canql 2.4.0 → 2.5.0
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- checksums.yaml +5 -5
- data/CHANGELOG.md +21 -0
- data/README.md +2 -2
- data/canql.gemspec +4 -2
- data/code_safety.yml +39 -19
- data/lib/canql/grammars/e_base_records.treetop +2 -11
- data/lib/canql/grammars/main.treetop +7 -1
- data/lib/canql/grammars/perinatal_hospital.treetop +31 -0
- data/lib/canql/grammars/provider.treetop +15 -0
- data/lib/canql/grammars.rb +2 -0
- data/lib/canql/nodes/e_base_records.rb +3 -2
- data/lib/canql/nodes/perinatal_hospital.rb +27 -0
- data/lib/canql/nodes.rb +1 -0
- data/lib/canql/version.rb +1 -1
- metadata +16 -14
- data/.travis.yml +0 -18
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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-
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metadata.gz:
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data.tar.gz:
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SHA256:
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metadata.gz: f8206dd11cfeb5875812b82062933650e2c97e56df252025633093705d73386a
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data.tar.gz: 14bfaa9148d2f3f5028f717ca48f7b4043254f194175fcaa3f4e7707f0fb69b0
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 94b07f6c37e22ff798f4966b29f2b3116720aaf2af1500e699fde1ddba1232e4f0370ca370366ce82dcbc9468caec19839e6e320a30ae8dbd2adab85be9f5677
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data.tar.gz: a79d86c334fb46c637a0fda89cb9b08996fab0923a942f2db91e913f865d745cc45755cce4af8669e671737fb5ff75805ad52d9ce57f6654bbad21111c240af8
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data/CHANGELOG.md
ADDED
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## [Unreleased]
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*no unreleased changes*
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## 2.5.0 / 2019-01-25
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### Added
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* Added the abiltity to filter actions by trust as well as hospital (#18)
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* Added the abiltity to filter cases by booking and delivery hospital & trust (#18)
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### Fixed
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* Support Ruby 2.6 - minimum is now 2.4
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## 2.4.0 / 2018-07-19
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### Added
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* add ability to filter by genetic tests (#17)
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## 2.3.0 / 2018-06-08
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### Added
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* Added action and ebr clauses for mother patients (#16)
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## 2.2.0 / 2018-06-05
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### Added
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* Added EDD and booking hospital to missing and populated field clause (#15)
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data/README.md
CHANGED
@@ -47,10 +47,10 @@ would output:
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```json
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{"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
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```
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-
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and booking at hospital RGT01 and delivery at addenbrookes trust
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The parser is case insensitive. An example of an almost fully involved CANQL query is:
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-
> First 27 Male Liveborn Thames Cases Due between 20/06/2015 and 25/06/2015 and Born on 22/06/2015 and that Died on 07/07/2015 with Suspected Prenatal Q20 Anomalies and Postnatal Tests and Missing Postcode and Date of Birth and QA Action and Unprocessed paediatric records and Mother Born between 01/10/1990 and 10/01/1999 and who Died on 01/08/2015 with Populated Postcode and NHS Number
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+
> First 27 Male Liveborn Thames Cases Due between 20/06/2015 and 25/06/2015 and Born on 22/06/2015 and that Died on 07/07/2015 with Suspected Prenatal Q20 Anomalies and Booking at hospital RGT01 and Delivery at addenbrookes trust and Postnatal Tests and Missing Postcode and Date of Birth and QA Action and Unprocessed paediatric records and Mother Born between 01/10/1990 and 10/01/1999 and who Died on 01/08/2015 with Populated Postcode and NHS Number
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Please see the tests for many more examples.
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data/canql.gemspec
CHANGED
@@ -16,10 +16,12 @@ Gem::Specification.new do |spec|
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spec.homepage = 'https://github.com/PublicHealthEngland/canql'
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spec.license = 'MIT'
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-
spec.required_ruby_version = '>= 2.
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spec.required_ruby_version = '>= 2.4'
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spec.files = `git ls-files -z`.split("\x0").
