0
  258. data/test/unit/ccls/subject_language_test.rb +43 -0
  259. data/test/unit/ccls/subject_race_test.rb +35 -0
  260. data/test/unit/ccls/subject_relationship_test.rb +43 -0
  261. data/test/unit/ccls/subject_type_test.rb +40 -0
  262. data/test/unit/ccls/tracing_status_test.rb +32 -0
  263. data/test/unit/ccls/transfer_test.rb +81 -0
  264. data/test/unit/ccls/translation_table_test.rb +40 -0
  265. data/test/unit/ccls/unit_test.rb +21 -0
  266. data/test/unit/ccls/user_test.rb +156 -0
  267. data/test/unit/ccls/vital_status_test.rb +36 -0
  268. data/test/unit/ccls/zip_code_test.rb +55 -0
  269. metadata +633 -0
@@ -0,0 +1,65 @@
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+ require 'test_helper'
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+
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+ class Ccls::StudySubjectEnrollmentsTest < ActiveSupport::TestCase
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+
5
+ test "should create study_subject and accept_nested_attributes_for enrollments" do
6
+ assert_difference( 'Enrollment.count', 2) { # ccls enrollment is auto-created, so 2
7
+ assert_difference( "StudySubject.count", 1 ) {
8
+ study_subject = create_study_subject(
9
+ :enrollments_attributes => [Factory.attributes_for(:enrollment,
10
+ :project_id => Project['non-specific'].id)])
11
+ assert !study_subject.new_record?,
12
+ "#{study_subject.errors.full_messages.to_sentence}"
13
+ } }
14
+ end
15
+
16
+ test "should NOT destroy enrollments with study_subject" do
17
+ assert_difference('StudySubject.count',1) {
18
+ assert_difference('Enrollment.count',2) { # due to the callback creation of ccls enrollment
19
+ @study_subject = Factory(:enrollment).study_subject
20
+ } }
21
+ assert_difference('StudySubject.count',-1) {
22
+ assert_difference('Enrollment.count',0) {
23
+ @study_subject.destroy
24
+ } }
25
+ end
26
+
27
+ test "should return nil hx_enrollment if not enrolled" do
28
+ study_subject = create_study_subject
29
+ assert_nil study_subject.enrollments.find_by_project_id(
30
+ Project['HomeExposures'].id)
31
+ end
32
+
33
+ test "should return valid hx_enrollment if enrolled" do
34
+ study_subject = create_study_subject
35
+ hxe = Factory(:enrollment,
36
+ :study_subject => study_subject,
37
+ :project => Project['HomeExposures']
38
+ )
39
+ assert_not_nil study_subject.enrollments.find_by_project_id(
40
+ Project['HomeExposures'].id)
41
+ end
42
+
43
+ test "should create ccls project enrollment on creation" do
44
+ study_subject = nil
45
+ assert_difference('Project.count',0) { # make sure it didn't create id
46
+ assert_difference('Enrollment.count',1) {
47
+ assert_difference('StudySubject.count',1) {
48
+ study_subject = create_study_subject
49
+ } } }
50
+ assert_not_nil study_subject.enrollments.find_by_project_id(Project['ccls'].id)
51
+ end
52
+
53
+ test "should only create 1 ccls project enrollment on creation if given one" do
54
+ study_subject = nil
55
+ assert_difference('Project.count',0) { # make sure it didn't create id
56
+ assert_difference('Enrollment.count',1) {
57
+ assert_difference('StudySubject.count',1) {
58
+ study_subject = create_study_subject(:enrollments_attributes => [
59
+ { :project_id => Project['ccls'].id }
60
+ ])
61
+ } } }
62
+ assert_not_nil study_subject.enrollments.find_by_project_id(Project['ccls'].id)
63
+ end
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+
65
+ end
@@ -0,0 +1,64 @@
1
+ require 'test_helper'
2
+
3
+ class Ccls::StudySubjectHomexOutcomeTest < ActiveSupport::TestCase
4
+
5
+ test "should create study_subject and accept_nested_attributes_for homex_outcome" do
6
+ assert_difference( 'HomexOutcome.count', 1) {
7
+ assert_difference( "StudySubject.count", 1 ) {
8
+ study_subject = create_study_subject(
9
+ :homex_outcome_attributes => Factory.attributes_for(:homex_outcome))
10
+ assert !study_subject.new_record?,
11
+ "#{study_subject.errors.full_messages.to_sentence}"
12
+ } }
13
+ end
14
+
15
+ # StudySubject currently accepts nested attributes for homex_outcome,
16
+ # but an empty homex_outcome is no longer invalid.
