Merge pull request #75 from GOmare/main

Automated flattening update
openmrs · Feb 13, 2024 · 3c5cb45 · 3c5cb45
2 parents 5139bef + 7f28f9c
commit 3c5cb45
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Showing 8 changed files with 56 additions and 41 deletions.
diff --git a/api/src/main/resources/_core/compiler/linux/compile-mysql.sh b/api/src/main/resources/_core/compiler/linux/compile-mysql.sh
@@ -70,12 +70,13 @@ function read_config_metadata() {
       -- \$BEGIN
           "$'
               SET @report_data = '%s';
+              CALL sp_mamba_extract_report_metadata(@report_data, '\''mamba_dim_concept_metadata'\'');
               SET @file_count = %d;
-              IF @file_count = 0 THEN
+              IF @file_count = 0 or @file_count > 0  THEN
                     CALL sp_mamba_dim_json();
-                    SET @report_data = fn_mamba_generate_report_array_from_automated_json_table();
+                    CALL sp_mamba_write_automated_json_config;
               END IF;
-              CALL sp_mamba_extract_report_metadata(@report_data, '\''mamba_dim_concept_metadata'\'');
+
           '"
       -- \$END
   "

diff --git a/api/src/main/resources/_core/database/mysql/dimensions/dim_json/sp_mamba_dim_json_create.sql b/api/src/main/resources/_core/database/mysql/dimensions/dim_json/sp_mamba_dim_json_create.sql
@@ -2,11 +2,13 @@
 
 CREATE TABLE mamba_dim_json
 (
+    id                      INT          NOT NULL AUTO_INCREMENT,
     report_name             VARCHAR(100) NOT NULL,
     encounter_type_id       INT NOT NULL UNIQUE,
     Json_data               JSON,
+    uuid                    CHAR(38),
 
-    PRIMARY KEY (encounter_type_id)
+    PRIMARY KEY (id)
 )
     CHARSET = UTF8MB4;
 
@@ -16,4 +18,7 @@ CREATE INDEX mamba_dim_json_encounter_type_id_index
 CREATE INDEX mamba_dim_json_report_name_index
     ON mamba_dim_json (report_name);
 
+CREATE INDEX mamba_dim_json_uuid_index
+    ON mamba_dim_json (uuid);
+
 -- $END
diff --git a/api/src/main/resources/_core/database/mysql/functions/fn_mamba_calculate_agegroup.sql b/api/src/main/resources/_core/database/mysql/functions/fn_mamba_calculate_agegroup.sql
@@ -7,7 +7,7 @@ CREATE FUNCTION fn_mamba_calculate_agegroup(age INT) RETURNS VARCHAR(15)
 BEGIN
     DECLARE agegroup VARCHAR(15);
     CASE age
-        WHEN age < 1 THEN  agegroup = '<1';
+        WHEN age < 1 THEN SET agegroup = '<1';
         WHEN age between 1 and 4 THEN SET agegroup = '1-4';
         WHEN age between 5 and 9 THEN SET agegroup = '5-9';
         WHEN age between 10 and 14 THEN SET agegroup = '10-14';

diff --git a/...ore/database/mysql/functions/fn_mamba_generate_report_array_from_automated_json_table.sql b/...ore/database/mysql/functions/fn_mamba_generate_report_array_from_automated_json_table.sql
@@ -7,9 +7,10 @@ CREATE FUNCTION fn_mamba_generate_report_array_from_automated_json_table() RETUR
 BEGIN
     DECLARE report_array JSON;
 
-    SELECT JSON_OBJECT('flat_report_metadata', JSON_ARRAYAGG(JSON_EXTRACT(Json_data, '$')))
+    SELECT JSON_OBJECT('flat_report_metadata',JSON_ARRAYAGG(JSON_EXTRACT(Json_data, '$')))
     INTO report_array
-    FROM mamba_dim_json;
+    FROM mamba_dim_json
+    WHERE uuid NOT IN (SELECT  DISTINCT encounter_type_uuid from mamba_dim_concept_metadata);
 
     RETURN report_array;
 END //

diff --git a/api/src/main/resources/_core/database/mysql/functions/fn_mamba_get_datatype_for_concept.sql b/api/src/main/resources/_core/database/mysql/functions/fn_mamba_get_datatype_for_concept.sql
@@ -7,13 +7,26 @@ CREATE FUNCTION fn_mamba_get_datatype_for_concept(conceptDatatype VARCHAR(20)) R
 BEGIN
     DECLARE mysqlDatatype VARCHAR(20);
 
-    CASE conceptDatatype
-        WHEN conceptDatatype IN ('Coded','N/A','Text') THEN SET  mysqlDatatype = 'TEXT';
-        WHEN conceptDatatype = 'Boolean' THEN SET mysqlDatatype = 'VARCHAR(50)';
-        WHEN conceptDatatype = 'Date' THEN SET mysqlDatatype = 'DATE';
-        WHEN conceptDatatype = 'Datetime' THEN  SET mysqlDatatype = 'DATETIME';
-        WHEN conceptDatatype = 'Numeric' THEN SET  mysqlDatatype = 'DOUBLE';
-    END CASE;
+    IF conceptDatatype = 'Coded'
+       OR conceptDatatype = 'N/A' THEN
+        SET mysqlDatatype = 'TEXT';
+
+    ELSEIF conceptDatatype = 'Text' THEN
+        SET mysqlDatatype = 'TEXT';
+
+    ELSEIF conceptDatatype = 'Boolean' THEN
+        SET mysqlDatatype = 'VARCHAR(30)';
+
+    ELSEIF conceptDatatype = 'Date' THEN
+        SET mysqlDatatype = 'DATE';
+
+    ELSEIF conceptDatatype = 'Datetime' THEN
+        SET mysqlDatatype = 'DATETIME';
+
+    ELSEIF conceptDatatype = 'Numeric' THEN
+        SET mysqlDatatype = 'DOUBLE';
+
+    END IF;
 
     RETURN mysqlDatatype;
 END //

diff --git a/api/src/main/resources/_core/database/mysql/functions/fn_mamba_get_obs_value_column.sql b/api/src/main/resources/_core/database/mysql/functions/fn_mamba_get_obs_value_column.sql
@@ -6,14 +6,16 @@ CREATE FUNCTION fn_mamba_get_obs_value_column(conceptDatatype VARCHAR(20)) RETUR
     DETERMINISTIC
 BEGIN
     DECLARE obsValueColumn VARCHAR(20);
+        IF (conceptDatatype = 'Text' OR conceptDatatype = 'Coded' OR conceptDatatype = 'N/A' OR
+            conceptDatatype = 'Boolean') THEN
+            SET obsValueColumn = 'obs_value_text';
+        ELSEIF conceptDatatype = 'Date' OR conceptDatatype = 'Datetime' THEN
+            SET obsValueColumn = 'obs_value_datetime';
+        ELSEIF conceptDatatype = 'Numeric' THEN
+            SET obsValueColumn = 'obs_value_numeric';
+        END IF;
 
-    CASE conceptDatatype
-        WHEN conceptDatatype IN ('Text','Coded','N/A','Boolean') THEN SET obsValueColumn = 'obs_value_text';
-        WHEN conceptDatatype IN ('Date','Datetime') THEN SET obsValueColumn = 'obs_value_datetime';
-        WHEN conceptDatatype  = 'Numeric' THEN SET obsValueColumn = 'obs_value_numeric';
-    END CASE;
-
-    RETURN obsValueColumn;
+    RETURN (obsValueColumn);
 END //
 
 DELIMITER ;
diff --git a/api/src/main/resources/_core/database/mysql/stored-procedures/sp_mamba_json_files_insert.sql b/api/src/main/resources/_core/database/mysql/stored-procedures/sp_mamba_json_files_insert.sql
@@ -30,7 +30,7 @@ BEGIN
     END IF;
 