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reject { |f| f.match(%r{^(test|spec|features)/}) }
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# SECURE BNS 2018-08-06: Minimise sharing of (public-key encrypted) slack secrets in .travis.yml
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spec.files -= %w[.travis.yml] # Not needed in the gem
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spec.bindir = 'exe'
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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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@@ -34,7 +36,7 @@ Gem::Specification.new do |spec|
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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', '~> 3.1', '>= 3.1.3'
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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
CHANGED
@@ -15,7 +15,11 @@ file safety:
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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: 16abb8206a3d36c7532427cd7137df79d2733d1d
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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: 6bbb80cd4d98411f7e263705074c3d55dcdaab5f
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CODE_OF_CONDUCT.md:
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comments:
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reviewed_by: drewthorp
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@@ -30,8 +34,8 @@ file safety:
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safe_revision: ee80c4bbd5e990d38b5fc954f4fd037177672db2
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README.md:
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comments:
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reviewed_by:
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safe_revision:
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reviewed_by: josh.pencheon
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safe_revision: 5241b851650e52fd094dad505a9bc0294b27204a
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Rakefile:
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comments:
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reviewed_by: timgentry
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@@ -46,8 +50,8 @@ file safety:
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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: josh.pencheon
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safe_revision: 16abb8206a3d36c7532427cd7137df79d2733d1d
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lib/canql.rb:
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comments:
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reviewed_by: timgentry
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@@ -59,7 +63,7 @@ file safety:
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lib/canql/grammars.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: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/grammars/age.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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safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
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lib/canql/grammars/e_base_records.treetop:
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comments:
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reviewed_by:
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safe_revision:
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reviewed_by: josh.pencheon
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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/grammars/genetic_test.treetop:
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comments:
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reviewed_by: josh.pencheon
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@@ -91,12 +95,20 @@ file safety:
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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: c431b8a476b84d077e9c39a2a13c2b17a296773d
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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: timgentry
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safe_revision: 1b73bdcf483c6e44979e183c5873a1f0612a49a1
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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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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/grammars/provider.treetop:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/grammars/registry.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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lib/canql/nodes.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: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/nodes/age.rb:
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comments:
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reviewed_by: timgentry
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@@ -129,8 +141,8 @@ file safety:
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safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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lib/canql/nodes/e_base_records.rb:
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comments:
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reviewed_by:
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safe_revision:
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reviewed_by: josh.pencheon
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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/nodes/genetic_test.rb:
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comments:
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reviewed_by: josh.pencheon
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comments:
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reviewed_by: josh.pencheon
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safe_revision: a1686a3905ee6d7ebc8c5b1786efba4f8df42a2d
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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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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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lib/canql/nodes/registry.rb:
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comments:
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reviewed_by: timgentry
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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: 6bbb80cd4d98411f7e263705074c3d55dcdaab5f
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test/anomaly_test_helper.rb:
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comments:
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reviewed_by: timgentry
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@@ -189,8 +205,8 @@ file safety:
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safe_revision: 695cec7ee61f36a9ef054a4079f290421d814666
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test/nodes/e_base_records_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: josh.pencheon
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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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test/nodes/genetic_tests_test.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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test/nodes/mother_e_base_records_test.rb:
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comments:
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safe_revision:
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reviewed_by: josh.pencheon
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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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test/nodes/patient_test.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: a1686a3905ee6d7ebc8c5b1786efba4f8df42a2d
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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: c431b8a476b84d077e9c39a2a13c2b17a296773d
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test/nodes/registry_test.rb:
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comments:
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reviewed_by: timgentry
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safe_revision: c39d24bb500719971969762e94545e82866bf92f
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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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safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
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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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@@ -61,21 +61,12 @@ module Canql
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space 'action' 's'? word_break