17
+ test "should create study_subject with empty homex_outcome" do
18
+ assert_difference( 'HomexOutcome.count', 1) {
19
+ assert_difference( 'StudySubject.count', 1) {
20
+ study_subject = create_study_subject( :homex_outcome_attributes => {})
21
+ } }
22
+ end
23
+
24
+ test "should NOT destroy homex_outcome with study_subject" do
25
+ assert_difference('StudySubject.count',1) {
26
+ assert_difference('HomexOutcome.count',1) {
27
+ @study_subject = Factory(:study_subject)
28
+ Factory(:homex_outcome, :study_subject => @study_subject)
29
+ } }
30
+ assert_difference('StudySubject.count',-1) {
31
+ assert_difference('HomexOutcome.count',0) {
32
+ @study_subject.destroy
33
+ } }
34
+ end
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+
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+ # Delegated homex_outcome fields
37
+ %w( interview_outcome sample_outcome
38
+ interview_outcome_on sample_outcome_on
39
+ ).each do |method_name|
40
+
41
+ test "should respond to #{method_name}" do
42
+ study_subject = create_study_subject
43
+ assert study_subject.respond_to?(method_name)
44
+ end
45
+
46
+ end
47
+
48
+ # Delegated homex_outcome fields except ... interview_outcome, sample_outcome
49
+ %w( interview_outcome_on sample_outcome_on ).each do |method_name|
50
+
51
+ test "should return nil #{method_name} without homex_outcome" do
52
+ study_subject = create_study_subject
53
+ assert_nil study_subject.send(method_name)
54
+ end
55
+
56
+ test "should return #{method_name} with homex_outcome" do
57
+ study_subject = create_study_subject(
58
+ :homex_outcome_attributes => Factory.attributes_for(:homex_outcome))
59
+ assert_not_nil study_subject.send(method_name)
60
+ end
61
+
62
+ end
63
+
64
+ end
@@ -0,0 +1,439 @@
1
+ require 'test_helper'
2
+
3
+ # This is just a collection of identifier related tests
4
+ # for StudySubject separated only for clarity due
5
+ # to the size of the StudySubjectTest class.
6
+ class Ccls::StudySubjectIdentifierTest < ActiveSupport::TestCase
7
+
8
+ test "studyid should be patid, case_control_type and orderno" do
9
+ StudySubject.any_instance.stubs(:get_next_patid).returns('123')
10
+ study_subject = Factory(:case_study_subject)
11
+ assert study_subject.is_case?
12
+ assert_not_nil study_subject.studyid
13
+ assert_nil study_subject.studyid_nohyphen
14
+ assert_nil study_subject.studyid_intonly_nohyphen
15
+ assert_equal "0123-C-0", study_subject.studyid
16
+ end
17
+
18
+ test "should create study subject with specified matchingid" do
19
+ # just to make sure that this method is defined
20
+ # get funny errors when accidentally comment out.
