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SQLite 3.41.0 and pearson correlation extension function (#106)

Browse Source 
* Build SQLite 3.41.0

* Update pivot_vtab

* Add Pearson correlation coefficient function extension, build

* Add an easy way to running test locally without Nodejs

* Use RSS sum to pick top2 processes for the report

* Try previous Ubuntu LTS as a workaround for Firefox worker not starting
This commit is contained in:
saaj
2023-03-04 22:51:25 +01:00
committed by GitHub
parent e4b117ffb9
commit 9c0103fd05
7 changed files with 89 additions and 35 deletions
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2
.github/workflows/test.yml vendored
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@@ -11,7 +11,7 @@ on:
jobs:
test:
name: Run tests
runs-on: ubuntu-latest
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- name: Use Node.js

24
Dockerfile.test Normal file
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@@ -0,0 +1,24 @@
# An easy way to run tests locally without Nodejs installed:
#
# docker build -t sqliteviz/test -f Dockerfile.test .
#
FROM node:12
RUN set -ex; \
apt update; \
apt install -y chromium firefox-esr; \
npm install -g npm@7
WORKDIR /tmp/build
COPY package.json package-lock.json ./
COPY lib lib
RUN npm install
COPY . .
RUN set -ex; \
sed -i 's/browsers: \[.*\],/browsers: ['"'FirefoxHeadlessTouch'"'],/' karma.conf.js
RUN npm run lint -- --no-fix && npm run test

4
lib/sql-js/README.md
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@@ -43,6 +43,8 @@ SQLite [miscellaneous extensions][3] included:
SQLite 3rd party extensions included:
1. [pivot_vtab][5] -- a pivot virtual table
2. `pearson` correlation coefficient function extension from [sqlean][21]
(which is part of [squib][20])
To ease the step to have working clone locally, the build is committed into
the repository.
@@ -99,3 +101,5 @@ described in [this message from SQLite Forum][12]:
[17]: https://sqlite.org/contrib/
[18]: https://sqlite.org/contrib//download/extension-functions.c?get=25
[19]: https://github.com/lana-k/sqliteviz/blob/master/tests/lib/database/sqliteExtensions.spec.js
[20]: https://github.com/mrwilson/squib/blob/master/pearson.c
[21]: https://github.com/nalgeon/sqlean/blob/incubator/src/pearson.c

2
lib/sql-js/benchmark/procpath/top2_rss.sql
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@@ -2,7 +2,7 @@ WITH one_time_pid_condition AS (
SELECT stat_pid
FROM record
GROUP BY 1
ORDER BY MAX(stat_rss) DESC
ORDER BY SUM(stat_rss) DESC
LIMIT 2
)
SELECT

5
lib/sql-js/configure.py
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@@ -8,7 +8,7 @@ from pathlib import Path
from urllib import request
amalgamation_url = 'https://sqlite.org/2022/sqlite-amalgamation-3390300.zip'
amalgamation_url = 'https://sqlite.org/2023/sqlite-amalgamation-3410000.zip'
# Extension-functions
# ===================
@@ -28,7 +28,8 @@ extension_urls = (
('https://sqlite.org/src/raw/09f967dc?at=decimal.c', 'sqlite3_decimal_init'),
# Third-party extension
# =====================
('https://github.com/jakethaw/pivot_vtab/raw/08ab0797/pivot_vtab.c', 'sqlite3_pivotvtab_init'),
('https://github.com/jakethaw/pivot_vtab/raw/9323ef93/pivot_vtab.c', 'sqlite3_pivotvtab_init'),
('https://github.com/nalgeon/sqlean/raw/95e8d21a/src/pearson.c', 'sqlite3_pearson_init'),
)
sqljs_url = 'https://github.com/sql-js/sql.js/archive/refs/tags/v1.7.0.zip'

