Add PG extension AGE (#18)

* add extension AGE * add notebooks * update docker-compose files
QPod · Apr 15, 2024 · 0312971 · 0312971
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diff --git a/README.md b/README.md
@@ -19,5 +19,6 @@ Building blocks for the following big data project use cases are supported in th
 
 - [Flink / Spark](https://hub.docker.com/r/qpod/bigdata)
 - [Kafka](https://hub.docker.com/r/qpod/kafka)
-- [Elasticsearch](https://hub.docker.com/r/qpod/elasticsearch)
+- [Postgresql with Extensions](https://hub.docker.com/r/qpod/postgres-ext): including pgvector, age, and [many others](https://github.com/QPod/lab-data/blob/main/docker_postgres/rootfs/opt/utils/install_list_pgext.tpl.apt)
 - [GreenplumDB](https://hub.docker.com/r/qpod/greenplum)
+- [Elasticsearch](https://hub.docker.com/r/qpod/elasticsearch)
diff --git a/docker_greenplum/example/gpdb-single-node/docker-compose.yml b/docker_greenplum/example/gpdb-single-node/docker-compose.yml
@@ -1,5 +1,3 @@
-version: "3"
-
 networks:
   greenplum:
     ipam:

diff --git a/docker_greenplum/example/gpdb-single-vm/docker-compose.yml b/docker_greenplum/example/gpdb-single-vm/docker-compose.yml
@@ -1,5 +1,3 @@
-version: "3"
-
 networks:
   greenplum:
     ipam:

diff --git a/docker_kafka_confluent/example/kafka-standalone-bitnami/docker-compose.yml b/docker_kafka_confluent/example/kafka-standalone-bitnami/docker-compose.yml
@@ -1,5 +1,3 @@
-version: "3"
-
 # Standalone kraft mode, ref: https://github.com/bitnami/containers/tree/main/bitnami/kafka#kafka-without-zookeeper-kraft
 # Note: the volume folder read/write permission is required for uid 1001 and gid 1000. use the command below for debug:
 # `KAFKA_DATA_DIR="/data/database/kafka-bitnami/broker" && mkdir -pv $KAFKA_DATA_DIR && chmod -R ugo+rws $KAFKA_DATA_DIR`

diff --git a/docker_kafka_confluent/example/kafka-standalone-confluent/docker-compose.yml b/docker_kafka_confluent/example/kafka-standalone-confluent/docker-compose.yml
@@ -1,5 +1,3 @@
-version: '3'
-
 ## Standalone kraft mode - confluent kafka: https://github.com/confluentinc/cp-all-in-one/blob/7.3.0-post/cp-all-in-one-kraft/docker-compose.yml
 # Note: the volume folder read/write permission is required for uid 1001 and gid 1000. use the command below for debug:
 # `KAFKA_DATA_DIR="/data/database/kafka-bitnami/broker" && mkdir -pv $KAFKA_DATA_DIR && chmod -R ugo+rws $KAFKA_DATA_DIR`