21
+ assert_difference('StudySubject.count',1) {
22
+ study_subject = create_study_subject(:matchingid => '54321')
23
+ assert_equal '054321', study_subject.matchingid
24
+ }
25
+ end
26
+
27
+ test "should not assign icf_master_id when there are none" do
28
+ study_subject = Factory(:study_subject, :icf_master_id => nil)
29
+ study_subject.assign_icf_master_id
30
+ assert_nil study_subject.icf_master_id
31
+ end
32
+
33
+ test "should not assign icf_master_id if already have one and one exists" do
34
+ study_subject = Factory(:study_subject)
35
+ assert_nil study_subject.reload.icf_master_id
36
+ imi1 = Factory(:icf_master_id,:icf_master_id => '12345678A')
37
+ study_subject.assign_icf_master_id
38
+ assert_equal imi1.icf_master_id, study_subject.reload.icf_master_id
39
+ imi2 = Factory(:icf_master_id,:icf_master_id => '12345678B')
40
+ study_subject.assign_icf_master_id
41
+ assert_equal imi1.icf_master_id, study_subject.reload.icf_master_id
42
+ end
43
+
44
+ test "should assign icf_master_id when there is one" do
45
+ study_subject = create_study_subject
46
+ imi = Factory(:icf_master_id,:icf_master_id => '12345678A')
47
+ study_subject.assign_icf_master_id
48
+ assert_not_nil study_subject.icf_master_id
49
+ assert_equal '12345678A', study_subject.icf_master_id
50
+ imi.reload
51
+ assert_not_nil imi.assigned_on
52
+ assert_equal Date.today, imi.assigned_on
53
+ assert_not_nil imi.study_subject_id
54
+ assert_equal imi.study_subject_id, study_subject.id
55
+ end
56
+
57
+ test "should assign icf_master_id to mother on creation if one exists" do
58
+ study_subject = create_study_subject
59
+ imi = Factory(:icf_master_id,:icf_master_id => '12345678A')
60
+ assert_equal '12345678A', imi.icf_master_id
61
+ mother = study_subject.create_mother
62
+ assert_not_nil mother.reload.icf_master_id
63
+ assert_equal '12345678A', mother.icf_master_id
64
+ end
65
+
66
+ test "should not assign icf_master_id to mother on creation if none exist" do
67
+ study_subject = create_study_subject
68
+ mother = study_subject.create_mother
69
+ assert_nil mother.reload.icf_master_id
70
+ end
71
+
72
+ test "should return 'no ID assigned' if study_subject has no icf_master_id" do
73
+ study_subject = create_study_subject
74
+ assert_nil study_subject.icf_master_id
75
+ assert_equal study_subject.icf_master_id_to_s, '[no ID assigned]'
76
+ end
77
+
78
+ test "should return icf_master_id if study_subject has icf_master_id" do
79
+ study_subject = create_study_subject
80
+ assert_nil study_subject.icf_master_id
81
+ assert_equal study_subject.icf_master_id_to_s, '[no ID assigned]'
82
+ imi = Factory(:icf_master_id,:icf_master_id => '12345678A')
83
+ study_subject.assign_icf_master_id
84
+ assert_not_nil study_subject.icf_master_id
85
+ assert_equal study_subject.icf_master_id, imi.icf_master_id
86
+ assert_equal study_subject.icf_master_id_to_s, imi.icf_master_id
87
+ end
88
+
89
+ test "should require unique icf_master_id" do
90
+ assert_difference('StudySubject.count',1){
91
+ Factory(:study_subject, :icf_master_id => 'Fake1234')
92
+ }
93
+ assert_difference('StudySubject.count',0){
94
+ study_subject = Factory.build(:study_subject, :icf_master_id => 'Fake1234')
95
+ study_subject.save
96
+ assert study_subject.errors.on_attr_and_type?(:icf_master_id, :taken)
97
+ }
98
+ end
99
+
100
+ test "should nullify blank state_id_no before validation" do
101
+ study_subject = Factory.build(:study_subject, :state_id_no => '')
102
+ assert study_subject.state_id_no.blank?
103
+ assert !study_subject.state_id_no.nil?
104
+ study_subject.valid?
105
+ assert study_subject.state_id_no.blank?
106
+ assert study_subject.state_id_no.nil?
107
+ end
108
+
109
+ test "should nullify blank state_registrar_no before validation" do
110
+ study_subject = Factory.build(:study_subject, :state_registrar_no => '')
111
+ assert study_subject.state_registrar_no.blank?
112
+ assert !study_subject.state_registrar_no.nil?
113
+ study_subject.valid?
114
+ assert study_subject.state_registrar_no.blank?
115
+ assert study_subject.state_registrar_no.nil?
116
+ end
117
+
118
+ test "should nullify blank local_registrar_no before validation" do
119
+ study_subject = Factory.build(:study_subject, :local_registrar_no => '')
120
+ assert study_subject.local_registrar_no.blank?
121
+ assert !study_subject.local_registrar_no.nil?
122
+ study_subject.valid?
123
+ assert study_subject.local_registrar_no.blank?
124
+ assert study_subject.local_registrar_no.nil?
125
+ end
126
+
127
+ # test "should pad subjectid with leading zeros before validation" do
128
+ # study_subject = Factory.build(:study_subject)
129
+ # assert study_subject.subjectid.length < 6
130
+ # study_subject.valid? #save
131
+ # assert study_subject.subjectid.length == 6
132
+ # end
133
+
134
+ test "should pad matchingid with leading zeros before validation" do
135
+ study_subject = Factory.build(:study_subject,{ :matchingid => '123' })
136
+ assert study_subject.matchingid.length < 6
137
+ assert_equal '123', study_subject.matchingid
138
+ study_subject.valid? #save
139
+ assert study_subject.matchingid.length == 6
140
+ assert_equal '000123', study_subject.matchingid
141
+ end
142
+
143
+ test "should pad patid with leading zeros before validation" do
144
+ study_subject = Factory.build(:study_subject)
145
+ study_subject.patid = '123'
146
+ assert study_subject.patid.length < 4
147
+ assert_equal '123', study_subject.patid
148
+ study_subject.valid? #save
149
+ assert study_subject.patid.length == 4
150
+ assert_equal '0123', study_subject.patid
151
+ end
152
+
153
+ # remove ssn from factory and don't use class level test
154
+ test "should require unique ssn" do
155
+ Factory(:study_subject,:ssn => '123-45-6789')
156
+ assert_difference('StudySubject.count',0){
157
+ study_subject = Factory.build(:study_subject,:ssn => '123-45-6789')
158
+ study_subject.save
159
+ assert study_subject.errors.on_attr_and_type?(:ssn,:taken)
160
+ }
161
+ end
162
+
163
+ test "should nullify blank ssn" do
164
+ assert_difference('StudySubject.count',1){
165
+ study_subject = Factory(:study_subject, :ssn => '')
166
+ assert study_subject.reload.ssn.nil?
167
+ }
168
+ end
169
+
170
+ test "should create with string standard format ssn" do
171
+ assert_difference( "StudySubject.count", 1 ) do
172
+ study_subject = create_study_subject(:ssn => '987-65-4321')
173
+ assert !study_subject.new_record?,
174
+ "#{study_subject.errors.full_messages.to_sentence}"
175
+ assert_equal '987-65-4321', study_subject.reload.ssn
176
+ end
177
+ end
178
+
179
+ test "should require standard formatted ssn" do
180
+ %w( 1s2n3-4k5=6;7sdfg89 123456789 12345678X 12345678 1-34-56-789 ).each do |invalid_ssn|
181
+ assert_difference( "StudySubject.count", 0 ) do
182
+ study_subject = create_study_subject(:ssn => invalid_ssn)
183
+ assert study_subject.errors.on_attr_and_type?(:ssn,:invalid)
184
+ end
185
+ end
186
+ end
187
+
188
+ # patid and childid should be protected as they are generated values
189
+
190
+ test "should generate orderno = 0 for case_control_type == 'c'" do
191
+ # case_control_type is NOT the trigger. SubjectType is.
