Renamed 'overlord' to 'core' as it is a more obvious name.

README.md

@@ -16,7 +16,7 @@ Each JSON schema is used to generate its a separate SQLite file that contains on
 
 ### File contents
 
-Each SQLite file contains a `primary` table.
+Each SQLite file contains a `core` table.
 Each row corresponds to an indexed object in **gypsum**.
 The table will have at least the following fields, all of which have the `TEXT` type:
 
@@ -37,17 +37,17 @@ The table contains at least the `_key` column (same as above), with one or more
 If the items are booleans, integers, strings or numbers, the table contains exactly one `item` column of the corresponding type;
 if the items are objects, the table contains columns corresponding to the properties of the object.
 
-For `primary` and `multi_<FIELD>` tables, we generate an index for each column.
+For `core` and `multi_<FIELD>` tables, we generate an index for each column.
 Clients can perform most complex queries efficiently with the relevant inner joins.
 
 ### Table generation rules
 
 Each JSON schema is used to generate a SQLite table according to some simple rules:
 
 - The schema must be a top-level `"type": "object"`.
-- An `integer` property is converted to an `INTEGER` field on the `primary` table.
-- A `boolean` property is converted to an `INTEGER` field on the `primary` table.
-- A `number` property is converted to a `REAL` field on the `primary` table. 
+- An `integer` property is converted to an `INTEGER` field on the `core` table.
+- A `boolean` property is converted to an `INTEGER` field on the `core` table.
+- A `number` property is converted to a `REAL` field on the `core` table. 
 - A `string` property is usually converted to a `TEXT` field.
   However, if its `_attributes` contain `"free_text"`, it will instead be converted into a column of `free_text`.
 - An `array` property is converted to a separate `multi_<FIELD>` table, where `<FIELD>` is the name of the property.

src/converterFromSchema.js

@@ -1,5 +1,5 @@
 export function converterFromSchema(schema) {
-    let overlord_inserts = [];
+    let core_inserts = [];
     let free_text_inserts = [];
     let array_simple = {};
     let array_complex = {};
@@ -9,7 +9,7 @@ export function converterFromSchema(schema) {
             if ("_attributes" in x && x._attributes.indexOf("free_text") >= 0) {
                 free_text_inserts.push(n);
             } else {
-                overlord_inserts.push(n);
+                core_inserts.push(n);
             }
 
         } else if (x.type == "array") {
@@ -21,7 +21,7 @@ export function converterFromSchema(schema) {
             }
 
         } else {
-            overlord_inserts.push(n);
+            core_inserts.push(n);
         }
     }
 
@@ -32,14 +32,14 @@ export function converterFromSchema(schema) {
         {
             let current_values = [key, project, asset, version, path, object];
             let current_columns = ["_key", "_project", "_asset", "_version", "_path", "_object"];
-            for (const y of overlord_inserts) {
+            for (const y of core_inserts) {
                 if (y in metadata) {
                     current_columns.push(y);
                     current_values.push(metadata[y]);
                 }
             }
             statements.push({ 
-                statement: `INSERT INTO overlord (${current_columns}) VALUES(${Array(current_columns.length).fill('?')});`,
+                statement: `INSERT INTO core (${current_columns}) VALUES(${Array(current_columns.length).fill('?')});`,
                 parameters: current_values
             });
         }

src/initializeFromSchema.js

@@ -54,10 +54,10 @@ export function initializeFromSchema(schema) {
         }
     }
 
-    commands.push("DROP TABLE IF EXISTS overlord;");
-    commands.push(`CREATE TABLE overlord (_key TEXT PRIMARY_KEY, ${main_table.map(y => y[0] + " " + y[1])});`);
+    commands.push("DROP TABLE IF EXISTS core;");
+    commands.push(`CREATE TABLE core (_key TEXT PRIMARY_KEY, ${main_table.map(y => y[0] + " " + y[1])});`);
     for (const y of main_table) {
-        commands.push(`CREATE INDEX index_overlord_${y[0]} ON overlord(${y[0]});`);
+        commands.push(`CREATE INDEX index_core_${y[0]} ON core(${y[0]});`);
     }
 
     commands.push("DROP TABLE IF EXISTS free_text;");

src/wiperFromSchema.js

@@ -1,5 +1,5 @@
 export function wiperFromSchema(schema) {
-    const tables = new Set(["overlord"]);
+    const tables = new Set(["core"]);
 
     for (const [n, x] of Object.entries(schema.properties)) {
         if (x.type == "string") {
@@ -12,7 +12,7 @@ export function wiperFromSchema(schema) {
     }
 
     return (project, asset, version) => {
-        let selector = "CREATE TEMP TABLE tmp_deleted AS SELECT _key FROM overlord WHERE _project = ?";
+        let selector = "CREATE TEMP TABLE tmp_deleted AS SELECT _key FROM core WHERE _project = ?";
         let params = [ project ];
 
         if (asset !== null) {

tests/converterFromSchema.test.js

@@ -21,7 +21,7 @@ test("converterFromSchema works as expected", () => {
     res = db.prepare("SELECT COUNT(*) FROM multi_taxonomy_id").all();
     expect(res[0]["COUNT(*)"]).toBe(2);
 