BIN
lib/sql-js/dist/sql-wasm.wasm vendored
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87
tests/lib/database/sqliteExtensions.spec.js
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@@ -160,39 +160,39 @@ describe('SQLite extensions', function () {
it('supports transitive_closure', async function () {
const actual = await db.execute(`
CREATE TABLE node(
node_id INTEGER NOT NULL PRIMARY KEY,
parent_id INTEGER,
name VARCHAR(127),
FOREIGN KEY (parent_id) REFERENCES node(node_id)
);
CREATE INDEX node_parent_id_idx ON node(parent_id);
CREATE VIRTUAL TABLE node_closure USING transitive_closure(
tablename = "node",
idcolumn = "node_id",
parentcolumn = "parent_id"
node_id INTEGER NOT NULL PRIMARY KEY,
parent_id INTEGER,
name VARCHAR(127),
FOREIGN KEY (parent_id) REFERENCES node(node_id)
);
CREATE INDEX node_parent_id_idx ON node(parent_id);
INSERT INTO node VALUES
(1, NULL, 'tests'),
(2, 1, 'lib'),
(3, 2, 'database'),
(4, 2, 'utils'),
(5, 2, 'storedQueries.spec.js'),
(6, 3, '_sql.spec.js'),
(7, 3, '_statements.spec.js'),
(8, 3, 'database.spec.js'),
(9, 3, 'sqliteExtensions.spec.js'),
(10, 4, 'fileIo.spec.js'),
(11, 4, 'time.spec.js');
CREATE VIRTUAL TABLE node_closure USING transitive_closure(
tablename = "node",
idcolumn = "node_id",
parentcolumn = "parent_id"
);
SELECT name
FROM node
WHERE node_id IN (
SELECT nc.id
FROM node_closure AS nc
WHERE nc.root = 2 AND nc.depth = 2
);
INSERT INTO node VALUES
(1, NULL, 'tests'),
(2, 1, 'lib'),
(3, 2, 'database'),
(4, 2, 'utils'),
(5, 2, 'storedQueries.spec.js'),
(6, 3, '_sql.spec.js'),
(7, 3, '_statements.spec.js'),
(8, 3, 'database.spec.js'),
(9, 3, 'sqliteExtensions.spec.js'),
(10, 4, 'fileIo.spec.js'),
(11, 4, 'time.spec.js');
SELECT name
FROM node
WHERE node_id IN (
SELECT nc.id
FROM node_closure AS nc
WHERE nc.root = 2 AND nc.depth = 2
);
`)
expect(actual.values).to.eql({
name: [
@@ -293,7 +293,7 @@ describe('SQLite extensions', function () {
it('supports decimal', async function () {
const actual = await db.execute(`
select
SELECT
decimal_add(decimal('0.1'), decimal('0.2')) "add",
decimal_sub(0.2, 0.1) sub,
decimal_mul(power(2, 69), 2) mul,
@@ -430,4 +430,29 @@ describe('SQLite extensions', function () {
]
})
})
it('supports pearson', async function () {
const actual = await db.execute(`
CREATE TABLE dataset(x REAL, y REAL, z REAL);
INSERT INTO dataset VALUES
(5,3,3.2), (5,6,4.3), (5,9,5.4),
(10,3,4), (10,6,3.8), (10,9,3.6),
(15,3,4.8), (15,6,4), (15,9,3.5);
SELECT
pearson(x, x) xx,
pearson(x, y) xy,
abs(-0.12666 - pearson(x, z)) < 0.00001 xz,
pearson(y, x) yx,
pearson(y, y) yy,
abs(0.10555 - pearson(y, z)) < 0.00001 yz,
abs(-0.12666 - pearson(z, x)) < 0.00001 zx,
abs(0.10555 - pearson(z, y)) < 0.00001 zy,
pearson(z, z) zz
FROM dataset;
`)
expect(actual.values).to.eql({
xx: [1], xy: [0], xz: [1], yx: [0], yy: [1], yz: [1], zx: [1], zy: [1], zz: [1]
})
})
})