Adding schema initialization and explicit refs

hms-dbmi · Jun 13, 2024 · e8d6253 · e8d6253
1 parent 1ccab83
commit e8d6253
Showing 1 changed file with 25 additions and 23 deletions.
diff --git a/db/schema.sql b/db/schema.sql
@@ -1,4 +1,6 @@
-CREATE TABLE dataset (
+CREATE schema dict;
+
+CREATE TABLE dict.dataset (
     DATASET_ID INT GENERATED ALWAYS AS IDENTITY,
     REF VARCHAR(512) NOT NULL,
     FULL_NAME VARCHAR(512) NOT NULL,
@@ -8,16 +10,16 @@ CREATE TABLE dataset (
     UNIQUE (REF)
 );
 
-CREATE TABLE dataset_meta (
+CREATE TABLE dict.dataset_meta (
     DATASET_META_ID INT GENERATED ALWAYS AS IDENTITY,
     DATASET_ID INT NOT NULL,
     KEY VARCHAR(256) NOT NULL,
     VALUE TEXT NOT NULL,
     UNIQUE (KEY, DATASET_ID),
-    CONSTRAINT fk_study FOREIGN KEY(DATASET_ID) REFERENCES dataset(DATASET_ID)
+    CONSTRAINT fk_study FOREIGN KEY(DATASET_ID) REFERENCES dict.dataset(DATASET_ID)
 );
 
-CREATE TABLE consent (
+CREATE TABLE dict.consent (
     CONSENT_ID INT GENERATED ALWAYS AS IDENTITY,
     DATASET_ID INT NOT NULL,
     CONSENT_CODE VARCHAR(512) NOT NULL,
@@ -27,7 +29,7 @@ CREATE TABLE consent (
     UNIQUE (CONSENT_CODE, DATASET_ID)
 );
 
-CREATE TABLE concept_node (
+CREATE TABLE dict.concept_node (
     CONCEPT_NODE_ID INT GENERATED ALWAYS AS IDENTITY,
     DATASET_ID INT NOT NULL,
     NAME VARCHAR(512) NOT NULL,
@@ -36,21 +38,21 @@ CREATE TABLE concept_node (
     CONCEPT_PATH VARCHAR(10000) NOT NULL DEFAULT 'INVALID',
     PARENT_ID INT,
     PRIMARY KEY (CONCEPT_NODE_ID),
-    CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES CONCEPT_NODE(CONCEPT_NODE_ID),
-    CONSTRAINT fk_study FOREIGN KEY (DATASET_ID) REFERENCES dataset(DATASET_ID)
+    CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES dict.CONCEPT_NODE(CONCEPT_NODE_ID),
+    CONSTRAINT fk_study FOREIGN KEY (DATASET_ID) REFERENCES dict.dataset(DATASET_ID)
 );
-CREATE UNIQUE INDEX concept_node_concept_path_idx ON CONCEPT_NODE (md5(CONCEPT_PATH));
+CREATE UNIQUE INDEX concept_node_concept_path_idx ON dict.CONCEPT_NODE (md5(CONCEPT_PATH));
 
-CREATE TABLE concept_node_meta (
+CREATE TABLE dict.concept_node_meta (
     CONCEPT_NODE_META_ID INT GENERATED ALWAYS AS IDENTITY,
     CONCEPT_NODE_ID INT NOT NULL,
     KEY VARCHAR(256) NOT NULL,
     VALUE TEXT NOT NULL,
     PRIMARY KEY (CONCEPT_NODE_META_ID),
     UNIQUE (KEY, CONCEPT_NODE_ID),
-    CONSTRAINT fk_CONCEPT_NODE FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES CONCEPT_NODE(CONCEPT_NODE_ID)
+    CONSTRAINT fk_CONCEPT_NODE FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.CONCEPT_NODE(CONCEPT_NODE_ID)
 );
-CREATE TABLE facet_category (
+CREATE TABLE dict.facet_category (
     FACET_CATEGORY_ID INT GENERATED ALWAYS AS IDENTITY,
     NAME VARCHAR(512) NOT NULL,
     DISPLAY VARCHAR(512) NOT NULL,
@@ -59,7 +61,7 @@ CREATE TABLE facet_category (
     UNIQUE (NAME)
 );
 
