renalware-core 2.0.0.pre.rc8 → 2.0.0.pre.rc9

data/db/migrate/20161124152732_add_deleted_at_to_patient_bookmarks.rb

@@ -12,7 +12,7 @@ class AddDeletedAtToPatientBookmarks < ActiveRecord::Migration[4.2]
     # deleted_at datetime. Because NULLs don't help in the index for our un-deleted
     # scenario (deleted_at == NULL) we have to coalesce those NULLs into the same
     # valid date. This lets us have a unique index when deleted_at is NULL.
-    ActiveRecord::Base.connection.execute(
+    connection.execute(
       "CREATE UNIQUE INDEX patient_bookmarks_uniqueness
       ON patient_bookmarks
       (patient_id, user_id, COALESCE(deleted_at, '1970-01-01'));"

data/db/migrate/20170608135553_create_functions_to_generate_secure_patient_id.rb

@@ -1,55 +1,11 @@
 class CreateFunctionsToGenerateSecurePatientId < ActiveRecord::Migration[5.0]
- def up
-    sql = <<-SQL.squish
-      CREATE OR REPLACE FUNCTION generate_secure_id(length integer default 24)
-        /*
-        Generates and returns a unique base 58 token of <length> length for use in for example
-        the obfuscation of database ids in URLs.
-        Note base58 tokens are case sensitive.
-        Example usage:
-          select generate_secure_id(24) #=> 0KPNXf4X5x1o6O4mXWE5MC9H
-        TC 8.6.2017
-        */
-        RETURNS text AS
-        $body$
-        SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789',
-                           ceil (random() * 62)::integer,
-                           1), '')
-        FROM   generate_series(1, length)
-        ;
-        $body$
-        LANGUAGE sql;
-    SQL
-    ActiveRecord::Base.connection.execute(sql)
-
-    sql = <<-SQL.squish
-    CREATE OR REPLACE FUNCTION generate_patient_secure_id()
-      /*
-        Generates and returns a unique base 58 token 24 characters long for use as a secure_id on
-        the Renalware patients table. If the generated token is in use already (very unlikely) it
-        retries until a unique one is generated.
-        Example usage:
-          select generate_patient_secure_id #=> 0KPNXf4X5x1o6O4mXWE5MC9H
-        TC 8.6.2017
-      */
-      RETURNS varchar AS $$
-      DECLARE
-      new_secure_id varchar;
-      BEGIN
-      LOOP
-        new_secure_id := generate_secure_id(24);
-        EXIT WHEN NOT EXISTS(select 1 from patients where 'secure_id' = new_secure_id);
-        RAISE NOTICE 'The generated secure_id % was already in use - now generating another', new_secure_id;
-      END LOOP;
-      RETURN new_secure_id;
-      END
-      $$ LANGUAGE plpgsql;
-    SQL
-    ActiveRecord::Base.connection.execute(sql)
+  def up
+    load_function("generate_secure_id_v01.sql")
+    load_function("generate_patient_secure_id_v01.sql")
   end
 
   def down
-    ActiveRecord::Base.connection.execute(
+    connection.execute(
       "DROP FUNCTION IF EXISTS generate_secure_id(integer); \
        DROP FUNCTION IF EXISTS generate_patient_secure_id();"
     )

data/db/migrate/20170705090219_create_refresh_all_materialized_views_fn.rb

@@ -1,44 +1,9 @@
 class CreateRefreshAllMaterializedViewsFn < ActiveRecord::Migration[5.0]
   def up
-    # Function to refresh all materialized views in all or a specified schema,
-    # optionally concurrently
-    # From https://github.com/frankhommers/RefreshAllMaterializedViews
-    sql = <<-SQL.squish
-      CREATE OR REPLACE FUNCTION
-      refresh_all_matierialized_views(_schema TEXT DEFAULT '*', _concurrently BOOLEAN DEFAULT false)
-      RETURNS INT AS $$
-        DECLARE
-          r RECORD;
-        BEGIN
-          RAISE NOTICE 'Refreshing materialized view(s) in % %',
-            CASE WHEN _schema = '*' THEN 'all schemas'
-            ELSE 'schema "'|| _schema || '"'
-            END,
-            CASE WHEN _concurrently
-            THEN 'concurrently'
-            ELSE '' END;
-          IF pg_is_in_recovery() THEN
-            RETURN 0;
-          ELSE
-            FOR r IN SELECT schemaname,
-                            matviewname FROM pg_matviews WHERE schemaname = _schema OR _schema = '*'
-            LOOP
-              RAISE NOTICE 'Refreshing materialized view "%"."%"', r.schemaname, r.matviewname;
-              EXECUTE 'REFRESH MATERIALIZED VIEW ' || CASE WHEN _concurrently THEN 'CONCURRENTLY '
-              ELSE '' END || '"' || r.schemaname || '"."' || r.matviewname || '"';
-            END LOOP;
-          END IF;
-          RETURN 1;
-        END
-      $$ LANGUAGE plpgsql;
-    SQL
-
-    ActiveRecord::Base.connection.execute(sql)
+    load_function("refresh_all_matierialized_views_v01.sql")
   end
 