192
+ study_subject = Factory(:case_study_subject).reload
193
+ assert_equal 0, study_subject.orderno
194
+ end
195
+
196
+ test "should not overwrite given studyid" do
197
+ study_subject = Factory(:study_subject,:studyid => 'MyStudyId').reload
198
+ assert_equal 'MyStudyId', study_subject.studyid
199
+ end
200
+
201
+ test "should set studyid with patid, case_control_type and orderno for" <<
202
+ " case_control_type c" do
203
+ StudySubject.any_instance.stubs(:get_next_patid).returns('123')
204
+ study_subject = Factory(:case_study_subject).reload
205
+ assert_equal "0123", study_subject.patid
206
+ assert_equal "C", study_subject.case_control_type
207
+ assert_equal "0", study_subject.orderno.to_s
208
+ assert_not_nil study_subject.studyid
209
+ assert_nil study_subject.studyid_nohyphen
210
+ assert_nil study_subject.studyid_intonly_nohyphen
211
+ assert_equal "0123-C-0", study_subject.studyid
212
+ end
213
+
214
+ test "should generate subjectid on creation for any study_subject" do
215
+ study_subject = Factory(:study_subject)
216
+ assert_not_nil study_subject.subjectid
217
+ assert study_subject.subjectid.length == 6
218
+ end
219
+
220
+ test "should generate patid on creation of case_control_type == 'c'" do
221
+ assert_difference('StudySubject.maximum(:patid).to_i', 1) {
222
+ study_subject = Factory(:case_study_subject).reload
223
+ assert_not_nil study_subject.patid
224
+ }
225
+ end
226
+
227
+ %w( c b f 4 5 6 ).each do |cct|
228
+
229
+ test "should generate childid on creation of case_control_type #{cct}" do
230
+ assert_difference('StudySubject.maximum(:childid).to_i', 1) {
231
+ study_subject = Factory(:study_subject, :case_control_type => cct )
232
+ assert_not_nil study_subject.childid
233
+ }
234
+ end
235
+
236
+ test "should generate familyid == subjectid on creation of case_control_type #{cct}" do
237
+ study_subject = Factory(:study_subject, :case_control_type => cct )
238
+ assert_not_nil study_subject.subjectid
239
+ assert_not_nil study_subject.familyid
240
+ assert_equal study_subject.subjectid, study_subject.familyid
241
+ end
242
+
243
+ end
244
+
245
+ test "should generate familyid == child's subjectid on creation of case's mother" do
246
+ case_study_subject = create_case_study_subject
247
+ assert_equal case_study_subject.subjectid, case_study_subject.familyid
248
+ mother = case_study_subject.create_mother
249
+ assert_equal case_study_subject.subjectid, mother.familyid
250
+ end
251
+
252
+ test "should generate familyid == child's subjectid on creation of control's mother" do
253
+ control_study_subject = create_control_study_subject
254
+ assert_equal control_study_subject.subjectid, control_study_subject.familyid
255
+ mother = control_study_subject.create_mother
256
+ assert_equal control_study_subject.subjectid, mother.familyid
257
+ end
258
+
259
+ test "should generate matchingid == subjectid on creation of case" do
260
+ study_subject = Factory(:case_study_subject).reload
261
+ assert_not_nil study_subject.subjectid
262
+ assert_not_nil study_subject.matchingid
263
+ assert_equal study_subject.subjectid, study_subject.matchingid
264
+ end
265
+
266
+ test "should not generate new patid for case if given" do
267
+ # existing data import
268
+ assert_difference( "StudySubject.maximum(:patid).to_i", 123 ) { # was 0, now 123
269
+ assert_difference( "StudySubject.count", 1 ) {
270
+ study_subject = Factory(:case_study_subject, :patid => '123').reload
271
+ assert_not_nil study_subject.studyid
272
+ assert_nil study_subject.studyid_nohyphen
273
+ assert_nil study_subject.studyid_intonly_nohyphen
274
+ assert_equal "0123-C-0", study_subject.studyid
275
+ assert_equal "0123", study_subject.patid
276
+ } } #}
277
+ end
278
+
279
+ test "should not generate new childid if given" do
280
+ # existing data import
281
+ assert_difference( "StudySubject.maximum(:childid).to_i", 123 ) { # was 0, now 123
282
+ assert_difference( "StudySubject.count", 1 ) {
283
+ study_subject = Factory(:case_study_subject, :childid => '123').reload
284
+ assert_equal 123, study_subject.childid
285
+ } } #}
286
+ end
287
+
288
+ test "should not generate new orderno if given" do
289
+ # existing data import
290
+ assert_difference( "StudySubject.count", 1 ) {
291
+ study_subject = Factory(:case_study_subject, :orderno => 9).reload
292
+ assert_equal 9, study_subject.orderno
293
+ }
294
+ end
295
+
296
+ test "should not generate new subjectid if given" do
297
+ # existing data import
298
+ assert_difference( "StudySubject.count", 1 ) {
299
+ study_subject = Factory(:case_study_subject, :subjectid => 'ABCDEF').reload
300
+ assert_equal "ABCDEF", study_subject.subjectid
301
+ }
302
+ end
303
+
304
+ test "should not generate new familyid if given" do
305
+ # existing data import
306
+ assert_difference( "StudySubject.count", 1 ) {
307
+ study_subject = Factory(:case_study_subject, :familyid => 'ABCDEF').reload
308
+ assert_equal "ABCDEF", study_subject.familyid
309
+ }
310
+ end
311
+
312
+ test "should not generate new matchingid if given" do
313
+ # existing data import
314
+ assert_difference( "StudySubject.count", 1 ) {
315
+ study_subject = Factory(:case_study_subject, :matchingid => '123456').reload
316
+ assert_equal "123456", study_subject.matchingid
317
+ }
318
+ end
319
+
320
+ test "should find by studyid or icf_master_id with studyid" do
321
+ study_subject1 = Factory(:case_study_subject)
322
+ study_subject2 = Factory(:case_study_subject)
323
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
324
+ study_subject1.studyid, nil )
325
+ assert study_subjects.include?(study_subject1)
326
+ assert !study_subjects.include?(study_subject2)
327
+ end
328
+
329
+ test "should find by studyid or icf_master_id with case studyid" do
330
+ subject = Factory(:complete_case_study_subject)
331
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
332
+ subject.studyid, nil )
333
+ assert study_subjects.include?(subject)
334
+ end
335
+
336
+ test "should find by studyid or icf_master_id with case icf_master_id" do
337
+ subject = Factory(:complete_case_study_subject)
338
+ Factory(:icf_master_id, :icf_master_id => '123456789' )
339
+ subject.assign_icf_master_id
340
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
341
+ nil, subject.icf_master_id )
342
+ assert study_subjects.include?(subject)
343
+ end
344
+
345
+ test "should find by studyid or icf_master_id with control studyid" do
346
+ subject = Factory(:complete_control_study_subject,
347
+ :patid => '1234', :case_control_type => 'X', :orderno => 9)
348
+ assert_equal subject.patid, '1234'
349
+ assert_equal subject.case_control_type, 'X'
350
+ assert_equal subject.orderno, 9
351
+ assert_equal subject.studyid, '1234-X-9'
352
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
353
+ subject.studyid, nil )
354
+ assert study_subjects.include?(subject)
355
+ end
356
+
357
+ test "should find by studyid or icf_master_id with control icf_master_id" do
358
+ subject = Factory(:complete_control_study_subject)
359
+ Factory(:icf_master_id, :icf_master_id => '123456789' )
360
+ subject.assign_icf_master_id
361
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
362
+ nil, subject.icf_master_id )
363
+ assert study_subjects.include?(subject)
364
+ end
365
+
366
+ # Mothers won't have a studyid
367
+ # test "should find by studyid or icf_master_id with mother studyid" do
368
+ # subject = Factory(:complete_mother_study_subject)
369
+ # puts subject.studyid
370
+ # study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
371
+ # subject.studyid, nil )
372
+ # assert study_subjects.include?(subject)
373
+ # end
374
+
375
+ test "should find by studyid or icf_master_id with mother icf_master_id" do
376
+ subject = Factory(:complete_mother_study_subject)
377
+ Factory(:icf_master_id, :icf_master_id => '123456789' )
378
+ subject.assign_icf_master_id
379
+ study_subjects = StudySubject.find_all_by_studyid_or_icf_master_id(
380
+ nil, subject.icf_master_id )
381
+ assert study_subjects.include?(subject)
382
+ end
383
+
384
+ # TODO what about both studyid and icf_master_id?
385
+
386
+
387
+
388
+
389
+
390
+
391
+
392
+
393
+
394
+
395
+
396
+ # The problems with autogeneration of childid, patid and subjectid are
397
+ # that they cannot be validated automatically. Validation would simply
398
+ # return this failure to the user, whom can do nothing about it.
399
+ # Autogeneration must work on its own. subjectid seems to effectively
400
+ # select an unused subjectid, but if many subjects were being created at
401
+ # the same time could theoretically select the same random number.
402
+ # If/When this occurs, a database error will be returned and confuse
403
+ # the user.