-CREATE TABLE facet (
+CREATE TABLE dict.facet (
     FACET_ID INT GENERATED ALWAYS AS IDENTITY,
     FACET_CATEGORY_ID INT NOT NULL,
     NAME VARCHAR(512) NOT NULL,
@@ -68,41 +70,41 @@ CREATE TABLE facet (
     PARENT_ID INT,
     PRIMARY KEY (FACET_ID),
     UNIQUE (NAME, FACET_CATEGORY_ID),
-    CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES facet(FACET_ID),
-    CONSTRAINT fk_category FOREIGN KEY (FACET_CATEGORY_ID) REFERENCES facet_category(FACET_CATEGORY_ID)
+    CONSTRAINT fk_parent FOREIGN KEY (PARENT_ID) REFERENCES dict.facet(FACET_ID),
+    CONSTRAINT fk_category FOREIGN KEY (FACET_CATEGORY_ID) REFERENCES dict.facet_category(FACET_CATEGORY_ID)
 );
 
-CREATE TABLE facet_meta (
+CREATE TABLE dict.facet_meta (
     FACET_META_ID INT GENERATED ALWAYS AS IDENTITY,
     FACET_ID INT NOT NULL,
     KEY VARCHAR(256) NOT NULL,
     VALUE TEXT NOT NULL,
     UNIQUE (KEY, FACET_ID),
-    CONSTRAINT fk_facet FOREIGN KEY(FACET_ID) REFERENCES facet(FACET_ID)
+    CONSTRAINT fk_facet FOREIGN KEY(FACET_ID) REFERENCES dict.facet(FACET_ID)
 );
 
-CREATE TABLE facet_category_meta (
+CREATE TABLE dict.facet_category_meta (
     FACET_CATEGORY_META_ID INT GENERATED ALWAYS AS IDENTITY,
     FACET_CATEGORY_ID INT NOT NULL,
     KEY VARCHAR(256) NOT NULL,
     VALUE TEXT NOT NULL,
     UNIQUE (KEY, FACET_CATEGORY_ID),
-    CONSTRAINT fk_facet_category FOREIGN KEY(FACET_CATEGORY_ID) REFERENCES facet_category(FACET_CATEGORY_ID)
+    CONSTRAINT fk_facet_category FOREIGN KEY(FACET_CATEGORY_ID) REFERENCES dict.facet_category(FACET_CATEGORY_ID)
 );
 
-CREATE TABLE facet__concept_node (
+CREATE TABLE dict.facet__concept_node (
     FACET__CONCEPT_NODE_ID INT GENERATED ALWAYS AS IDENTITY,
     FACET_ID INT NOT NULL,
     CONCEPT_NODE_ID INT NOT NULL,
     PRIMARY KEY (FACET__CONCEPT_NODE_ID),
     UNIQUE (FACET_ID, CONCEPT_NODE_ID),
-    CONSTRAINT fk_facet FOREIGN KEY (FACET_ID) REFERENCES facet(FACET_ID),
-    CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES concept_node(CONCEPT_NODE_ID)
+    CONSTRAINT fk_facet FOREIGN KEY (FACET_ID) REFERENCES dict.facet(FACET_ID),
+    CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.concept_node(CONCEPT_NODE_ID)
 );
 
 -- Commenting out because I don't remember what these do.
 
---CREATE TABLE harmonized_concept_node (
+--CREATE TABLE dict.harmonized_concept_node (
 --    HARMONIZED_CONCEPT_NODE_ID INT GENERATED ALWAYS AS IDENTITY,
 --    NAME VARCHAR(512) NOT NULL,
 --    DISPLAY VARCHAR(512) NOT NULL,
@@ -113,7 +115,7 @@ CREATE TABLE facet__concept_node (
 --);
 --CREATE UNIQUE INDEX harmonized_concept_node_concept_path_idx ON harmonized_concept_node(md5(CONCEPT_PATH));
 --
---CREATE TABLE harmonized_concept_node__concept_node (
+--CREATE TABLE dict.harmonized_concept_node__concept_node (
 --    HARMONIZED_CONCEPT_NODE__CONCEPT_NODE INT GENERATED ALWAYS AS IDENTITY,
 --    HARMONIZED_CONCEPT_NODE_ID INT NOT NULL,
 --    CONCEPT_NODE_ID INT NOT NULL,