   def down
-    ActiveRecord::Base.connection.execute(
-      "DROP FUNCTION refresh_all_matierialized_views(TEXT,BOOLEAN);"
-    )
+    connection.execute("DROP FUNCTION refresh_all_matierialized_views(TEXT,BOOLEAN);")
   end
 end

data/db/migrate/20170707110155_rename_access_plans_to_access_plan_types.rb

@@ -23,7 +23,7 @@ class RenameAccessPlansToAccessPlanTypes < ActiveRecord::Migration[5.0]
     add_foreign_key :access_plans, :users, column: :updated_by_id
 
     # There can only ever be one un-terminated plan per user - is the current one
-    ActiveRecord::Base.connection.execute(
+    connection.execute(
       "CREATE UNIQUE INDEX access_plan_uniqueness ON access_plans
       (patient_id, COALESCE(terminated_at, '1970-01-01'));"
     )

data/db/migrate/20170831142819_enable_crosstab_extension.rb

@@ -1,9 +1,9 @@
 class EnableCrosstabExtension < ActiveRecord::Migration[5.1]
   def up
-    ActiveRecord::Base.connection.execute("CREATE extension IF NOT EXISTS tablefunc;")
+    connection.execute("CREATE extension IF NOT EXISTS tablefunc;")
   end
 
   def down
-    ActiveRecord::Base.connection.execute("DROP extension IF EXISTS tablefunc;")
+    connection.execute("DROP extension IF EXISTS tablefunc;")
   end
 end

data/db/migrate/20170911133224_add_type_to_messaging_messages.rb

@@ -3,7 +3,7 @@ class AddTypeToMessagingMessages < ActiveRecord::Migration[5.1]
   def up
     add_column :messaging_messages, :type, :string, null: true
     add_index :messaging_messages, :type
-    ActiveRecord::Base.connection.execute(
+    connection.execute(
       "update messaging_messages set type = 'Renalware::Messaging::Internal::Message' where type is null;"
     )
     change_column_null(:messaging_messages, :type, false)

data/db/migrate/20170915115228_add_schedule_diurnal_period_id_to_hd_profiles.rb

@@ -2,7 +2,7 @@ class AddScheduleDiurnalPeriodIdToHDProfiles < ActiveRecord::Migration[5.1]
   def change
 
     #ActiveRecord::Base.clear_all_connections!
-    conn = ActiveRecord::Base.connection
+    conn = connection
 
     # Enable the intarray extension which is required if we want to index the days[] array
     # - see below

data/db/migrate/20171013145849_set_patients_secure_id.rb

@@ -6,7 +6,7 @@ class SetPatientsSecureId < ActiveRecord::Migration[5.1]
 
     reversible do |direction|
       direction.up do
-        ActiveRecord::Base.connection.execute(
+        connection.execute(
           "DROP FUNCTION IF EXISTS generate_secure_id(integer); \
            DROP FUNCTION IF EXISTS generate_patient_secure_id();"
         )

data/db/migrate/20171101121130_create_function_to_render_audit_view_as_json.rb

@@ -1,37 +1,10 @@
 class CreateFunctionToRenderAuditViewAsJson < ActiveRecord::Migration[5.1]
   def up
-    sql = <<-SQL.squish
-      CREATE OR REPLACE FUNCTION audit_view_as_json(view_name text)
-        /*
-        Converts the specified view into its json representation suitable for feeding for example
-        into jQuery datatables plugin, or creating a historical snapshot.
-        Example usage:
-          select audit_view_as_json('reporting_bone_audit')
-        TC 1.11.2017
-        */
-        RETURNS json
-        LANGUAGE 'plpgsql'
-        as $$
-        DECLARE result json;
-        BEGIN
-        EXECUTE format('
-        select row_to_json(t)
-          from (
-            select
-              current_timestamp as runat,
-              (select array_to_json(array_agg(row_to_json(d))
-            )
-          from (select * from %s) d) as data) t;
-          ', quote_ident(view_name)) into result;
-        return result;
-      END
-      $$;
-    SQL
-    ActiveRecord::Base.connection.execute(sql)
+    load_function("audit_view_as_json_v01.sql")
   end
 
   def down
-    ActiveRecord::Base.connection.execute(
+    connection.execute(
       "DROP FUNCTION IF EXISTS audit_view_as_json(text);"
     )
   end

