Relax db

qiita_db/support_files/patches/23.sql

@@ -0,0 +1,150 @@
+-- Apr 16, 2015
+-- This patch relaxes the sample template metadata constraints on the database,
+-- so from now on they're going to be enforced by code, except
+-- required_sample_info_status which is completely deprecated
+
+DO $do$
+DECLARE
+    dyn_t varchar;
+    dyn_table varchar;
+    st_id bigint;
+BEGIN
+
+-- First, sample template
+FOR dyn_t IN
+    SELECT DISTINCT table_name
+    FROM information_schema.columns
+    WHERE SUBSTR(table_name, 1, 7) = 'sample_'
+        AND table_schema = 'qiita'
+        AND table_name != 'sample_template_filepath'
+LOOP
+    st_id := SUBSTR(dyn_t, 8)::int;
+    dyn_table := 'qiita.' || dyn_t;
+
+    -- Add the new columns to the study_sample_columns table
+    INSERT INTO qiita.study_sample_columns (study_id, column_name, column_type)
+        VALUES (st_id, 'physical_specimen_location', 'varchar'),
+               (st_id, 'physical_specimen_remaining', 'bool'),
+               (st_id, 'dna_extracted', 'bool'),
+               (st_id, 'sample_type', 'varchar'),
+               (st_id, 'collection_timestamp', 'timestamp'),
+               (st_id, 'host_subject_id', 'varchar'),
+               (st_id, 'description', 'varchar'),
+               (st_id, 'latitude', 'float8'),
+               (st_id, 'longitude', 'float8'),
+               (st_id, 'required_sample_info_status', 'varchar');
+
+    -- Add the new columns to the dynamic table
+    EXECUTE 'ALTER TABLE ' || dyn_table || '
+                ADD COLUMN physical_specimen_location varchar, 
+                ADD COLUMN physical_specimen_remaining boolean, 
+                ADD COLUMN dna_extracted boolean, 
+                ADD COLUMN sample_type varchar, 
+                ADD COLUMN collection_timestamp timestamp, 
+                ADD COLUMN host_subject_id varchar, 
+                ADD COLUMN description varchar, 
+                ADD COLUMN latitude float8, 
+                ADD COLUMN longitude float8, 
+                ADD COLUMN required_sample_info_status varchar;';
+
+    -- Copy the values from the required_sample_info table to the dynamic table
+    EXECUTE '
+        WITH sv AS (SELECT * FROM qiita.required_sample_info
+                    JOIN qiita.required_sample_info_status
+                        USING (required_sample_info_status_id)
+                    WHERE study_id = ' || st_id || ')
+        UPDATE ' || dyn_table || '
+            SET physical_specimen_location=sv.physical_location,
+                physical_specimen_remaining=sv.has_physical_specimen,
+                dna_extracted=sv.has_extracted_data,
+                sample_type=sv.sample_type,
+                collection_timestamp=sv.collection_timestamp,
+                host_subject_id=sv.host_subject_id,
+                description=sv.description,
+                latitude=sv.latitude,
+                longitude=sv.longitude,
+                required_sample_info_status=sv.status
+            FROM sv
+            WHERE ' || dyn_table || '.sample_id = sv.sample_id;';
+
+END LOOP;
+END $do$;
+
+-- We can now drop the columns in the required_sample_info_table
+ALTER TABLE qiita.required_sample_info
+    DROP COLUMN physical_location,
+    DROP COLUMN has_physical_specimen,
+    DROP COLUMN has_extracted_data,
+    DROP COLUMN sample_type,
+    DROP COLUMN required_sample_info_status_id,
+    DROP COLUMN collection_timestamp,
+    DROP COLUMN host_subject_id,
+    DROP COLUMN description,
+    DROP COLUMN latitude,
+    DROP COLUMN longitude;
+
+-- Since that table no longer stores required metadata,
+-- we will rename it
+ALTER TABLE qiita.required_sample_info RENAME TO study_sample;
+
+-- The table required_sample_info_status_id is no longer needed
+DROP TABLE qiita.required_sample_info_status;
+
+-- Now, let's move the data for the prep templates
+DO $do$
+DECLARE
+    dyn_t varchar;
+    dyn_table varchar;
+    prep_id bigint;
+BEGIN
+FOR dyn_t IN
+    SELECT DISTINCT table_name
+    FROM information_schema.columns
+    WHERE SUBSTR(table_name, 1, 5) = 'prep_'
+        AND table_schema = 'qiita'
+        AND table_name NOT IN ('prep_template',
+                               'prep_template_preprocessed_data',
+                               'prep_template_filepath',
+                               'prep_columns')
+LOOP
+    prep_id := SUBSTR(dyn_t, 6)::int;
+    dyn_table := 'qiita.' || dyn_t;
+
+    -- Add the new columns to the prep_template_columns table
+    INSERT INTO qiita.prep_columns (prep_template_id, column_name, column_type)
+        VALUES (prep_id, 'center_name', 'varchar'),
+               (prep_id, 'center_project_name', 'varchar'),
+               (prep_id, 'emp_status', 'varchar');
+
+    -- Add the new columns to the dynamic table
+    EXECUTE 'ALTER TABLE ' || dyn_table || '
+                ADD COLUMN center_name varchar,
+                ADD COLUMN center_project_name varchar,
+                ADD COLUMN emp_status varchar;';
+
+    -- Copy the values from the common_prep_info table to the dynamic table
+    EXECUTE '
+        WITH sv AS (SELECT * FROM qiita.common_prep_info
+                        JOIN qiita.emp_status USING (emp_status_id)
+                    WHERE prep_template_id = ' || prep_id || ')
+        UPDATE ' || dyn_table || '
+            SET center_name=sv.center_name,
+                center_project_name=sv.center_project_name,
+                emp_status=sv.emp_status
+            FROM sv
+            WHERE ' || dyn_table || '.sample_id=sv.sample_id;';
+
+END LOOP;
+END $do$;
+
+-- We can now drop the columns in the required_sample_info_table
+ALTER TABLE qiita.common_prep_info
+    DROP COLUMN center_name,
+    DROP COLUMN center_project_name,
+    DROP COLUMN emp_status_id;
+
+-- Since that table no longer stores common metadata, we will rename it
+ALTER TABLE qiita.common_prep_info RENAME to prep_template_sample;
+
+-- The table emp_status is no longer needed
+DROP TABLE qiita.emp_status;