canql 3.0.0 → 4.3.0
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- checksums.yaml +4 -4
- data/CHANGELOG.md +23 -0
- data/README.md +1 -1
- data/canql.gemspec +2 -2
- data/code_safety.yml +18 -18
- data/lib/canql/grammars/anomaly.treetop +1 -1
- data/lib/canql/grammars/main.treetop +2 -2
- data/lib/canql/grammars/patient.treetop +9 -3
- data/lib/canql/nodes/anomaly.rb +6 -1
- data/lib/canql/nodes/patient.rb +31 -11
- data/lib/canql/version.rb +1 -1
- metadata +6 -12
checksums.yaml
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 2b054c9d0f56e07afcd4521b2e56b23fc21647f419f9bef7f04104bd2544e3b5
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data.tar.gz: 48bf63bc902135454291778e23905535570bc5fd3019c13acb55709c9795e827
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ad41792d7cfb4d5c79077ac53ca462e03cac72042095c51f41a03c53b92a01e3b16777e4f55d7c3167ab589be134cdf35547724a35b61b496bf9beb58f37ae1a
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data.tar.gz: ca725da517e80d207eaaed88a7128461bfdadc3a23e5754682e342367762d2dbc7d69ae9d1b462fc8529f7135a1486c90d57516882b972964642cacf8b265618
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data/CHANGELOG.md
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## [Unreleased]
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*no unreleased changes*
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## 4.3.0 / 2020-06-10
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### Added
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* Added additional field existance options (#45)
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## 4.2.0 / 2020-03-25
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### Added
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* Added additional EUROCAT category filters for RAG combination
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## 4.1.0 / 2020-03-19
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### Added
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* Added filters for EUROCAT RAG rating (#39)
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## 4.0.1 / 2019-10-29
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### Fixed
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* Relax `chronic` dependency
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## 4.0.0 / 2019-09-06
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### Changed
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* Added case filters for delivery and booking postcode fields and removed all simple postcode field filters (#36)
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### Added
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* Added fasp and fasp plus code groups (#37)
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## 3.0.0 / 2019-06-04
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### Changed
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* Added new branch of CANQL for querying all patient not just child patients - modifies DIR (#29)
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data/README.md
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# CANQL [![Build Status](https://travis-ci.org/PublicHealthEngland/canql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/canql)
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# CANQL [![Build Status](https://travis-ci.org/PublicHealthEngland/canql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/canql) [![Gem Version](https://badge.fury.io/rb/canql.svg)](https://rubygems.org/gems/canql)
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Congenital Anomaly Natural Query Language (CANQL) is a [Treetop](http://treetop.rubyforge.org/) driven Domain Specific Language (DSL) used by the Public Health England (PHE) National Congenital Anomaly and Rare Disease Registration Service (NCARDRS) to identify cohorts of cases.
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data/canql.gemspec
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spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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spec.require_paths = ['lib']
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-
spec.add_dependency 'chronic', '~> 0.3
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spec.add_dependency 'chronic', '~> 0.3'
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spec.add_dependency 'ndr_support', '>= 3.0', '< 6'
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spec.add_dependency 'rails', '>= 4.1', '< 6'
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spec.add_dependency 'treetop', '>= 1.4.10'
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spec.add_development_dependency 'guard-minitest'
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spec.add_development_dependency 'guard-rubocop'
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spec.add_development_dependency 'minitest'
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spec.add_development_dependency 'ndr_dev_support', '~>
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spec.add_development_dependency 'ndr_dev_support', '~> 5.6'
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spec.add_development_dependency 'pry'
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spec.add_development_dependency 'rake'
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spec.add_development_dependency 'terminal-notifier-guard' if RUBY_PLATFORM =~ /darwin/
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data/code_safety.yml
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".travis.yml":
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 8adb767031a19aa6b3cea3f1cb05b4a9bcc964f3
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CHANGELOG.md:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 23852bc731fdf82a87fd06070a89ec81affe8155
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CODE_OF_CONDUCT.md:
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comments:
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reviewed_by: drewthorp
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README.md:
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 33feeeaa4b2089e33f563e4c766e91c38b108e36
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Rakefile:
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comments:
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reviewed_by: timgentry
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safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
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canql.gemspec:
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comments:
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reviewed_by:
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safe_revision:
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reviewed_by: timgentry
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safe_revision: 6cb13f43b4353ab7c90ff0406ec13ac169b8e64c
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lib/canql.rb:
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comments:
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reviewed_by: timgentry
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comments: It is a known issue that this is potentially susceptible to certain
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kinds of DoS attack
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
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lib/canql/grammars/batch_types.treetop:
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comments:
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reviewed_by: josh.pencheon
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lib/canql/grammars/main.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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kinds of DoS attack
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reviewed_by:
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safe_revision:
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reviewed_by: timgentry
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safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
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lib/canql/grammars/patient.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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kinds of DoS attack