data/db/migrate/20171127092158_create_function_to_import_practices.rb

@@ -1,123 +1,9 @@
 class CreateFunctionToImportPractices < ActiveRecord::Migration[5.0]
-
-  def down
-    ActiveRecord::Base.connection.execute(
-      "DROP FUNCTION IF EXISTS import_practices_csv(file text);"
-    )
-  end
-
   def up
-    sql = <<-SQL
-      CREATE OR REPLACE FUNCTION renalware.import_practices_csv(file text) RETURNS void AS $$
-      BEGIN
-      /*
-      Imports a practices.csv file created by parsing out an HSCOrgRefData_Full_xxxxx.xml file.
-      */
-      DROP TABLE IF EXISTS tmp_practices;
-
-      CREATE TEMP TABLE tmp_practices (
-        code text NOT NULL,
-        name text NOT NULL,
-        tel text,
-        street_1 text,
-        street_2 text,
-        street_3 text,
-        town text,
-        county text,
-        postcode text NOT NULL,
-        region text,
-        country_id integer,
-        active text NOT NULL,
-        CONSTRAINT tmp_practices_pkey PRIMARY KEY (code)
-      );
-
-      /* Import the CSV file into tmp_practices, ignoring the first row which is a header */
-      EXECUTE format ('COPY tmp_practices FROM %L DELIMITER %L CSV HEADER', file, ',');
-
-      /* Upsert practices */
-      WITH data(
-          code,
-          name,
-          telephone,
-          street_1,
-          street_2,
-          street_3,
-          town,
-          county,
-          postcode,
-          region,
-          country_id,
-          active)
-        AS (select * from tmp_practices)
-        , practice_changes AS (
-            INSERT INTO patient_practices (code, name, telephone, created_at, updated_at)
-            SELECT code, name, telephone, clock_timestamp(), clock_timestamp()
-            FROM data
-            ON CONFLICT (code) DO UPDATE
-              SET
-                name = excluded.name,
-                telephone = excluded.telephone,
-                updated_at = excluded.updated_at
-              RETURNING code, id
-          )
-
-      /* Upsert practice addresses */
-      INSERT INTO addresses (
-        addressable_type,
-        addressable_id,
-        street_1,
-        street_2,
-        street_3,
-        town,
-        county,
-        postcode,
-        region,
-        country_id,
-        created_at,
-        updated_at)
-      SELECT
-        'Renalware::Patients::Practice',
-        practice_changes.id,
-        street_1,
-        street_2,
-        street_3,
-        town,
-        county,
-        postcode,
-        region,
-        country_id,
-        CURRENT_TIMESTAMP,
-        CURRENT_TIMESTAMP
-        FROM data join practice_changes using(code)
-      ON CONFLICT (addressable_type, addressable_id) DO UPDATE
-        SET
-        street_1 = excluded.street_1,
-        street_2 = excluded.street_2,
-        street_3 = excluded.street_3,
-        town = excluded.town,
-        county = excluded.county,
-        postcode = excluded.postcode,
-        region = excluded.region,
-        country_id = excluded.country_id,
-        updated_at = clock_timestamp();
-
-      /* Update the deleted_at column of any practices which do not have an Active status_code */
-      UPDATE patient_practices AS p
-      SET deleted_at = CURRENT_TIMESTAMP
-      FROM tmp_practices AS tp
-      WHERE p.code = tp.code AND tp.active = 'false';
-
-      /* Set deleted_at tp NULL for active practices */
-      UPDATE patient_practices AS p
-      SET deleted_at = NULL
-      FROM tmp_practices AS tp
-      WHERE p.code = tp.code AND tp.active != 'false';
-
-      DROP TABLE tmp_practices;
+    load_function("import_practices_csv_v01.sql")
+  end
 
-      END;
-      $$ LANGUAGE plpgsql;
-    SQL
-    ActiveRecord::Base.connection.execute(sql)
+  def down
+    connection.execute("DROP FUNCTION IF EXISTS import_practices_csv(file text);")
   end
 end

data/db/migrate/20171127092359_create_fn_to_insert_gps.rb

@@ -1,145 +1,9 @@
 class CreateFnToInsertGps < ActiveRecord::Migration[5.0]
-
   def up
-    sql = <<-SQL
-      CREATE OR REPLACE FUNCTION import_gps_csv(file text) RETURNS void
-
-        AS $$
-        BEGIN
-        -- Imports a egpcur.csv.csv file created from ODS.
-        -- Returns counts of changed (insert/updated) and (soft) deleted rows.
-
-        DROP TABLE IF EXISTS tmp_gps_copy;
-
-        -- Create a tmp table to hold the ODS-defined standard 27 field format into which we will insert out CSV data
-        CREATE TEMP TABLE tmp_gps_copy (
-        code text NOT NULL,
-        name text NOT NULL,
-        unused3 text,
-        unused4 text,
-        street_1 text,
-        street_2 text,
-        street_3 text,
-        town text,
-        county text,
-        postcode text,
-        unused11 text,
-        unused12 text,
-        status text, -- A = Active B = Retired C = Closed P = Proposed
-        unused14 text,
-        unused15 text,
-        unused16 text,
-        unused17 text,
-        telephone text,
-        unused19 text,
-        unused20 text,
-        unused21 text,
-        amended_record_indicator text,
-        unused23 text,
-        unused24 text,
-        unused25 text,
-        unused26 text,
-        unused27 text,
-        CONSTRAINT tmp_gps_pkey PRIMARY KEY (code)
-        );
-
-        -- Import the CSV file into tmp_practices - note there is no CSV header in this file
-        EXECUTE format ('COPY tmp_gps_copy FROM %L DELIMITER %L CSV ', file, ',');
-
-        DROP TABLE IF EXISTS tmp_gps;
-        CREATE TEMP TABLE tmp_gps AS SELECT
-          code,
-          name,
-          telephone,
-          street_1,
-          street_2,
-          street_3,
-          town,
-          county,
-          postcode,
-          left(status,1) as status from tmp_gps_copy ;
-        ALTER TABLE tmp_gps ADD PRIMARY KEY (code);
-
-  RAISE NOTICE 'Calling cs_create_job(%)', (select status from tmp_gps limit 1);
-
-        -- Upsert GPs
-        WITH
-         data AS (select * from  tmp_gps),
-         gp_changes AS (
-          INSERT INTO renalware.patient_primary_care_physicians (code, name, telephone, practitioner_type, created_at, updated_at)
-          SELECT code, name, telephone, 'GP', clock_timestamp(), clock_timestamp()
-          FROM data
-          ON CONFLICT (code) DO UPDATE
-            SET
-             telephone = excluded.telephone,
-             name = excluded.name,
-             updated_at = excluded.updated_at
-            where (patient_primary_care_physicians.telephone) is distinct from (excluded.telephone)
-            RETURNING code, id
-           )
-
-        -- Upsert GP addresses
-        INSERT INTO renalware.addresses (
-          addressable_type,
-          addressable_id,
-          street_1,
-          street_2,
-          street_3,
-          town,
-          county,
-          postcode,
-          created_at,
-          updated_at)
-        SELECT
-          'Renalware::Patients::PrimaryCarePhysician' as addressable_type,
-          gps.id as addressable_id,
-          street_1,
-          street_2,
-          street_3,
-          town,
-          county,
-          postcode,
-          CURRENT_TIMESTAMP as created_at,
-          CURRENT_TIMESTAMP as updated_at
-          FROM data join patient_primary_care_physicians gps using(code)
-        ON CONFLICT (addressable_type, addressable_id) DO UPDATE
-          SET
-          street_1 = excluded.street_1,
-          street_2 = excluded.street_2,
-          street_3 = excluded.street_3,
-          town = excluded.town,
-          county = excluded.county,
-          postcode = excluded.postcode,
-          updated_at = clock_timestamp()
-          where (addresses.street_1, addresses.street_2, addresses.street_3)
-          is distinct from (excluded.street_1, excluded.street_2, excluded.street_3);
-
-        --GET DIAGNOSTICS changed_count = ROW_COUNT;
-
-        -- Update the deleted_at column of any gps which do not have an Active status_code
-        UPDATE renalware.patient_primary_care_physicians AS p
-        SET deleted_at = CURRENT_TIMESTAMP
-        FROM tmp_gps AS tp
-        WHERE p.code = tp.code AND tp.status IN ('C', 'P', 'B');
-
-        -- Un-delete any previously deleted GPs
-        UPDATE renalware.patient_primary_care_physicians AS gp
-        SET deleted_at = NULL
-        FROM tmp_gps
-        WHERE gp.code = tmp_gps.code AND tmp_gps.status IN ('A') AND gp.code NOT IN ('A');
-
-        --GET DIAGNOSTICS deleted_count = ROW_COUNT;
-        --select changed_count, deleted_count;
-        END;
-       $$ LANGUAGE plpgsql;
-    SQL
-
-    ActiveRecord::Base.connection.execute(sql)
+    load_function("import_gps_csv_v01.sql")
   end
 
-   def down
-    ActiveRecord::Base.connection.execute(
-      "DROP FUNCTION IF EXISTS import_gps_csv(file text);"
-    )
+  def down
+    connection.execute("DROP FUNCTION IF EXISTS import_gps_csv(file text);")
   end
 end