canql 2.10.0 → 3.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,6 +1,10 @@
 ## [Unreleased]
 *no unreleased changes*
 
+## 3.0.0 / 2019-06-04
+### Changed
+* Added new branch of CANQL for querying all patient not just child patients - modifies DIR (#29)
+
 ## 2.10.0 / 2019-05-29
 ### Added
 * Add filter for processing region (#32)

data/README.md

@@ -45,7 +45,7 @@ end
 would output:
 
 ```json
-{"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
+{"results.subject":{"equals":"case"},"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:

data/code_safety.yml

@@ -19,7 +19,7 @@ file safety:
   CHANGELOG.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: '098751876ada572fd6dd7137e7c8eab28ca3b8e5'
+    safe_revision: ff70470e8fa9613a6968a7579b206b6107ef5312
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -35,7 +35,7 @@ file safety:
   README.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 1b5795e8b5e20395f17277050f17ff0db6f0f556
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   Rakefile:
     comments: 
     reviewed_by: timgentry
@@ -95,12 +95,12 @@ 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: 1b5795e8b5e20395f17277050f17ff0db6f0f556
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   lib/canql/grammars/patient.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: josh.pencheon
-    safe_revision: 38369f1f26167f396d1705ec88611103d5262726
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   lib/canql/grammars/perinatal_hospital.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -150,7 +150,7 @@ file safety:
   lib/canql/nodes/main.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   lib/canql/nodes/patient.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -178,7 +178,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: '098751876ada572fd6dd7137e7c8eab28ca3b8e5'
+    safe_revision: ff70470e8fa9613a6968a7579b206b6107ef5312
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -191,14 +191,18 @@ file safety:
     comments: 
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
-  test/nodes/age_test.rb:
-    comments: 
-    reviewed_by: timgentry
-    safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   test/nodes/anomaly_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 73a7dac17b20fcc77bcbd9d38777c8aa4d524816
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/case_age_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/case_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/code_test.rb:
     comments: 
     reviewed_by: timgentry
@@ -206,40 +210,48 @@ file safety:
   test/nodes/e_base_records_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 4e26ac746098452b01dac88373e401e39f309b74
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/genetic_tests_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
-  test/nodes/main_test.rb:
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/main_case_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/main_patient_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/mother_e_base_records_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 4805609963f75639e2444df8f42d2d6d65005b7c
+  test/nodes/patient_age_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/patient_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 38369f1f26167f396d1705ec88611103d5262726
+    safe_revision: 33597126dbd2f720bd867fc357003634b73e6d0a
   test/nodes/perinatal_hospital_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/registry_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/test_results_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: c39d24bb500719971969762e94545e82866bf92f
+    reviewed_by: josh.pencheon
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/parser_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 1b5795e8b5e20395f17277050f17ff0db6f0f556
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: a1686a3905ee6d7ebc8c5b1786efba4f8df42a2d
+    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb

data/lib/canql/grammars/main.treetop

@@ -13,8 +13,15 @@ grammar Canql
 
   # The root grammar
   rule query
-    #quantity:record_count? pre:preconditions* cases_keyword post:additional_conditions*
-    quantity:record_count? pre:preconditions* cases_keyword post:additional_conditions* with_clause?
+    case_query / patient_query
+  end
+
+  rule case_query
+    quantity:record_count? pre:case_preconditions* cases_keyword post:case_additional_conditions* case_with_clause?
+  end
+
+  rule patient_query
+    quantity:record_count? pre:patient_preconditions* patient_keyword post:patient_additional_conditions* patient_with_clause?
   end
 
   rule word_break
@@ -44,19 +51,35 @@ grammar Canql
   end
 
   rule cases_keyword
-     space subject:('cases' / 'babies') word_break
+     space subject:('cases' / 'babies') word_break <Nodes::SubjectNode>
   end
 
-  rule preconditions
+  rule patient_keyword
+    space subject:'patients' word_break <Nodes::SubjectNode>
+  end
+
+  rule case_preconditions
     registry / gender / outcome / primacy
   end
 
-  rule additional_conditions
+  rule patient_preconditions
+     gender / primacy
+  end
+
+  rule case_additional_conditions
     and_keyword? (expected / with_birth_date / with_death_date)
   end
 
-  rule with_clause
-    with_keyword post:with_conditions+ <Nodes::WithConditions>
+  rule patient_additional_conditions
+    and_keyword? (with_birth_date / with_death_date)
+  end
+
+  rule case_with_clause
+    with_keyword post:case_with_conditions+ <Nodes::WithConditions>
+  end
+
+  rule patient_with_clause
+    with_keyword post:patient_with_conditions+ <Nodes::WithConditions>
   end
 
   rule with_keyword
@@ -103,7 +126,11 @@ grammar Canql
     space 'at' word_break
   end
 
-  rule with_conditions
-     anomalies / genetic_tests / test_results / perinatal_hospital / patient_field_existance / mother_conditions / action_or_ebr
+  rule case_with_conditions
+     anomalies / genetic_tests / test_results / perinatal_hospital / case_field_existance / mother_conditions / action_or_ebr
+  end
+
+  rule patient_with_conditions
+     anomalies / genetic_tests / test_results / patient_field_existance / action_or_ebr
   end
 end

data/lib/canql/grammars/patient.treetop

@@ -20,6 +20,10 @@ module Canql
       expected_keyword fuzzy_date <Nodes::Patient::ExpectedDateRangeNode>
     end
 
+    rule case_field_existance
+      and_keyword? field_existance_modifier:existance_keyword patient_field_list:case_field_list  <Nodes::Patient::FieldExists>
+    end
+
     rule patient_field_existance
       and_keyword? field_existance_modifier:existance_keyword patient_field_list:patient_field_list  <Nodes::Patient::FieldExists>
     end
@@ -28,11 +32,15 @@ module Canql
       space 'field' 's'? word_break
     end
 
+    rule case_field_list
+      space case_field_names (comma case_field_names)*
+    end
+
     rule patient_field_list
       space patient_field_names (comma patient_field_names)*
     end
 
-    rule patient_field_names
+    rule case_field_names
       patient_field_name:(
         'date of birth' / 'dob' / 'nhs number' / 'postcode' / 'birth weight' /
         'place of delivery' / 'sex' / 'outcome' / 'edd' /
@@ -40,6 +48,12 @@ module Canql
       )
     end
 
+    rule patient_field_names
+      patient_field_name:(
+        'date of birth' / 'dob' / 'nhs number' / 'postcode' / 'sex'
+      )
+    end
+
     rule mother_conditions
       and_keyword? space subject:'mother' word_break mother_additional_conditions mother_with_clause?
     end

data/lib/canql/nodes/main.rb

@@ -14,6 +14,16 @@ end
 
 module Canql #:nodoc: all
   module Nodes
+    # Returns a filter detailing the require result type (cases or patients)
+    module SubjectNode
+      def meta_data_item
+        type_map = { cases: 'case', babies: 'case', patients: 'patient' }
+        raise 'Unknown result type' if type_map[subject.text_value.to_sym].nil?
+
+        { 'results.subject' => { Canql::EQUALS => type_map[subject.text_value.to_sym] } }
+      end
+    end
+
     # Provides meta data for with conditions that return
     # multiple instances of a condition type as an array
     module WithConditions

data/lib/canql/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '2.10.0'
+  VERSION = '3.0.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 2.10.0
+  version: 3.0.0
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-05-29 00:00:00.000000000 Z
+date: 2019-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic