canql 2.4.0 → 2.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: ca21ec21e84cecfab26ed4f687caa307d46d848b
+SHA256:
+  metadata.gz: f8206dd11cfeb5875812b82062933650e2c97e56df252025633093705d73386a
+  data.tar.gz: 14bfaa9148d2f3f5028f717ca48f7b4043254f194175fcaa3f4e7707f0fb69b0
 SHA512:
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data/CHANGELOG.md

@@ -0,0 +1,21 @@
+## [Unreleased]
+*no unreleased changes*
+
+## 2.5.0 / 2019-01-25
+### Added
+* Added the abiltity to filter actions by trust as well as hospital (#18)
+* Added the abiltity to filter cases by booking and delivery hospital & trust (#18)
+### Fixed
+* Support Ruby 2.6 - minimum is now 2.4
+
+## 2.4.0 / 2018-07-19
+### Added
+* add ability to filter by genetic tests (#17)
+
+## 2.3.0 / 2018-06-08
+### Added
+* Added action and ebr clauses for mother patients (#16)
+
+## 2.2.0 / 2018-06-05
+### Added
+* Added EDD and booking hospital to missing and populated field clause (#15)

data/README.md

@@ -47,10 +47,10 @@ would output:
 ```json
 {"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
 ```
-
+      and booking at hospital RGT01 and delivery at addenbrookes trust
 The parser is case insensitive. An example of an almost fully involved CANQL query is:
 
-> 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
+> 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
 
 Please see the tests for many more examples.
 

data/canql.gemspec

@@ -16,10 +16,12 @@ Gem::Specification.new do |spec|
   spec.homepage      = 'https://github.com/PublicHealthEngland/canql'
   spec.license       = 'MIT'
 
-  spec.required_ruby_version = '>= 2.2'
+  spec.required_ruby_version = '>= 2.4'
 
   spec.files         = `git ls-files -z`.split("\x0").
                        reject { |f| f.match(%r{^(test|spec|features)/}) }
+  # SECURE BNS 2018-08-06: Minimise sharing of (public-key encrypted) slack secrets in .travis.yml
+  spec.files         -= %w[.travis.yml] # Not needed in the gem
   spec.bindir        = 'exe'
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
@@ -34,7 +36,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'guard-minitest'
   spec.add_development_dependency 'guard-rubocop'
   spec.add_development_dependency 'minitest'
-  spec.add_development_dependency 'ndr_dev_support', '>= 3.0', '<6'
+  spec.add_development_dependency 'ndr_dev_support', '~> 3.1', '>= 3.1.3'
   spec.add_development_dependency 'pry'
   spec.add_development_dependency 'rake'
   spec.add_development_dependency 'terminal-notifier-guard' if RUBY_PLATFORM =~ /darwin/

data/code_safety.yml

@@ -15,7 +15,11 @@ file safety:
   ".travis.yml":
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: ce5d961ef757500c8d12d7ca72a900ff7040378a
+    safe_revision: 16abb8206a3d36c7532427cd7137df79d2733d1d
+  CHANGELOG.md:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 6bbb80cd4d98411f7e263705074c3d55dcdaab5f
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -30,8 +34,8 @@ file safety:
     safe_revision: ee80c4bbd5e990d38b5fc954f4fd037177672db2
   README.md:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 695cec7ee61f36a9ef054a4079f290421d814666
+    reviewed_by: josh.pencheon
+    safe_revision: 5241b851650e52fd094dad505a9bc0294b27204a
   Rakefile:
     comments: 
     reviewed_by: timgentry
@@ -46,8 +50,8 @@ file safety:
     safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
   canql.gemspec:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
+    reviewed_by: josh.pencheon
+    safe_revision: 16abb8206a3d36c7532427cd7137df79d2733d1d
   lib/canql.rb:
     comments: 
     reviewed_by: timgentry
@@ -59,7 +63,7 @@ file safety:
   lib/canql/grammars.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/age.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
@@ -81,8 +85,8 @@ file safety:
     safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
   lib/canql/grammars/e_base_records.treetop:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 03f7a8fbee06a947e60bc554dcc1d1311c5632ac
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/genetic_test.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -91,12 +95,20 @@ file safety:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: josh.pencheon
-    safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/patient.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: timgentry
     safe_revision: 1b73bdcf483c6e44979e183c5873a1f0612a49a1
+  lib/canql/grammars/perinatal_hospital.treetop:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
+  lib/canql/grammars/provider.treetop:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/registry.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
@@ -110,7 +122,7 @@ file safety:
   lib/canql/nodes.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/nodes/age.rb:
     comments: 
     reviewed_by: timgentry
@@ -129,8 +141,8 @@ file safety:
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/nodes/e_base_records.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 1b73bdcf483c6e44979e183c5873a1f0612a49a1
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/nodes/genetic_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -143,6 +155,10 @@ file safety:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: a1686a3905ee6d7ebc8c5b1786efba4f8df42a2d
+  lib/canql/nodes/perinatal_hospital.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/nodes/registry.rb:
     comments: 
     reviewed_by: timgentry
@@ -162,7 +178,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 60f7281fd6ef911b932992b2c965c6f8ace182c5
+    safe_revision: 6bbb80cd4d98411f7e263705074c3d55dcdaab5f
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: timgentry
@@ -189,8 +205,8 @@ file safety:
     safe_revision: 695cec7ee61f36a9ef054a4079f290421d814666
   test/nodes/e_base_records_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   test/nodes/genetic_tests_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -201,12 +217,16 @@ file safety:
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   test/nodes/mother_e_base_records_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 1b73bdcf483c6e44979e183c5873a1f0612a49a1
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   test/nodes/patient_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: a1686a3905ee6d7ebc8c5b1786efba4f8df42a2d
+  test/nodes/perinatal_hospital_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   test/nodes/registry_test.rb:
     comments: 
     reviewed_by: timgentry
@@ -217,8 +237,8 @@ file safety:
     safe_revision: c39d24bb500719971969762e94545e82866bf92f
   test/parser_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: c39d24bb500719971969762e94545e82866bf92f
+    reviewed_by: josh.pencheon
+    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon

data/lib/canql/grammars/e_base_records.treetop

@@ -61,21 +61,12 @@ module Canql
       space 'action' 's'? word_break
     end
 
-    rule at_keyword
-      space 'at' word_break
-    end
-
     rule action_provider_code
-      provider_type space code:(!' ' .)+ <Nodes::ActionProviderCodeNode>
+      provider_code <Nodes::ActionProviderCodeNode>
     end
 
     rule action_provider_name
-      short_desc:(!(space provider_type) .)+ space provider_type <Nodes::ActionProviderNameNode>
-    end
-
-    # TODO: support cancer network?
-    rule provider_type
-      'hospital'
+      provider_name <Nodes::ActionProviderNameNode>
     end
 
     rule unprocessed_keyword

data/lib/canql/grammars/main.treetop

@@ -1,12 +1,14 @@
 grammar Canql
   include Registry
   include Patient
+  include Provider
   include Anomaly
   include GeneticTest
   include TestResult
   include Dates
   include EBaseRecords
   include BatchTypes
+  include PerinatalHospital
   include Age
 
   # The root grammar
@@ -97,7 +99,11 @@ grammar Canql
     space 'diagnosed' word_break
   end
 
+  rule at_keyword
+    space 'at' word_break
+  end
+
   rule with_conditions
-     anomalies / genetic_tests / test_results / patient_field_existance / mother_conditions / action_or_ebr
+     anomalies / genetic_tests / test_results / perinatal_hospital / patient_field_existance / mother_conditions / action_or_ebr
   end
 end

data/lib/canql/grammars/perinatal_hospital.treetop

@@ -0,0 +1,31 @@
+module Canql
+  grammar PerinatalHospital
+    rule perinatal_hospital
+      and_keyword? space hospital_event:perinatal_hospital_type space perinatal_provider word_break
+    end
+
+    rule perinatal_provider
+      'at' space provider:(perinatal_provider_code / perinatal_provider_name)
+    end
+
+    rule perinatal_provider_code
+      provider_code <Nodes::PerinatalProviderCodeNode>
+    end
+
+    rule perinatal_provider_name
+      provider_name <Nodes::PerinatalProviderNameNode>
+    end
+
+    rule perinatal_hospital_type
+      booking_hospital_keyword / delivery_hospital_keyword
+    end
+
+    rule booking_hospital_keyword
+      'booking'
+    end
+
+    rule delivery_hospital_keyword
+      'delivery'
+    end
+  end
+end

data/lib/canql/grammars/provider.treetop

@@ -0,0 +1,15 @@
+module Canql
+  grammar Provider
+    rule provider_type
+      'hospital' / 'trust'
+    end
+
+    rule provider_code
+      provider_type space code:(!' ' .)+
+    end
+
+    rule provider_name
+      short_desc:(!(space provider_type) .)+ space provider_type
+    end
+  end
+end

data/lib/canql/grammars.rb

@@ -11,4 +11,6 @@ Treetop.load File.expand_path('grammars/genetic_test', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/test_result', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/patient', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/registry', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/provider', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/perinatal_hospital', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/main', File.dirname(__FILE__))

data/lib/canql/nodes/e_base_records.rb

@@ -54,7 +54,8 @@ module Canql #:nodoc: all
         # default to provider
         subject = reverse_scan_for_marker(:subject) == 'mother' ? '.mother' : ''
         key = 'providercode'
-        { "action#{subject}.#{key}" => { Canql::EQUALS => code.text_value.upcase } }
+        condition = provider_type.text_value == 'trust' ? Canql::BEGINS : Canql::EQUALS
+        { "action#{subject}.#{key}" => { condition => code.text_value.upcase } }
       end
     end
 
