canql 2.10.0 → 3.0.0
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- checksums.yaml +4 -4
- data/CHANGELOG.md +4 -0
- data/README.md +1 -1
- data/code_safety.yml +36 -24
- data/lib/canql/grammars/main.treetop +36 -9
- data/lib/canql/grammars/patient.treetop +15 -1
- data/lib/canql/nodes/main.rb +10 -0
- data/lib/canql/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 935d92e9e0fa6135540db6a7acfdf127d9fdf395ddbd8f1c93f328b8e708983e
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data.tar.gz: 0b55234d83f824b71c66beb3e761ce0687393bb9e2695aaa21bda055883cdec0
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c97e4d469ee36061bfd75b6c27c28ec47ed63c626bfd1412a84e9d0139cc2510f2d8c429b5793eded4e174cb9ec4a7401664492ae8dc52e2bddc6ca9382bf147
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data.tar.gz: 6f0998e8c64dd33322c70ca72c610a5b69c96956758e94a646489bf4eb14f7ee892bd268f01e6809e0cf42356591e8cedb7a6b15ffec4529001c56b000c9c191
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data/CHANGELOG.md
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## [Unreleased]
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*no unreleased changes*
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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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## 2.10.0 / 2019-05-29
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### Added
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* Add filter for processing region (#32)
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data/README.md
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would output:
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```json
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-
{"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
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{"results.subject":{"equals":"case"},"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
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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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data/code_safety.yml
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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:
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safe_revision: ff70470e8fa9613a6968a7579b206b6107ef5312
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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: 511e4238f83eb5b32839c25d94ec2a59145539bb
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Rakefile:
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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: 511e4238f83eb5b32839c25d94ec2a59145539bb
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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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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/main.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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lib/canql/nodes/patient.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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reviewed_by: josh.pencheon
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test/anomaly_test_helper.rb:
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reviewed_by: josh.pencheon
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comments:
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reviewed_by: timgentry
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safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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test/nodes/age_test.rb:
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comments:
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reviewed_by: timgentry
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safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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test/nodes/anomaly_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/nodes/case_age_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/nodes/case_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/nodes/code_test.rb:
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comments:
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reviewed_by: timgentry
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test/nodes/e_base_records_test.rb:
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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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test/nodes/
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test/nodes/main_case_test.rb:
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test/nodes/main_patient_test.rb:
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comments:
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test/nodes/mother_e_base_records_test.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 4805609963f75639e2444df8f42d2d6d65005b7c
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test/nodes/patient_age_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/nodes/patient_test.rb:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 33597126dbd2f720bd867fc357003634b73e6d0a
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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/nodes/registry_test.rb:
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comments:
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test/nodes/test_results_test.rb:
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comments:
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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: josh.pencheon
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safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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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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safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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@@ -13,8 +13,15 @@ grammar Canql
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# The root grammar
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rule query
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-
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-
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case_query / patient_query
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end
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rule case_query
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quantity:record_count? pre:case_preconditions* cases_keyword post:case_additional_conditions* case_with_clause?
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end
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rule patient_query
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quantity:record_count? pre:patient_preconditions* patient_keyword post:patient_additional_conditions* patient_with_clause?
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end
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rule word_break
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@@ -44,19 +51,35 @@ grammar Canql
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end
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rule cases_keyword
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space subject:('cases' / 'babies') word_break
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space subject:('cases' / 'babies') word_break <Nodes::SubjectNode>
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end
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-
rule
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rule patient_keyword
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space subject:'patients' word_break <Nodes::SubjectNode>
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end
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+
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rule case_preconditions
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registry / gender / outcome / primacy
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end
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-
rule
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rule patient_preconditions
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gender / primacy
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end
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rule case_additional_conditions
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and_keyword? (expected / with_birth_date / with_death_date)
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end
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rule
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-
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rule patient_additional_conditions
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and_keyword? (with_birth_date / with_death_date)
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end
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rule case_with_clause
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with_keyword post:case_with_conditions+ <Nodes::WithConditions>
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end
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rule patient_with_clause
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with_keyword post:patient_with_conditions+ <Nodes::WithConditions>
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end
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rule with_keyword
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@@ -103,7 +126,11 @@ grammar Canql
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space 'at' word_break
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end
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-
rule
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-
anomalies / genetic_tests / test_results / perinatal_hospital /
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rule case_with_conditions
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anomalies / genetic_tests / test_results / perinatal_hospital / case_field_existance / mother_conditions / action_or_ebr
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end
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+
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rule patient_with_conditions
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anomalies / genetic_tests / test_results / patient_field_existance / action_or_ebr
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end
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end
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expected_keyword fuzzy_date <Nodes::Patient::ExpectedDateRangeNode>
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end
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rule case_field_existance
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and_keyword? field_existance_modifier:existance_keyword patient_field_list:case_field_list <Nodes::Patient::FieldExists>
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end
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rule patient_field_existance
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and_keyword? field_existance_modifier:existance_keyword patient_field_list:patient_field_list <Nodes::Patient::FieldExists>
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end
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space 'field' 's'? word_break
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end
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rule case_field_list
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space case_field_names (comma case_field_names)*
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end
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+
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rule patient_field_list
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space patient_field_names (comma patient_field_names)*
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end
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-
rule
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rule case_field_names
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patient_field_name:(
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'date of birth' / 'dob' / 'nhs number' / 'postcode' / 'birth weight' /
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'place of delivery' / 'sex' / 'outcome' / 'edd' /
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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' / 'nhs number' / 'postcode' / 'sex'
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)
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end
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+
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rule mother_conditions
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and_keyword? space subject:'mother' word_break mother_additional_conditions mother_with_clause?
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end
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data/lib/canql/nodes/main.rb
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module Canql #:nodoc: all
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module Nodes
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# Returns a filter detailing the require result type (cases or patients)
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module SubjectNode
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def meta_data_item
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type_map = { cases: 'case', babies: 'case', patients: 'patient' }
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raise 'Unknown result type' if type_map[subject.text_value.to_sym].nil?
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+
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{ 'results.subject' => { Canql::EQUALS => type_map[subject.text_value.to_sym] } }
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end
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end
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# Provides meta data for with conditions that return
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# multiple instances of a condition type as an array
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module WithConditions
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data/lib/canql/version.rb
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metadata
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--- !ruby/object:Gem::Specification
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name: canql
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version: !ruby/object:Gem::Version
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version:
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version: 3.0.0
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platform: ruby
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authors:
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- PHE NDR Development Team
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autorequire:
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bindir: exe
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cert_chain: []
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-
date: 2019-
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+
date: 2019-06-04 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: chronic
|