RubyGems - bonnie_bundler - Versions diffs - 2.0.3 → 2.1.0 - Mend

bonnie_bundler 2.0.3 → 2.1.0

Files changed (42) hide show

checksums.yaml +4 -4
data/Gemfile +1 -1
data/Gemfile.lock +6 -6
data/bonnie-bundler.gemspec +1 -1
data/lib/bonnie_bundler.rb +1 -0
data/lib/measures/loading/cql_loader.rb +25 -12
data/lib/measures/loading/exceptions.rb +0 -2
data/lib/measures/loading/value_set_loader.rb +77 -97
data/lib/util/vsac_api.rb +274 -0
data/test/fixtures/PVC2_v5_4_Unused_Support_Libraries.zip +0 -0
data/test/fixtures/vcr_cassettes/valid_vsac_response_pvc_unused_libraries.yml +4286 -0
data/test/fixtures/vcr_cassettes/vs_loading_500_response.yml +633 -0
data/test/fixtures/vcr_cassettes/vs_loading_empty_concept_list.yml +174 -0
data/test/fixtures/vcr_cassettes/vs_loading_meausre_defined_no_backup_profile.yml +1237 -0
data/test/fixtures/vcr_cassettes/vs_loading_release.yml +17035 -0
data/test/fixtures/vcr_cassettes/vsac_auth_bad_credentials.yml +57 -0
data/test/fixtures/vcr_cassettes/vsac_auth_bad_ticket.yml +57 -0
data/test/fixtures/vcr_cassettes/vsac_auth_good_credentials.yml +57 -0
data/test/fixtures/vcr_cassettes/vsac_auth_good_credentials_and_simple_call.yml +177 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_profiles.yml +74 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_CMS_Hybrid.yml +57 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_CMS_eCQM.yml +64 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_HL7_C-CDA.yml +58 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_invalid.yml +53 -0
data/test/fixtures/vcr_cassettes/vsac_util_get_programs.yml +64 -0
data/test/fixtures/vcr_cassettes/vsac_vs_include_draft_no_profile.yml +57 -0
data/test/fixtures/vcr_cassettes/vsac_vs_include_draft_with_profile.yml +177 -0
data/test/fixtures/vcr_cassettes/vsac_vs_no_options.yml +177 -0
data/test/fixtures/vcr_cassettes/vsac_vs_not_found.yml +164 -0
data/test/fixtures/vcr_cassettes/vsac_vs_release.yml +4802 -0
data/test/fixtures/vcr_cassettes/vsac_vs_version.yml +370 -0
data/test/test_helper.rb +9 -4
data/test/unit/cql_loader_test.rb +42 -15
data/test/unit/load_mat_export_test.rb +10 -13
data/test/unit/measure_complexity_test.rb +1 -1
data/test/unit/measure_diff_test.rb +4 -4
data/test/unit/storing_mat_export_package_test.rb +1 -1
data/test/unit/value_set_loading_test.rb +58 -16
data/test/unit/vsac_api_auth_test.rb +129 -0
data/test/unit/vsac_api_test.rb +77 -0
data/test/unit/vsac_api_util_test.rb +139 -0
metadata +29 -3

data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_CMS_eCQM.yml ADDED

@@ -0,0 +1,64 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://vsac.nlm.nih.gov/vsac/program/CMS%20eCQM
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      User-Agent:
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+  response:
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+      message: ''
+    headers:
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+      Pragma:
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+      X-Content-Type-Options:
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+      X-Vip-Info:
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+      X-Pool-Info:
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+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+    body:
+      encoding: UTF-8
+      string: '{"name":"CMS eCQM","description":"eCQMs use data from electronic health
+        records (EHR) and/or health information technology systems to measure health
+        care quality. eCQM value sets specify terminology codes required for eCQM
+        measurement and are updated by CMS one or more times each year.","release":[{"name":"eCQM
+        Update 2018-05-04","releaseDate":20180504},{"name":"eCQM Update 2018 EP-EC
+        and EH","releaseDate":20170929},{"name":"eCQM Update 4Q2017 EH","releaseDate":20170915},{"name":"eCQM
+        Update 2017-05-05","releaseDate":20170505},{"name":"MU2 Update 2017-01-06","releaseDate":20170106},{"name":"MU2
+        Update 2016-04-01","releaseDate":20160401},{"name":"MU2 Update 2015-05-01","releaseDate":20150501},{"name":"MU2
+        EP Update 2014-07-01","releaseDate":20140701},{"name":"MU2 EP Update 2014-05-30","releaseDate":20140530},{"name":"MU2
+        EH Update 2014-04-01","releaseDate":20140401},{"name":"MU2 EP Update 2013-06-14","releaseDate":20130614},{"name":"MU2
+        EH Update 2013-04-01","releaseDate":20130401},{"name":"MU2 Update 2012-12-21","releaseDate":20121221},{"name":"MU2
+        Update 2012-10-25","releaseDate":20121025}]}'
+    http_version:
+  recorded_at: Wed, 28 Mar 2018 15:17:51 GMT
+recorded_with: VCR 3.0.3