-    res = db.prepare("SELECT COUNT(*) FROM overlord").all();
+    res = db.prepare("SELECT COUNT(*) FROM core").all();
     expect(res[0]["COUNT(*)"]).toBe(1);
 
     res = db.prepare("SELECT COUNT(*) FROM free_text").all();

tests/initializeFromSchema.test.js

@@ -9,7 +9,7 @@ test("initializerFromSchema works as expected", () => {
 
     let listing = db.pragma("table_list");
     let available = listing.filter(y => y.type == "table" || y.type == "virtual").map(y => y.name);
-    expect(available.indexOf("overlord") >= 0).toBe(true);
+    expect(available.indexOf("core") >= 0).toBe(true);
     expect(available.indexOf("free_text") >= 0).toBe(true);
     expect(available.indexOf("multi_sources") >= 0).toBe(true);
     expect(available.indexOf("multi_genome") >= 0).toBe(true);

tests/scripts/handleAction.test.js

@@ -28,7 +28,7 @@ const asset = "zeisel-brain-2015";
 const version = "2023-12-14";
 
 function extract_count(handle) {
-    let res = handle.prepare("SELECT COUNT(*) FROM overlord").all();
+    let res = handle.prepare("SELECT COUNT(*) FROM core").all();
     return res[0]["COUNT(*)"];
 }
 
@@ -74,7 +74,7 @@ test("handleAction works correctly when deleting a version", async () => {
     // Injecting a bunch of crap.
     for (const db of Object.values(handles)) {
         for (const key of ["foo", "bar"]) {
-            db.prepare("INSERT INTO overlord(_key, _project, _asset) VALUES(?,?,?)").run(key, project, asset);
+            db.prepare("INSERT INTO core(_key, _project, _asset) VALUES(?,?,?)").run(key, project, asset);
         }
     }
     expect(extract_count(handles.bioconductor)).toEqual(2);
@@ -98,8 +98,8 @@ test("handleAction works correctly when deleting an asset", async () => {
 
     // Injecting a bunch of crap.
     for (const db of Object.values(handles)) {
-        db.prepare("INSERT INTO overlord(_key, _project, _asset) VALUES(?,?,?)").run("YAY", project, asset);
-        db.prepare("INSERT INTO overlord(_key, _project, _asset) VALUES(?,?,?)").run("YAY2", project, asset + "2");
+        db.prepare("INSERT INTO core(_key, _project, _asset) VALUES(?,?,?)").run("YAY", project, asset);
+        db.prepare("INSERT INTO core(_key, _project, _asset) VALUES(?,?,?)").run("YAY2", project, asset + "2");
     }
     expect(extract_count(handles.bioconductor)).toEqual(2);
     expect(extract_count(handles.scRNAseq)).toEqual(2);
@@ -119,8 +119,8 @@ test("handleAction works correctly when deleting a project", async () => {
 
     // Injecting a bunch of crap.
     for (const db of Object.values(handles)) {
-        db.prepare("INSERT INTO overlord(_key, _project, _asset) VALUES(?,?,?)").run("YAY", project, asset);
-        db.prepare("INSERT INTO overlord(_key, _project, _asset) VALUES(?,?,?)").run("YAY2", project, asset + "2");
+        db.prepare("INSERT INTO core(_key, _project, _asset) VALUES(?,?,?)").run("YAY", project, asset);
+        db.prepare("INSERT INTO core(_key, _project, _asset) VALUES(?,?,?)").run("YAY2", project, asset + "2");
     }
     expect(extract_count(handles.bioconductor)).toEqual(2);
     expect(extract_count(handles.scRNAseq)).toEqual(2);

tests/scripts/indexVersion.test.js

@@ -18,9 +18,9 @@ test("indexAction works correctly", async () => {
     let statements = await indexVersion(project, asset, version, cv, cc);
 
     expect(statements.bioconductor.length).toBeGreaterThan(1);
-    expect(statements.bioconductor[0].statement).toMatch("overlord");
+    expect(statements.bioconductor[0].statement).toMatch("core");
     expect(statements.bioconductor[1].statement).toMatch("free_text");
 
     expect(statements.scRNAseq.length).toBeGreaterThan(0);
-    expect(statements.bioconductor[0].statement).toMatch("overlord");
+    expect(statements.bioconductor[0].statement).toMatch("core");
 })

tests/wiperFromSchema.test.js

@@ -25,7 +25,7 @@ test("wiperFromSchema works as expected", () => {
     res = db.prepare("SELECT COUNT(*) FROM multi_taxonomy_id").all();
     expect(res[0]["COUNT(*)"]).toBe(3);
 
-    res = db.prepare("SELECT COUNT(*) FROM overlord").all();
+    res = db.prepare("SELECT COUNT(*) FROM core").all();
     expect(res[0]["COUNT(*)"]).toBe(2);
 
     res = db.prepare("SELECT COUNT(*) FROM free_text").all();
@@ -43,7 +43,7 @@ test("wiperFromSchema works as expected", () => {
     res = db.prepare("SELECT COUNT(*) FROM multi_taxonomy_id").all();
     expect(res[0]["COUNT(*)"]).toBe(1);
 
-    res = db.prepare("SELECT COUNT(*) FROM overlord").all();
+    res = db.prepare("SELECT COUNT(*) FROM core").all();
     expect(res[0]["COUNT(*)"]).toBe(1);
 
     res = db.prepare("SELECT COUNT(*) FROM free_text").all();