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end
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-
rule at_keyword
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space 'at' word_break
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-
end
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-
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rule action_provider_code
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-
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+
provider_code <Nodes::ActionProviderCodeNode>
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end
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68
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rule action_provider_name
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-
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-
end
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-
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-
# TODO: support cancer network?
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-
rule provider_type
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-
'hospital'
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+
provider_name <Nodes::ActionProviderNameNode>
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end
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rule unprocessed_keyword
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@@ -1,12 +1,14 @@
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grammar Canql
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include Registry
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include Patient
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+
include Provider
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include Anomaly
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include GeneticTest
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include TestResult
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include Dates
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9
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include EBaseRecords
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include BatchTypes
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11
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+
include PerinatalHospital
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include Age
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13
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# The root grammar
|
@@ -97,7 +99,11 @@ grammar Canql
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97
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space 'diagnosed' word_break
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end
|
99
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|
102
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rule at_keyword
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103
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space 'at' word_break
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end
|
105
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+
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106
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rule with_conditions
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101
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-
anomalies / genetic_tests / test_results / patient_field_existance / mother_conditions / action_or_ebr
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+
anomalies / genetic_tests / test_results / perinatal_hospital / patient_field_existance / mother_conditions / action_or_ebr
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end
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end
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@@ -0,0 +1,31 @@
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module Canql
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grammar PerinatalHospital
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rule perinatal_hospital
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and_keyword? space hospital_event:perinatal_hospital_type space perinatal_provider word_break
|
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+
end
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6
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+
|
7
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+
rule perinatal_provider
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8
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+
'at' space provider:(perinatal_provider_code / perinatal_provider_name)
|
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+
end
|
10
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+
|
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rule perinatal_provider_code
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12
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provider_code <Nodes::PerinatalProviderCodeNode>
|
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+
end
|
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+
|
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rule perinatal_provider_name
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16
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+
provider_name <Nodes::PerinatalProviderNameNode>
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+
end
|
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+
|
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rule perinatal_hospital_type
|
20
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booking_hospital_keyword / delivery_hospital_keyword
|
21
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+
end
|
22
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+
|
23
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+
rule booking_hospital_keyword
|
24
|
+
'booking'
|
25
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+
end
|
26
|
+
|
27
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+
rule delivery_hospital_keyword
|
28
|
+
'delivery'
|
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+
end
|
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+
end
|
31
|
+
end
|
@@ -0,0 +1,15 @@
|
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module Canql
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grammar Provider
|
3
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rule provider_type
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4
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+
'hospital' / 'trust'
|
5
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+
end
|
6
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+
|
7
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+
rule provider_code
|
8
|
+
provider_type space code:(!' ' .)+
|
9
|
+
end
|
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+
|
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+
rule provider_name
|
12
|
+
short_desc:(!(space provider_type) .)+ space provider_type
|
13
|
+
end
|
14
|
+
end
|
15
|
+
end
|
data/lib/canql/grammars.rb
CHANGED
@@ -11,4 +11,6 @@ Treetop.load File.expand_path('grammars/genetic_test', File.dirname(__FILE__))
|
|
11
11
|
Treetop.load File.expand_path('grammars/test_result', File.dirname(__FILE__))
|
12
12
|
Treetop.load File.expand_path('grammars/patient', File.dirname(__FILE__))
|
13
13
|
Treetop.load File.expand_path('grammars/registry', File.dirname(__FILE__))
|
14
|
+
Treetop.load File.expand_path('grammars/provider', File.dirname(__FILE__))
|
15
|
+
Treetop.load File.expand_path('grammars/perinatal_hospital', File.dirname(__FILE__))
|
14
16
|
Treetop.load File.expand_path('grammars/main', File.dirname(__FILE__))
|
@@ -54,7 +54,8 @@ module Canql #:nodoc: all
|
|
54
54
|
# default to provider
|
55
55
|
subject = reverse_scan_for_marker(:subject) == 'mother' ? '.mother' : ''
|
56
56
|
key = 'providercode'
|
57
|
-
|
57
|
+
condition = provider_type.text_value == 'trust' ? Canql::BEGINS : Canql::EQUALS
|
58
|
+
{ "action#{subject}.#{key}" => { condition => code.text_value.upcase } }
|
58
59
|
end
|
59
60
|
end
|
60
61
|
|
@@ -62,7 +63,7 @@ module Canql #:nodoc: all
|
|
62
63
|
def meta_data_item
|
63
64
|
# default to provider
|
64
65
|
subject = reverse_scan_for_marker(:subject) == 'mother' ? '.mother' : ''
|
65
|
-
key =
|
66
|
+
key = 'providername'
|
66
67
|
{
|
67
68
|
"action#{subject}.#{key}" => {
|
68
69
|
Canql::BEGINS => short_desc.text_value.upcase,
|
@@ -0,0 +1,27 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module Canql #:nodoc: all
|
4
|
+
module Nodes
|
5
|
+
module PerinatalProviderCodeNode
|
6
|
+
def meta_data_item
|
7
|
+
hospital_event = reverse_scan_for_marker(:hospital_event)
|
8
|
+
key = 'providercode'
|
9
|
+
condition = provider_type.text_value == 'trust' ? Canql::BEGINS : Canql::EQUALS
|
10
|
+
{ "#{hospital_event}.#{key}" => { condition => code.text_value.upcase } }
|
11
|
+
end
|
12
|
+
end
|
13
|
+
|
14
|
+
module PerinatalProviderNameNode
|
15
|
+
def meta_data_item
|
16
|
+
hospital_event = reverse_scan_for_marker(:hospital_event)
|
17
|
+
key = 'providername'
|
18
|
+
{
|
19
|
+
"#{hospital_event}.#{key}" => {
|
20
|
+
Canql::BEGINS => short_desc.text_value.upcase,
|
21
|
+
:interval => interval
|
22
|
+
}
|
23
|
+
}
|
24
|
+
end
|
25
|
+
end
|
26
|
+
end
|
27
|
+
end
|
data/lib/canql/nodes.rb
CHANGED
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: 2.