data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_HL7_C-CDA.yml ADDED

@@ -0,0 +1,58 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://vsac.nlm.nih.gov/vsac/program/HL7%20C-CDA
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      User-Agent:
+      - Ruby
+  response:
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+      message: ''
+    headers:
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+      X-Content-Type-Options:
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+      Date:
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+      Strict-Transport-Security:
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+        templated clinical information (e.g., Allergies, Encounters, Immunizations,
+        Problems, Procedures, etc.) from electronic health records.","release":[{"name":"C-CDA
+        R2.1 2018-02-01","releaseDate":20180201},{"name":"C-CDA R2.1 2017-06-09","releaseDate":20170609},{"name":"C-CDA
+        R1.1 2016-06-23","releaseDate":20160623}]}'
+    http_version:
+  recorded_at: Wed, 28 Mar 2018 15:20:43 GMT
+recorded_with: VCR 3.0.3

data/test/fixtures/vcr_cassettes/vsac_util_get_program_details_invalid.yml ADDED

@@ -0,0 +1,53 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://vsac.nlm.nih.gov/vsac/program/Fake%20Program
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      User-Agent:
+      - Ruby
+  response:
+    status:
+      code: 404
+      message: ''
+    headers:
+      Cache-Control:
+      - no-cache, no-store, max-age=0, must-revalidate
+      Pragma:
+      - no-cache
+      Expires:
+      - '0'
+      X-Xss-Protection:
+      - 1; mode=block
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+      X-Content-Type-Options:
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+      Content-Type:
+      - application/json
+      Content-Length:
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+      Date:
+      - Thu, 29 Mar 2018 18:30:22 GMT
+      Set-Cookie:
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+        expires=Thu, 29-Mar-2018 20:30:22 GMT; path=/; Httponly; Secure
+      X-Vip-Info:
+      - 130.14.16.40:443
+      X-Pool-Info:
+      - "/Common/vsacweb_p 10.1.5.110 8080"
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+    body:
+      encoding: UTF-8
+      string: '{"status":"info","message":"Not found"}'
+    http_version:
+  recorded_at: Thu, 29 Mar 2018 18:30:22 GMT
+recorded_with: VCR 3.0.3

data/test/fixtures/vcr_cassettes/vsac_util_get_programs.yml ADDED

@@ -0,0 +1,64 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://vsac.nlm.nih.gov/vsac/programs
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      User-Agent:
+      - Ruby
+  response:
+    status:
+      code: 200
+      message: ''
+    headers:
+      Cache-Control:
+      - no-cache, no-store, max-age=0, must-revalidate
+      Pragma:
+      - no-cache
+      Expires:
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+      - 1; mode=block
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Content-Type-Options:
+      - nosniff
+      Content-Type:
+      - application/json
+      Content-Length:
+      - '910'
+      Date:
+      - Wed, 28 Mar 2018 15:05:36 GMT
+      Set-Cookie:
+      - BIGipServervsacweb_p=!oJB3GT1Q8fqYrd3NtNHn4GsLooFbU/OCI8YRnoJbAmKcXbV/vw7qNd5JchiaAp3SnbSBmoH+pQfBuuE=;
+        expires=Wed, 28-Mar-2018 17:05:36 GMT; path=/; Httponly; Secure
+      X-Vip-Info:
+      - 130.14.16.40:443
+      X-Pool-Info:
+      - "/Common/vsacweb_p 10.1.5.114 8080"
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+    body:
+      encoding: UTF-8
+      string: '{"Program":[{"name":"CMS Hybrid","description":"Core Clinical Data
+        Elements and Hybrid Measures use a set of core clinical data elements, clinical
+        variables from electronic health records (EHRs), that are routinely collected
+        and can be feasibly extracted for use in risk-adjusted hospital-level hybrid
+        outcome measures."},{"name":"CMS eCQM","description":"eCQMs use data from
+        electronic health records (EHR) and/or health information technology systems
+        to measure health care quality. eCQM value sets specify terminology codes
+        required for eCQM measurement and are updated by CMS one or more times each
+        year."},{"name":"HL7 C-CDA","description":"Consolidated Clinical Document
+        Architecture (C-CDA) value sets provide standardized terminology data elements
+        for exchanging templated clinical information (e.g., Allergies, Encounters,
+        Immunizations, Problems, Procedures, etc.) from electronic health records."}]}'
+    http_version:
+  recorded_at: Wed, 28 Mar 2018 15:05:36 GMT
+recorded_with: VCR 3.0.3

