AJ-2008: json-based entities POC

core/src/main/resources/org/broadinstitute/dsde/rawls/liquibase/changelog.xml

@@ -125,6 +125,7 @@
     <include file="changesets/20240418_workspace_monitor_args.xml" relativeToChangelogFile="true"/>
     <include file="changesets/20240723_workspace_settings.xml" relativeToChangelogFile="true"/>
     <include file="changesets/20240820_submission_cost_cap_threshold.xml" relativeToChangelogFile="true"/>
+    <include file="changesets/20240910_entity_json_support.xml" relativeToChangelogFile="true"/>
     <include file="changesets/20240830_workflow_cost.xml" relativeToChangelogFile="true"/>
     <include file="changesets/20241106_streamline_entity_attr_temp_table_procedure.xml" relativeToChangelogFile="true"/>
     <include file="changesets/20241106_streamline_workspace_attr_temp_table_procedure.xml" relativeToChangelogFile="true"/>

core/src/main/resources/org/broadinstitute/dsde/rawls/liquibase/changesets/20240910_entity_json_support.xml

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog logicalFilePath="dummy" xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.29.xsd">
+
+    <!-- add the ENTITY.attributes JSON column -->
+    <changeSet logicalFilePath="dummy" author="davidan" id="add_attributes_col_to_entity">
+        <addColumn tableName="ENTITY">
+            <column name="attributes" type="JSON"/>
+        </addColumn>
+    </changeSet>
+
+    <!-- create the ENTITY_KEYS table -->
+    <changeSet logicalFilePath="dummy" author="davidan" id="create_table_entity_keys">
+        <createTable tableName="ENTITY_KEYS">
+            <column name="id" type="BIGINT UNSIGNED">
+                <constraints primaryKey="true"
+                             nullable="false"
+                             referencedTableName="ENTITY" referencedColumnNames="id"
+                             foreignKeyName="fk_entity_keys_entity_id" deleteCascade="true"/>
+            </column>
+            <column name="workspace_id" type="BINARY(16)">
+                <constraints nullable="false"
+                             referencedTableName="WORKSPACE" referencedColumnNames="id"
+                             foreignKeyName="fk_entity_keys_workspace_id" deleteCascade="true"/>
+            </column>
+            <column name="entity_type" type="VARCHAR(254)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="attribute_keys" type="JSON">
+                <constraints nullable="false"/>
+            </column>
+            <column name="last_updated" type="TIMESTAMP(3)">
+                <constraints nullable="false"/>
+            </column>
+        </createTable>
+        <createIndex indexName="idx_entity_keys_workspace_and_entity_type" tableName="ENTITY_KEYS" unique="false">
+            <column name="workspace_id"/>
+            <column name="entity_type"/>
+        </createIndex>
+        <createIndex indexName="idx_entity_keys_last_updated_desc" tableName="ENTITY_KEYS" unique="false">
+            <column name="last_updated" descending="true"/>
+        </createIndex>
+    </changeSet>
+
+    <!-- create the ENTITY triggers to populate ENTITY_KEYS -->
+    <changeSet logicalFilePath="dummy" author="davidan" id="entity_keys_triggers">
+        <sql stripComments="true" endDelimiter="~">
+            DROP TRIGGER IF EXISTS after_entity_insert ~
+            DROP TRIGGER IF EXISTS after_entity_update ~
+
+            CREATE TRIGGER after_entity_insert AFTER INSERT ON ENTITY
+                FOR EACH ROW
+                if new.attributes is not null then
+                    INSERT INTO ENTITY_KEYS
+                        (id, workspace_id, entity_type, attribute_keys, last_updated)
+                    VALUES
+                        (new.id, new.workspace_id, new.entity_type, JSON_KEYS(new.attributes), now(3));
+                end if ~
+
+            CREATE TRIGGER after_entity_update AFTER UPDATE ON ENTITY
+                FOR EACH ROW
+                BEGIN
+                    -- is this row soft-deleted?
+                    if old.deleted = 0 and new.deleted = 1 then
+                        DELETE FROM ENTITY_KEYS WHERE id = new.id;
+                    elseif new.attributes is not null then
+                        -- compare old keys to new keys; update the ENTITY_KEYS table only if they are different
+                        set @new_keys := JSON_KEYS(new.attributes);
+                        set @old_keys := JSON_KEYS(old.attributes);
+                        if JSON_LENGTH(@new_keys) != JSON_LENGTH(@old_keys) OR JSON_CONTAINS(@new_keys, @old_keys) = 0 then
+                            UPDATE ENTITY_KEYS SET attribute_keys=@new_keys, last_updated=now(3)
+                            WHERE id = new.id;
+                        end if;
+                    end if;
+                END ~
+        </sql>
+        <rollback>
+            DROP TRIGGER IF EXISTS after_entity_insert;
+            DROP TRIGGER IF EXISTS after_entity_update;
+        </rollback>
+    </changeSet>
+
+    <!-- create the ENTITY_REFS table -->
+    <changeSet logicalFilePath="dummy" author="davidan" id="create_table_entity_refs">
+        <createTable tableName="ENTITY_REFS">
+            <column name="from_id" type="BIGINT UNSIGNED">
+                <constraints nullable="false" />
+            </column>
+            <column name="to_id" type="BIGINT UNSIGNED">
+                <constraints nullable="false" />
+            </column>
+        </createTable>
+        <!-- index for lookups against to_id -->
+        <createIndex tableName="ENTITY_REFS" indexName="idx_to">
+            <column name="to_id" />
+        </createIndex>
+        <!-- unique constraint for from+to, which covers lookups against from_id -->
+        <addUniqueConstraint columnNames="from_id, to_id" constraintName="unq_from_to" tableName="ENTITY_REFS"/>
+    </changeSet>
+
+
+
+
+</databaseChangeLog>

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/DataAccess.scala

@@ -13,6 +13,7 @@ trait DataAccess
     with RawlsBillingProjectComponent
     with WorkspaceComponent
     with EntityComponent
+    with JsonEntityComponent
     with AttributeComponent
     with MethodConfigurationComponent
     with SubmissionComponent