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-- Query Template: find synonyms between source strings and an OMOP terminology concept codes 
SELECT DISTINCT
lower(source_string) AS source_code,
lower(concept_synonym_name) AS source_name,
"String" AS input_type,
domain_id AS source_domain,
"None" AS source_vocabulary

FROM 
(SELECT DISTINCT

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SELECT 
  DISTINCT CONCAT('"', c.concept_code, '"') AS standard_code, 
  c.concept_name AS standard_name, 
  c.domain_id AS standard_domain, 
  c.vocabulary_id AS standard_vocabulary, 
  COUNT(occ.{count_concept}_id) AS occ_count 
FROM 
  {database}.concept c 
  JOIN {database}.{count_concept} occ ON occ.{concept}_concept_id = c.concept_id 
WHERE 

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WITH age_criteria_1 AS (
SELECT co.person_id, cohort.standard_code_set AS code_set 
FROM 
  {database}.person p, 
  {database}.condition_occurrence co, 
  {database}.ADHD_COHORT_VARS cohort 
WHERE p.person_id = co.person_id 
  AND co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1
  AND cohort.standard_code_set = {code_set_group}

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WITH dx_case_inclusion_criteria_1 AS (
  SELECT co.person_id, cohort.standard_code_set AS code_set 
  FROM 
    {database}.condition_occurrence co,
    {database}.SICKLECELLDISEASE_COHORT_VARS cohort
  WHERE 
    co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
    AND cohort.standard_code_set = {code_set_group}
    GROUP BY co.person_id, cohort.standard_code_set
  HAVING

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WITH dx_case_inclusion_criteria_1 AS (
  SELECT co.person_id, cohort.standard_code_set AS code_set
    FROM 
     {database}.condition_occurrence co, 
     {database}.SLEEPAPNEA_COHORT_VARS cohort 
   WHERE co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
     AND cohort.phenotype_definition_number = 1 
     AND cohort.standard_code_set = {code_set_group} 
   GROUP BY
      co.person_id, code_set

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WITH dx_case_inclusion_criteria_1 AS (
SELECT co.person_id, cohort.standard_code_set AS code_set 
FROM 
  {database}.condition_occurrence co, 
  {database}.CROHNSDISEASE_COHORT_VARS cohort 
WHERE 
  co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 

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WITH dx_case_inclusion_criteria_1 AS (
SELECT co.person_id, cohort.standard_code_set AS code_set 
FROM 
  {database}.condition_occurrence co, 
  {database}.APPENDICITIS_COHORT_VARS cohort 
WHERE 
  co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 

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WITH dx_case_inclusion_criteria_1 AS (
SELECT co.person_id, cohort.standard_code_set AS code_set
  FROM 
   {database}.condition_occurrence co, 
   {database}.SYSTEMICLUPUSERYTHEMATOSUS_COHORT_VARS cohort 
 WHERE co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
   AND cohort.phenotype_definition_number = 1
   AND cohort.standard_code_set = {code_set_group} 
 GROUP BY
    co.person_id, code_set

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#!/usr/bin/python
# -*- coding: utf-8 -*-

def xpath_soup(element):
    """
    Generate xpath from BeautifulSoup4 element

    :param element: BeautifulSoup4 element.
    :type element: bs4.element.Tag or bs4.element.NavigableString
    :return: xpath as string

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WITH all_case_inclusion_criteria_1 AS (
SELECT person_id, {code_set_group} AS code_set FROM
(SELECT co.person_id
FROM 
  {database}.condition_occurrence co, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}