data/test/fixtures/vcr_cassettes/vsac_vs_include_draft_no_profile.yml ADDED

@@ -0,0 +1,57 @@
+---
+http_interactions:
+- request:
+    method: post
+    uri: https://vsac.nlm.nih.gov/vsac/ws/Ticket
+    body:
+      encoding: UTF-8
+      string: username=<VSAC_USERNAME>&password=<VSAC_PASSWORD>
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      Content-Length:
+      - '38'
+      Content-Type:
+      - application/x-www-form-urlencoded
+      User-Agent:
+      - Ruby
+  response:
+    status:
+      code: 200
+      message: ''
+    headers:
+      Cache-Control:
+      - no-cache, no-store, max-age=0, must-revalidate
+      Pragma:
+      - no-cache
+      Expires:
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+      - 1; mode=block
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+      X-Content-Type-Options:
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+      Content-Length:
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+      Date:
+      - Wed, 28 Mar 2018 21:42:03 GMT
+      Set-Cookie:
+      - BIGipServervsacweb_p=!KMRBIj8hQBk4QIPm9OGvBt4MxRMcjnASuPJT0OodpqRbPTmyVnOmPkOoB3WJd94G9Oaq9VzBg8wKeac=;
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+      X-Vip-Info:
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+      X-Pool-Info:
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+      Strict-Transport-Security:
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+      string: TGT-2822-zbZ7hDeuUV19mZ4RCbJi99BD5Th6xZgg0Jgf9XlbjZ5W0tVWGw-cas
+    http_version:
+  recorded_at: Wed, 28 Mar 2018 21:42:03 GMT
+recorded_with: VCR 3.0.3

data/test/fixtures/vcr_cassettes/vsac_vs_include_draft_with_profile.yml ADDED

@@ -0,0 +1,177 @@
+---
+http_interactions:
+- request:
+    method: post
+    uri: https://vsac.nlm.nih.gov/vsac/ws/Ticket
+    body:
+      encoding: UTF-8
+      string: username=<VSAC_USERNAME>&password=<VSAC_PASSWORD>
+    headers:
+      Accept:
+      - "*/*; q=0.5, application/xml"
+      Accept-Encoding:
+      - gzip, deflate
+      Content-Length:
+      - '38'
+      Content-Type:
+      - application/x-www-form-urlencoded
+      User-Agent:
+      - Ruby
+  response:
+    status:
+      code: 200
+      message: ''
+    headers:
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+      Pragma:
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+    http_version:
+  recorded_at: Wed, 28 Mar 2018 21:40:43 GMT
+- request:
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+    uri: https://vsac.nlm.nih.gov/vsac/ws/Ticket/TGT-2798-OUaMUk7yGMcrWCJRHkcCKYRvReJEgyxFHmn6sRup4y3vJwQeeV-cas
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+    http_version:
+  recorded_at: Wed, 28 Mar 2018 21:40:43 GMT
+- request:
+    method: get
+    uri: https://vsac.nlm.nih.gov/vsac/svs/RetrieveMultipleValueSets?id=2.16.840.1.113762.1.4.1&includeDraft=yes&profile=eCQM%20Update%202018-05-04&ticket=ST-49130-oakPAN3DQYbiLeTdbOyV-cas
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+            <ns0:DescribedValueSet ID="2.16.840.1.113762.1.4.1" displayName="ONC Administrative Sex" version="N/A">
+                <ns0:ConceptList>
+                    <ns0:Concept code="F" codeSystem="2.16.840.1.113883.5.1" codeSystemName="AdministrativeGender" codeSystemVersion="HL7V3.0_2017-07" displayName="Female"/>
+                    <ns0:Concept code="M" codeSystem="2.16.840.1.113883.5.1" codeSystemName="AdministrativeGender" codeSystemVersion="HL7V3.0_2017-07" displayName="Male"/>
+                </ns0:ConceptList>
+                <ns0:Source>Office of the National Coordinator for Health Information Technology</ns0:Source>
+                <ns0:Purpose>(Clinical Focus: Gender identity restricted to only Male and Female used in administrative situations requiring a restriction to these two categories.),(Data Element Scope: Gender),(Inclusion Criteria: Male and Female only.),(Exclusion Criteria: Any gender identity that is not male or female.)</ns0:Purpose>
+                <ns0:Type>Extensional</ns0:Type>
+                <ns0:Binding>Dynamic</ns0:Binding>
+                <ns0:Status>Active</ns0:Status>
+                <ns0:RevisionDate>2018-03-28</ns0:RevisionDate>
+            </ns0:DescribedValueSet>
+        </ns0:RetrieveMultipleValueSetsResponse>
+    http_version:
+  recorded_at: Wed, 28 Mar 2018 21:40:44 GMT
+recorded_with: VCR 3.0.3