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
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lib/canql/grammars/perinatal_hospital.treetop:
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comments:
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reviewed_by: josh.pencheon
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lib/canql/nodes/anomaly.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
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lib/canql/nodes/batch_types.rb:
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comments:
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reviewed_by: josh.pencheon
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lib/canql/nodes/patient.rb:
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comments:
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reviewed_by: josh.pencheon
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lib/canql/nodes/perinatal_hospital.rb:
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comments:
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reviewed_by: josh.pencheon
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lib/canql/version.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 23852bc731fdf82a87fd06070a89ec81affe8155
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test/anomaly_test_helper.rb:
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comments:
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reviewed_by: josh.pencheon
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test/nodes/case_test.rb:
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comments:
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reviewed_by: josh.pencheon
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test/nodes/code_test.rb:
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comments:
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test/nodes/e_base_records_test.rb:
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comments:
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reviewed_by: josh.pencheon
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test/nodes/patient_test.rb:
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reviewed_by: josh.pencheon
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test/nodes/perinatal_hospital_test.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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test/parser_test.rb:
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comments:
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reviewed_by:
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safe_revision:
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reviewed_by: timgentry
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safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
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test/test_helper.rb:
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comments:
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reviewed_by: josh.pencheon
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@@ -59,11 +59,11 @@ grammar Canql
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end
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rule case_preconditions
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-
registry / gender / outcome / primacy
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registry / gender / outcome / primacy / category
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end
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rule patient_preconditions
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gender / primacy
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gender / primacy / category
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end
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rule case_additional_conditions
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@@ -12,6 +12,10 @@ module Canql
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space primacy:('primary' / 'alias' ) word_break <Nodes::Patient::PrimacyNode>
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end
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rule category
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space category:('eurocat amber and green' / 'eurocat red and amber' / 'eurocat red' / 'eurocat amber' / 'eurocat green' / 'eurocat') word_break <Nodes::Patient::CategoryNode>
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end
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+
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rule expected_keyword
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space ('expected' / 'due') word_break
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end
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@@ -42,15 +46,17 @@ module Canql
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rule case_field_names
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patient_field_name:(
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-
'date of birth' / 'dob' / '
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'date of birth' / 'dob' / 'date of vital status' / 'nhs number' /
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'delivery postcode' / 'booking postcode' / 'birth weight' /
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'place of delivery' / 'sex' / 'outcome' / 'edd' /
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'expected delivery date' / 'booking hospital' / 'screening status'
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'expected delivery date' / 'booking hospital' / 'screening status' /
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'number of fetuses at delivery' / 'malformed in set'
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)
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end
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rule patient_field_names
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patient_field_name:(
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'date of birth' / 'dob' / '
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'date of birth' / 'dob' / 'date of vital status' / 'nhs number' / 'sex'
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)
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end
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data/lib/canql/nodes/anomaly.rb
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end
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anomaly_hash['icd_codes'] = code_filter[:icd_code] if code_filter[:icd_code].present?
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return anomaly_hash if code_filter[:code_group].blank?
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+
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anomaly_hash['code_groups'] = code_filter[:code_group]
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anomaly_hash
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end
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def code_type(code)
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return :icd_code if code.respond_to?(:to_code) && code.to_code.present?
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return :code_group if code.respond_to?(:to_code_group) && code.to_code_group.present?
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+
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raise 'Unable to find code type'
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end
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def code_value(code)
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return code.to_code if :icd_code == code_type(code)
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+
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code.to_code_group
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end
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@@ -67,6 +70,7 @@ module Canql #:nodoc: all
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code_filters[:icd_code] = { Canql::BEGINS => code_array[:icd_code] }
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end
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return code_filters if code_array[:code_group].blank?
