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CPT4

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manual work
manual work
 
 
load_stage.sql
load_stage.sql
 
 
readme.md
readme.md
 
 
vocab_specific_QA.sql
vocab_specific_QA.sql
 
 

readme.md

Update of CPT4

Prerequisites:

  • Schema DevV5 with copies of tables concept, concept_relationship and concept_synonym from ProdV5, fully indexed.
  • UMLS in SOURCES schema
  • SNOMED must be loaded first
  • Working directory CPT4
  1. Run
SELECT devv5.FastRecreateSchema(main_schema_name=>'devv5', include_concept_ancestor=>true, include_deprecated_rels=>true, include_synonyms=>true);

  1. Run load_stage.sql (The pVocabularyDate will be automatically retrieved from the UMLS [SOURCES.MRSMAP.vocabulary_date])

  2. Run generic_update:

DO $_$
BEGIN
	PERFORM devv5.GenericUpdate();
END $_$;
  1. Run basic tables check (should retrieve NULL):
SELECT * FROM qa_tests.get_checks();
  1. Work with 'manual work' directory

Repeat steps 1-5

  1. Run manual_checks_after_generic.sql, and interpret the results.

  2. Run scripts to get summary, and interpret the results:

SELECT * FROM qa_tests.get_summary('concept');
SELECT * FROM qa_tests.get_summary('concept_relationship');
  1. Run scripts to collect statistics, and interpret the results:
SELECT * FROM qa_tests.get_domain_changes();
SELECT * FROM qa_tests.get_newly_concepts();
SELECT * FROM qa_tests.get_standard_concept_changes();
SELECT * FROM qa_tests.get_newly_concepts_standard_concept_status();
SELECT * FROM qa_tests.get_changes_concept_mapping();
  1. If no problems, enjoy!

Manual tables directory permalink: https://drive.google.com/drive/u/0/folders/1TWGdyVy95AT-9GfK7KaKY2HQA4rDqxrH