@@ -62,7 +63,7 @@ module Canql #:nodoc: all
       def meta_data_item
         # default to provider
         subject = reverse_scan_for_marker(:subject) == 'mother' ? '.mother' : ''
-        key = provider_type.text_value == 'cancer network' ? 'cn_ukacrname' : 'providername'
+        key = 'providername'
         {
           "action#{subject}.#{key}" => {
             Canql::BEGINS => short_desc.text_value.upcase,

data/lib/canql/nodes/perinatal_hospital.rb

@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+module Canql #:nodoc: all
+  module Nodes
+    module PerinatalProviderCodeNode
+      def meta_data_item
+        hospital_event = reverse_scan_for_marker(:hospital_event)
+        key = 'providercode'
+        condition = provider_type.text_value == 'trust' ? Canql::BEGINS : Canql::EQUALS
+        { "#{hospital_event}.#{key}" => { condition => code.text_value.upcase } }
+      end
+    end
+
+    module PerinatalProviderNameNode
+      def meta_data_item
+        hospital_event = reverse_scan_for_marker(:hospital_event)
+        key = 'providername'
+        {
+          "#{hospital_event}.#{key}" => {
+            Canql::BEGINS => short_desc.text_value.upcase,
+            :interval => interval
+          }
+        }
+      end
+    end
+  end
+end

data/lib/canql/nodes.rb

@@ -20,3 +20,4 @@ require 'canql/nodes/test_result'
 require 'canql/nodes/patient'
 require 'canql/nodes/main'
 require 'canql/nodes/registry'
+require 'canql/nodes/perinatal_hospital'

data/lib/canql/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '2.4.0'
+  VERSION = '2.5.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 2.4.0
+  version: 2.5.0
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-07-19 00:00:00.000000000 Z
+date: 2019-01-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -152,22 +152,22 @@ dependencies:
   name: ndr_dev_support
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
-    - - "<"
+        version: '3.1'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '6'
+        version: 3.1.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
-    - - "<"
+        version: '3.1'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '6'
+        version: 3.1.3
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -219,7 +219,7 @@ files:
 - ".gitignore"
 - ".hound.yml"
 - ".rubocop.yml"
-- ".travis.yml"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
 - LICENSE.txt
@@ -240,6 +240,8 @@ files:
 - lib/canql/grammars/genetic_test.treetop
 - lib/canql/grammars/main.treetop
 - lib/canql/grammars/patient.treetop
+- lib/canql/grammars/perinatal_hospital.treetop
+- lib/canql/grammars/provider.treetop
 - lib/canql/grammars/registry.treetop
 - lib/canql/grammars/test_result.treetop
 - lib/canql/nodes.rb
@@ -251,6 +253,7 @@ files:
 - lib/canql/nodes/genetic_test.rb
 - lib/canql/nodes/main.rb
 - lib/canql/nodes/patient.rb
+- lib/canql/nodes/perinatal_hospital.rb
 - lib/canql/nodes/registry.rb
 - lib/canql/nodes/test_result.rb
 - lib/canql/parser.rb
@@ -268,15 +271,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.2'
+      version: '2.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.2.3
+rubygems_version: 3.0.2
 signing_key: 
 specification_version: 4
 summary: Congenital Anomaly Natural Query Language

data/.travis.yml

@@ -1,18 +0,0 @@
-language: ruby
-rvm:
-- 2.3
-- 2.4
-- 2.5
-sudo: false
-cache: bundler
-before_install:
-- gem update --system
-- gem install bundler
-before_script: bundle update
-notifications:
-  slack:
-    on_pull_requests: false
-    on_success: always
-    on_failure: always
-    rooms:
-      secure: ixok7nqnRMtP4IqhLhSetpK8AI70aUhqUYiijoCkQ65I/TwRz0cbkl4PChTBLMbUiN1lhXtujg8CcVf++6QMj+vzrpfTIPkw3W/TG4zTJa0FaSg9h1zHX/9hXXw4QOIUvwstH51ay2ONZDVvm2Z1dIMkOFkcw2ndl4VnvtX5Xnekf3jUUvAmCNboLaKiUx5mqKo6KvMq3w7yakik5kQ3462QXoaI7PCEYiPK+CoskqX6aEyDREhCjV6nnzbEaZPBfpJjDp5KLRoFN6BT+Px8tD/lrAHMrW5gkzOtN5zGw9jjgjxp8cOsPoaYsCApQWjnSnRjcXy+g2Pw+SyxIshPE07cazB9fjTVDEiz2P+tb7hh/YEjM3uSJQFs37mIqir2NaUlFQSLwLP2HAX3DvYZeVKQMj8X+pH7Ad6iYGs8soGxrjznL7e1hfUoB89SkNHYTzBbsFy7pMVmTEfPG/MvjFmUgTai40lEvWyRJ4CbDsJ6W/KaLKUOMZpFZ+x/Sc10r9O1FZCKVpfnuRHLQXUj8cqcDags9evB5x6/ECn8zEGs7aX6ZTebPx+2D9sywmvy2LFL9Sjx+L8FYtzTXGBwip3rZOTNZhByzPDVwb0gJqamqRF0cET5RwNqb0Pohs9ScMMQwJnZGznvUbmjMQcemq/s51A6n+5g/Z31j+T482g=