404
+ #
405
+
406
+ # ActiveRecord::StatementInvalid: Mysql::Error: Duplicate entry '12345' for key 'index_identifiers_on_childid': INSERT INTO `identifiers` (`familyid`, `created_at`, `case_control_type`, `childidwho`, `ssn`, `updated_at`, `state_id_no`, `matchingid`, `gbid`, `idno_wiemels`, `related_childid`, `state_registrar_no`, `study_subject_id`, `studyid`, `childid`, `studyid_nohyphen`, `icf_master_id`, `orderno`, `lab_no`, `lab_no_wiemels`, `accession_no`, `subjectid`, `newid`, `studyid_intonly_nohyphen`, `local_registrar_no`, `patid`, `related_case_childid`) VALUES('407928', '2011-10-28 12:36:07', '3', NULL, '000000002', '2011-10-28 12:36:07', '2', NULL, '2', '2', NULL, '2', 2, NULL, 12345, NULL, '2', NULL, NULL, '2', '2', '407928', NULL, NULL, '2', NULL, NULL)
407
+ test "duplicating childid should raise database error" do
408
+ StudySubject.any_instance.stubs(:get_next_childid).returns(12345)
409
+ study_subject1 = Factory(:study_subject)
410
+ assert_not_nil study_subject1.childid
411
+ assert_raises(ActiveRecord::StatementInvalid){
412
+ study_subject2 = Factory(:study_subject)
413
+ }
414
+ end
415
+
416
+ # ActiveRecord::StatementInvalid: Mysql::Error: Duplicate entry '0123-C-0' for key 'piccton': INSERT INTO `identifiers` (`familyid`, `created_at`, `case_control_type`, `childidwho`, `ssn`, `updated_at`, `state_id_no`, `matchingid`, `gbid`, `idno_wiemels`, `related_childid`, `state_registrar_no`, `study_subject_id`, `studyid`, `childid`, `studyid_nohyphen`, `icf_master_id`, `orderno`, `lab_no`, `lab_no_wiemels`, `accession_no`, `subjectid`, `newid`, `studyid_intonly_nohyphen`, `local_registrar_no`, `patid`, `related_case_childid`) VALUES('975152', '2011-10-28 12:36:08', 'C', NULL, '000000004', '2011-10-28 12:36:08', '4', '975152', '4', '4', NULL, '4', 4, NULL, 2, NULL, '4', 0, NULL, '4', '4', '975152', NULL, NULL, '4', '0123', NULL)
417
+ test "duplicating patid should raise database error" do
418
+ StudySubject.any_instance.stubs(:get_next_patid).returns('0123')
419
+ study_subject1 = Factory(:case_study_subject)
420
+ assert_not_nil study_subject1.patid
421
+ assert_raises(ActiveRecord::StatementInvalid){
422
+ study_subject2 = Factory(:case_study_subject)
423
+ }
424
+ end
425
+
426
+ # This should never actually happen as the code actually removes all those that exist.
427
+ # But it does show that if/when creation of an identifier with an existing
428
+ # is attempted, it will raise a database error.
429
+ # ActiveRecord::StatementInvalid: Mysql::Error: Duplicate entry '012345' for key 'index_identifiers_on_subjectid': INSERT INTO `identifiers` (`familyid`, `created_at`, `case_control_type`, `childidwho`, `ssn`, `updated_at`, `state_id_no`, `matchingid`, `gbid`, `idno_wiemels`, `related_childid`, `state_registrar_no`, `study_subject_id`, `studyid`, `childid`, `studyid_nohyphen`, `icf_master_id`, `orderno`, `lab_no`, `lab_no_wiemels`, `accession_no`, `subjectid`, `newid`, `studyid_intonly_nohyphen`, `local_registrar_no`, `patid`, `related_case_childid`) VALUES('012345', '2011-10-28 12:36:08', '5', NULL, '000000006', '2011-10-28 12:36:08', '6', NULL, '6', '6', NULL, '6', 6, NULL, 4, NULL, '6', NULL, NULL, '6', '6', '012345', NULL, NULL, '6', NULL, NULL)
430
+ test "duplicating subjectid should raise database error" do
431
+ StudySubject.any_instance.stubs(:generate_subjectid).returns('012345')
432
+ study_subject1 = Factory(:study_subject)
433
+ assert_not_nil study_subject1.subjectid
434
+ assert_raises(ActiveRecord::StatementInvalid){
435
+ study_subject2 = Factory(:study_subject)
436
+ }
437
+ end
438
+
439
+ end