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+
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code_filters[:code_group] = { Canql::EQUALS => code_array[:code_group] }
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code_filters
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end
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@@ -86,6 +90,7 @@ module Canql #:nodoc: all
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module AdditionalCodeNode
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def code_type
|
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return :icd_code if anomalies_icd_code.respond_to?(:to_code)
|
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+
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:code_group
|
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end
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@@ -106,7 +111,7 @@ module Canql #:nodoc: all
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111
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module SingleCodeGroupNode
|
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def to_code_group
|
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-
text_value.upcase
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+
text_value.gsub(/( )/, '_').upcase
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end
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end
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end
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data/lib/canql/nodes/patient.rb
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end
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end
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module CategoryNode
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25
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+
def meta_data_item
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+
{ 'patient.category' => { Canql::EQUALS => clean_category } }
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+
end
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+
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+
def clean_category
|
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+
return 'eurocat_red' if 'eurocat red' == category.text_value
|
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+
return 'eurocat_amber' if 'eurocat amber' == category.text_value
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32
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+
return 'eurocat_green' if 'eurocat green' == category.text_value
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+
return 'eurocat_amber_green' if 'eurocat amber and green' == category.text_value
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+
return 'eurocat_red_amber' if 'eurocat red and amber' == category.text_value
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+
|
36
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+
category.text_value
|
37
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+
end
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+
end
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+
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module FieldExists
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FIELDS = {
|
26
|
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'date of birth':
|
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-
'dob':
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-
'
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-
'
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-
'
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'
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'
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'
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'
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'date of birth': { patient: 'birthdate', mother: 'birthdate' },
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'dob': { patient: 'birthdate', mother: 'birthdate' },
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'date of vital status': { patient: 'dateofvitalstatus', mother: 'dateofvitalstatus' },
|
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+
'delivery postcode': { patient: 'delivery_postcode' },
|
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+
'booking postcode': { patient: 'booking_postcode' },
|
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+
'nhs number': { patient: 'nhsnumber', mother: 'nhsnumber' },
|
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+
'birth weight': { patient: 'weight' },
|
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+
'place of delivery': { patient: 'placeofdelivery' },
|
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+
'sex': { patient: 'sex' },
|
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+
'outcome': { patient: 'outcome' },
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+
'edd': { patient: 'expecteddeliverydate' },
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|
'expected delivery date': { patient: 'expecteddeliverydate' },
|
36
|
-
'booking hospital':
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-
'screening status':
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+
'booking hospital': { patient: 'booking_hospital' },
|
55
|
+
'screening status': { patient: 'screeningstatus' },
|
56
|
+
'number of fetuses at delivery': { patient: 'numoffetusesatdelivery' },
|
57
|
+
'malformed in set': { patient: 'malformedinset' }
|
38
58
|
}.freeze
|
39
59
|
|
40
60
|
def meta_data_item
|
data/lib/canql/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: canql
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.0
|
4
|
+
version: 4.3.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- PHE NDR Development Team
|
8
8
|
autorequire:
|
9
9
|
bindir: exe
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2020-06-10 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: chronic
|
@@ -16,14 +16,14 @@ dependencies:
|
|
16
16
|
requirements:
|
17
17
|
- - "~>"
|
18
18
|
- !ruby/object:Gem::Version
|
19
|
-
version: 0.3
|
19
|
+
version: '0.3'
|
20
20
|
type: :runtime
|
21
21
|
prerelease: false
|
22
22
|
version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
24
|
- - "~>"
|
25
25
|
- !ruby/object:Gem::Version
|
26
|
-
version: 0.3
|
26
|
+
version: '0.3'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: ndr_support
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
@@ -154,20 +154,14 @@ dependencies:
|
|
154
154
|
requirements:
|
155
155
|
- - "~>"
|
156
156
|
- !ruby/object:Gem::Version
|
157
|
-
version: '
|
158
|
-
- - ">="
|
159
|
-
- !ruby/object:Gem::Version
|
160
|
-
version: 3.1.3
|
157
|
+
version: '5.6'
|
161
158
|
type: :development
|
162
159
|
prerelease: false
|
163
160
|
version_requirements: !ruby/object:Gem::Requirement
|
164
161
|
requirements:
|
165
162
|
- - "~>"
|
166
163
|
- !ruby/object:Gem::Version
|
167
|
-
version: '
|
168
|
-
- - ">="
|
169
|
-
- !ruby/object:Gem::Version
|
170
|
-
version: 3.1.3
|
164
|
+
version: '5.6'
|
171
165
|
- !ruby/object:Gem::Dependency
|
172
166
|
name: pry
|
173
167
|
requirement: !ruby/object:Gem::Requirement
|