MySQL snippets and other material relating to reporting from the Onyx database.

In the early phase of BRICCS, before i2b2 is deployed, obtaining data on BRICCS participants is possible only from within the Onyx database, via MySQL queries.

There is a web page for reporting from the Onyx database, accessible via password within the UHL network, contact Nick or Vasil for information. In addition, the following is provided as useful material to assist when writing custom MySQL queries for reporting:


== Table Structure ==

{{{

mysql> describe participant;
+------------------+--------------+------+-----+---------+----------------+
| Field            | Type         | Null | Key | Default | Extra          |
+------------------+--------------+------+-----+---------+----------------+
| id               | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| barcode          | varchar(250) | YES  |     | NULL    |                |
| birth_date       | date         | YES  |     | NULL    |                |
| enrollment_id    | varchar(255) | YES  |     | NULL    |                |
| first_name       | varchar(250) | NO   |     | NULL    |                |
| gender           | varchar(255) | YES  |     | NULL    |                |
| last_name        | varchar(250) | NO   |     | NULL    |                |
| recruitment_type | varchar(255) | YES  |     | NULL    |                |
| site_no          | varchar(255) | NO   |     | NULL    |                |
+------------------+--------------+------+-----+---------+----------------+
9 rows in set (0.00 sec)

mysql> describe question_answer;
+------------------------------+---------------+------+-----+---------+----------------+
| Field                        | Type          | Null | Key | Default | Extra          |
+------------------------------+---------------+------+-----+---------+----------------+
| id                           | bigint(20)    | NO   | PRI | NULL    | auto_increment |
| active                       | bit(1)        | NO   |     | NULL    |                |
| comment                      | varchar(2000) | YES  |     | NULL    |                |
| question_name                | varchar(255)  | NO   | MUL | NULL    |                |
| questionnaire_participant_id | bigint(20)    | NO   | MUL | NULL    |                |
+------------------------------+---------------+------+-----+---------+----------------+
5 rows in set (0.00 sec)


mysql> describe open_answer;
+-----------------------------+---------------+------+-----+---------+----------------+
| Field                       | Type          | Null | Key | Default | Extra          |
+-----------------------------+---------------+------+-----+---------+----------------+
| id                          | bigint(20)    | NO   | PRI | NULL    | auto_increment |
| data_type                   | varchar(255)  | YES  |     | NULL    |                |
| date_value                  | datetime      | YES  |     | NULL    |                |
| decimal_value               | double        | YES  |     | NULL    |                |
| integer_value               | bigint(20)    | YES  |     | NULL    |                |
| open_answer_definition_name | varchar(255)  | NO   | MUL | NULL    |                |
| text_value                  | varchar(2000) | YES  |     | NULL    |                |
| category_answer_id          | bigint(20)    | NO   | MUL | NULL    |                |
+-----------------------------+---------------+------+-----+---------+----------------+
8 rows in set (0.00 sec)


mysql> describe category_answer;
+---------------------------+--------------+------+-----+---------+----------------+
| Field                     | Type         | Null | Key | Default | Extra          |
+---------------------------+--------------+------+-----+---------+----------------+
| id                        | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| active                    | bit(1)       | NO   |     | NULL    |                |
| category_name             | varchar(255) | NO   | MUL | NULL    |                |
| occurence                 | int(11)      | YES  |     | NULL    |                |
| parent_category_answer_id | bigint(20)   | YES  | MUL | NULL    |                |
| question_answer_id        | bigint(20)   | NO   | MUL | NULL    |                |
+---------------------------+--------------+------+-----+---------+----------------+
6 rows in set (0.00 sec)


mysql> describe questionnaire_participant;
+-----------------------+--------------+------+-----+---------+----------------+
| Field                 | Type         | Null | Key | Default | Extra          |
+-----------------------+--------------+------+-----+---------+----------------+
| id                    | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| locale                | varchar(255) | NO   |     | NULL    |                |
| questionnaire_name    | varchar(255) | NO   |     | NULL    |                |
| questionnaire_version | varchar(255) | NO   |     | NULL    |                |
| resume_page           | varchar(255) | YES  |     | NULL    |                |
| time_end              | datetime     | YES  |     | NULL    |                |
| time_start            | datetime     | NO   |     | NULL    |                |
| participant_id        | bigint(20)   | NO   | MUL | NULL    |                |
| user_id               | bigint(20)   | NO   | MUL | NULL    |                |
+-----------------------+--------------+------+-----+---------+----------------+
9 rows in set (0.00 sec)