|
4
|
+
version: 2.5.0
|
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: 2019-01-25 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: chronic
|
@@ -152,22 +152,22 @@ dependencies:
|
|
152
152
|
name: ndr_dev_support
|
153
153
|
requirement: !ruby/object:Gem::Requirement
|
154
154
|
requirements:
|
155
|
-
- - "
|
155
|
+
- - "~>"
|
156
156
|
- !ruby/object:Gem::Version
|
157
|
-
version: '3.
|
158
|
-
- - "
|
157
|
+
version: '3.1'
|
158
|
+
- - ">="
|
159
159
|
- !ruby/object:Gem::Version
|
160
|
-
version:
|
160
|
+
version: 3.1.3
|
161
161
|
type: :development
|
162
162
|
prerelease: false
|
163
163
|
version_requirements: !ruby/object:Gem::Requirement
|
164
164
|
requirements:
|
165
|
-
- - "
|
165
|
+
- - "~>"
|
166
166
|
- !ruby/object:Gem::Version
|
167
|
-
version: '3.
|
168
|
-
- - "
|
167
|
+
version: '3.1'
|
168
|
+
- - ">="
|
169
169
|
- !ruby/object:Gem::Version
|
170
|
-
version:
|
170
|
+
version: 3.1.3
|
171
171
|
- !ruby/object:Gem::Dependency
|
172
172
|
name: pry
|
173
173
|
requirement: !ruby/object:Gem::Requirement
|
@@ -219,7 +219,7 @@ files:
|
|
219
219
|
- ".gitignore"
|
220
220
|
- ".hound.yml"
|
221
221
|
- ".rubocop.yml"
|
222
|
-
-
|
222
|
+
- CHANGELOG.md
|
223
223
|
- CODE_OF_CONDUCT.md
|
224
224
|
- Gemfile
|
225
225
|
- LICENSE.txt
|
@@ -240,6 +240,8 @@ files:
|
|
240
240
|
- lib/canql/grammars/genetic_test.treetop
|
241
241
|
- lib/canql/grammars/main.treetop
|
242
242
|
- lib/canql/grammars/patient.treetop
|
243
|
+
- lib/canql/grammars/perinatal_hospital.treetop
|
244
|
+
- lib/canql/grammars/provider.treetop
|
243
245
|
- lib/canql/grammars/registry.treetop
|
244
246
|
- lib/canql/grammars/test_result.treetop
|
245
247
|
- lib/canql/nodes.rb
|
@@ -251,6 +253,7 @@ files:
|
|
251
253
|
- lib/canql/nodes/genetic_test.rb
|
252
254
|
- lib/canql/nodes/main.rb
|
253
255
|
- lib/canql/nodes/patient.rb
|
256
|
+
- lib/canql/nodes/perinatal_hospital.rb
|
254
257
|
- lib/canql/nodes/registry.rb
|
255
258
|
- lib/canql/nodes/test_result.rb
|
256
259
|
- lib/canql/parser.rb
|
@@ -268,15 +271,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
268
271
|
requirements:
|
269
272
|
- - ">="
|
270
273
|
- !ruby/object:Gem::Version
|
271
|
-
version: '2.
|
274
|
+
version: '2.4'
|
272
275
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
273
276
|
requirements:
|
274
277
|
- - ">="
|
275
278
|
- !ruby/object:Gem::Version
|
276
279
|
version: '0'
|
277
280
|
requirements: []
|
278
|
-
|
279
|
-
rubygems_version: 2.5.2.3
|
281
|
+
rubygems_version: 3.0.2
|
280
282
|
signing_key:
|
281
283
|
specification_version: 4
|
282
284
|
summary: Congenital Anomaly Natural Query Language
|
data/.travis.yml
DELETED
@@ -1,18 +0,0 @@
|
|
1
|
-
language: ruby
|
2
|
-
rvm:
|
3
|
-
- 2.3
|
4
|
-
- 2.4
|
5
|
-
- 2.5
|
6
|
-
sudo: false
|
7
|
-
cache: bundler
|
8
|
-
before_install:
|
9
|
-
- gem update --system
|
10
|
-
- gem install bundler
|
11
|
-
before_script: bundle update
|
12
|
-
notifications:
|
13
|
-
slack:
|
14
|
-
on_pull_requests: false
|
15
|
-
on_success: always
|
16
|
-
on_failure: always
|
17
|
-
rooms:
|
18
|
-
secure: 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
|