     SET @insert_stmt = CONCAT(
-            'INSERT INTO mamba_dim_json
+            'INSERT INTO mamba_dim_json(report_name,encounter_type_id,Json_data,uuid)
                 SELECT
                     name,
                     encounter_type_id,
@@ -40,7 +40,7 @@ BEGIN
                     ''encounter_type_uuid'',uuid,
                     ''concepts_locale'',locale,
                     ''table_columns'',json_obj
-                    )
+                    ), encounter_type_uuid
                 FROM (
                     SELECT DISTINCT
                         et.name,
@@ -54,7 +54,7 @@ BEGIN
                             FROM (
                                     SELECT
                                         DISTINCT et.encounter_type_id,
-                                        LOWER(LEFT(REPLACE(REPLACE(REGEXP_REPLACE(cn.name, ''[^0-9a-zÀ-ÿ ]'', ''''), '' '', ''_''),''__'', ''_''),35)) name,
+                                        LOWER(LEFT(REPLACE(REPLACE(REGEXP_REPLACE(cn.name, ''[^0-9a-z ]'', ''''), '' '', ''_''),''__'', ''_''),35)) name,
                                         c.uuid
                                     FROM mamba_source_db.obs o
                                     INNER JOIN mamba_source_db.encounter e
@@ -71,7 +71,8 @@ BEGIN
                                     AND cn.locale_preferred = 1
                                     AND et.retired = 0
                                 ) json_obj
-                        ) json_obj
+                        ) json_obj,
+                       et.uuid as encounter_type_uuid
                     FROM mamba_source_db.encounter_type et
                     INNER JOIN mamba_source_db.encounter e
                         ON e.encounter_type = et.encounter_type_id

diff --git a/...resources/_core/database/mysql/stored-procedures/sp_mamba_write_automated_json_config.sql b/...resources/_core/database/mysql/stored-procedures/sp_mamba_write_automated_json_config.sql
@@ -5,44 +5,36 @@ DELIMITER //
 CREATE PROCEDURE sp_mamba_write_automated_json_config()
 BEGIN
 
-    DECLARE countRows INT;
     DECLARE done INT DEFAULT FALSE;
     DECLARE jsonData JSON;
     DECLARE cur CURSOR FOR
         SELECT json_data FROM mamba_dim_json;
     DECLARE CONTINUE HANDLER FOR NOT FOUND SET done = TRUE;
 
-    SELECT COUNT(*) INTO countRows FROM mamba_dim_concept_metadata;
-    IF countRows = 0 THEN
-
         SET @report_data = '{"flat_report_metadata":[';
 
         OPEN cur;
         FETCH cur INTO jsonData;
 
         IF NOT done THEN
-            SET @report_data = CONCAT(@report_data, jsonData);
-            FETCH cur INTO jsonData; -- Fetch next record after the first one
+                    SET @report_data = CONCAT(@report_data, jsonData);
+        FETCH cur INTO jsonData; -- Fetch next record after the first one
         END IF;
 
-        read_loop: LOOP
-            IF done THEN
-                LEAVE read_loop;
-            END IF;
+                read_loop: LOOP
+                    IF done THEN
+                        LEAVE read_loop;
+        END IF;
 
-            SET @report_data = CONCAT(@report_data, ',', jsonData);
-            FETCH cur INTO jsonData;
+                    SET @report_data = CONCAT(@report_data, ',', jsonData);
+        FETCH cur INTO jsonData;
         END LOOP;
         CLOSE cur;
 
         SET @report_data = CONCAT(@report_data, ']}');
 
         CALL sp_mamba_extract_report_metadata(@report_data, 'mamba_dim_concept_metadata');
 
-        ELSE
-            SELECT 'mamba_dim_concept_metadata is not empty, no data copied.';
-    END IF;
-
 END //
 
 DELIMITER ;