}}}

== MySQL snippets ==

Lists primary diagnoses with a count (used in the reporting table):

SELECT category_name, count(category_name)
          FROM question_answer, category_answer
          where question_answer.question_name = 'epi_pridiag'
         and category_answer.question_answer_id = question_answer.id
         group by category_name order by count(category_name) desc


Lists BPt numbers, grouped and counted by primary diagnosis:

SELECT category_name, barcode, count(*)
	FROM participant, questionnaire_participant, question_answer, category_answer
	WHERE participant.id = questionnaire_participant.participant_id
	AND question_answer.questionnaire_participant_id = questionnaire_participant.id
	AND question_answer.question_name = 'epi_pridiag'
        AND category_answer.question_answer_id = question_answer.id
	GROUP BY category_name, barcode WITH ROLLUP;

From the command line, to query for gender and birth date for specific diagnosis, into an outfile:

mysql -h briccsdb -u auditor -p briccs -e "
SELECT category_name, birth_date, gender
FROM participant, questionnaire_participant, question_answer, category_answer 
WHERE participant.id = questionnaire_participant.participant_id 
AND question_answer.questionnaire_participant_id = questionnaire_participant.id 
AND question_answer.question_name = 'epi_pridiag' 
AND category_answer.question_answer_id = question_answer.id 
AND ( category_answer.category_name LIKE '%ACS%' OR category_answer.category_name = 'STEMI' OR category_answer.category_name = 'Stable Angina' )
; 
" > mysql-output.txt


Single diagnosis, count:

SELECT count(participant.id) as 'Number of Participants' 
FROM participant, questionnaire_participant, question_answer, category_answer  
WHERE participant.id = questionnaire_participant.participant_id  
AND question_answer.questionnaire_participant_id = questionnaire_participant.id  
AND ( question_answer.question_name = 'epi_pridiag' OR question_answer.question_name = 'epi_secdiag' ) 
AND category_answer.question_answer_id = question_answer.id  
AND category_answer.category_name = 'Aortic_Stenosis';


Complex query, using two references to the same tables, to derive those of a certain diagnosis (primary or secondary) where the recruitment context is not 'Study specific':

SELECT count(participant.id) as 'AS not study recruited' 
FROM participant, questionnaire_participant as diag_questionnaire, questionnaire_participant as context_questionnaire, question_answer as diag_question, category_answer as diag_answer, question_answer as context_question, category_answer as context_answer
WHERE participant.id = diag_questionnaire.participant_id  
AND participant.id = context_questionnaire.participant_id  
AND diag_questionnaire.id = diag_question.questionnaire_participant_id
AND ( diag_question.question_name = 'epi_pridiag' OR diag_question.question_name = 'epi_secdiag' )
AND diag_answer.question_answer_id = diag_question.id 
AND diag_answer.category_name = 'Aortic_Stenosis'
AND context_questionnaire.id = context_question.questionnaire_participant_id
AND context_question.question_name = 'epi_type'
AND context_answer.question_answer_id = context_question.id 
AND context_answer.category_name <> 'Study_specific' 
;

Using UNION to produce a list of S numbers and DOBs for participants who are either study specific recruits or have a specific primary or secondary diagnosis (UNION combines two SELECTs with duplicates removed):

mysql -h briccsdb -u auditor -p briccs -e " 
SELECT enrollment_id as 'Participant', birth_date as 'DOB'
FROM participant, questionnaire_participant, question_answer, category_answer 
WHERE participant.id = questionnaire_participant.participant_id 
AND question_answer.questionnaire_participant_id = questionnaire_participant.id 
AND ( question_answer.question_name = 'epi_pridiag' OR question_answer.question_name = 'epi_secdiag' ) 
AND category_answer.question_answer_id = question_answer.id 
AND category_answer.category_name = 'Aortic_Stenosis'
UNION
SELECT enrollment_id as 'Participant', birth_date as 'DOB'
FROM participant, questionnaire_participant, question_answer, category_answer 
WHERE participant.id = questionnaire_participant.participant_id 
AND question_answer.questionnaire_participant_id = questionnaire_participant.id 
AND question_answer.question_name = 'epi_type' 
AND category_answer.question_answer_id = question_answer.id 
AND category_answer.category_name = 'Study_specific'
; " > mysql-output.txt