diff --git a/docker_postgres/README.md b/docker_postgres/README.md
diff --git a/docker_postgres/demo/docker-compose.yml b/docker_postgres/demo/docker-compose.yml
@@ -0,0 +1,26 @@
+services:
+  db-postgres:
+  # su postgres && psql -d casdoor -U pg-casdoor-username
+      image: qpod0dev/postgres-ext
+      container_name: db-postgres
+      environment:
+        POSTGRES_DB: postgres
+        POSTGRES_USER: postgres
+        POSTGRES_PASSWORD: postgres
+
+  svc-jupyter:
+      image: quay.io/jupyter/minimal-notebook
+      depends_on:
+        - db-postgres
+      container_name: dev-jupyter
+      hostname: jupyter
+      user: root
+      environment:
+        NB_USER: root
+        NB_UID: 0
+        NB_GID: 0
+      ports:
+        - 8888:8888
+      volumes:
+        - "./:/home/root/work"
+      command: ["start-notebook.py", "--allow-root"]
diff --git a/docker_postgres/demo/test-apache-age.ipynb b/docker_postgres/demo/test-apache-age.ipynb
@@ -0,0 +1,106 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0e5737ed-ad83-4902-b551-ddd413f13475",
+   "metadata": {},
+   "source": [
+    "# Example - Using Python to connect to PG Apache AGE\n",
+    "\n",
+    "- reference: https://age.apache.org/getstarted/quickstart\n",
+    "- to install `apache-age-python`, code compile is currently required:\n",
+    "\n",
+    "```shell\n",
+    "sudo apt-get -y install gcc libpq-dev \"postgresql-client-${VER_PG}\"\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c0fa8e36-c263-4f95-b715-670ee760167d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! pip install apache-age-python"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1700acf5-8cc6-495a-ab7d-44115cdc7b94",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import age\n",
+    "import psycopg2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dac7a486-6fc8-43f5-88f9-ed57d507becb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "conn = psycopg2.connect(host=\"db-postgres\", port=\"5432\", dbname=\"postgres\", user=\"postgres\", password=\"postgres\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "759fe54a-7897-4eaa-a304-ff9d084c0704",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DSN = \"host=db-postgres port=5432 dbname=postgres user=postgres password=postgres\"\n",
+    "TEST_GRAPH_NAME = 'agens'\n",
+    "\n",
+    "conn = age.connect(dsn=DSN, graph=TEST_GRAPH_NAME)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "56c19b14-aaa5-4d73-b049-88f51fb983e6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cursor = conn.execCypher(\"CREATE (n:Person {name: %s, title: 'Developer'}) RETURN n\", params=('Andy',))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "affae3fa-bad0-4685-a05b-fb689287fce3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from age.models import Vertex\n",
+    "for row in cursor:\n",
+    "    print(\"Vertex: %s , Type: %s \" % (Vertex, type(row[0])))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docker_postgres/demo/test-pgvector.ipynb b/docker_postgres/demo/test-pgvector.ipynb
@@ -0,0 +1,163 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0e5737ed-ad83-4902-b551-ddd413f13475",
+   "metadata": {},
+   "source": [
+    "# Example - Using Python to connect to PG vector\n",
+    "\n",
+    "https://github.com/pgvector/pgvector-python/blob/master/examples/openai_embeddings.py"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c0fa8e36-c263-4f95-b715-670ee760167d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! pip install psycopg[binary] pgvector"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1700acf5-8cc6-495a-ab7d-44115cdc7b94",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pgvector.psycopg import register_vector\n",
+    "import psycopg"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dac7a486-6fc8-43f5-88f9-ed57d507becb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "conn = psycopg.connect(\n",
+    "    conninfo='postgresql://postgres:postgres@db-postgres/postgres',\n",
+    "    autocommit=True\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9e399b5c-e11b-4fd9-b430-7774d2bb8457",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "conn.execute('CREATE EXTENSION IF NOT EXISTS vector')\n",
+    "register_vector(conn)\n",
+    "conn.execute('DROP TABLE IF EXISTS documents')\n",
+    "conn.execute('CREATE TABLE documents (id bigserial PRIMARY KEY, content text, embedding vector(1536))')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "36c139e8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "def get_embeddings(inputs: list):\n",
+    "    dimensions = 1536\n",
+    "    embeddings = [np.random.rand(dimensions) for _ in inputs]\n",
+    "    return embeddings\n",
+    "\n",
+    "# The real code should by something like:\n",
+    "# from openai import OpenAI\n",
+    "# OPENAI_API_KEY=\"*\"\n",
+    "# client = OpenAI(api_key=OPENAI_API_KEY)\n",
+    "# response = client.embeddings.create(input=input, model='text-embedding-3-small')\n",
+    "# embeddings = [v.embedding for v in response.data]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b52db809-d008-448a-99bd-9db57dc35218",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "inputs = [\n",
+    "    'The dog is barking',\n",
+    "    'The cat is purring',\n",
+    "    'The bear is growling'\n",
+    "]\n",
+    "\n",
+    "embeddings = get_embeddings(inputs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dff8234a-4bf2-4abc-8d3f-68a233225792",
+   "metadata": {},
+   "source": [
+    "## Insert doc contents and embeddings into DB table"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b507cff0-dae1-42ea-b71b-c8f230474cb0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for content, embedding in zip(inputs, embeddings):\n",
+    "    conn.execute('INSERT INTO documents (content, embedding) VALUES (%s, %s)', (content, embedding))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c7b240ae-1d24-45a7-b96a-de89f50f0c14",
+   "metadata": {},
+   "source": [
+    "## Query DB table using embedding"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "65391dfc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "document_id = 1\n",
+    "neighbors = conn.execute(\n",
+    "    'SELECT content FROM documents WHERE id != %(id)s ORDER BY embedding <=> (SELECT embedding FROM documents WHERE id = %(id)s) LIMIT 5',\n",
+    "    {'id': document_id}\n",
+    ").fetchall()\n",
+    "for neighbor in neighbors:\n",
+    "    print(neighbor[0])"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docker_postgres/postgres-ext.Dockerfile b/docker_postgres/postgres-ext.Dockerfile
@@ -9,14 +9,14 @@ LABEL maintainer="[email protected]"
 COPY rootfs /
 
 RUN set -x && . /opt/utils/script-utils.sh && . /opt/utils/script-setup-pg_ext_mirror.sh \
+ ## Generate a package list based on PG_MAJOR version
  && apt-get update && apt-get install -y gettext \
  && envsubst < /opt/utils/install_list_pgext.tpl.apt > /opt/utils/install_list_pgext.apt \
  && rm -rf /opt/utils/install_list_pgext.tpl.apt \
- && echo "To install PG extensions: $(cat /opt/utils/install_list_pgext.apt)" \
- && install_apt /opt/utils/install_list_pgext.apt \
+ ## Install extensions
  && . /opt/utils/script-setup-pg_ext.sh \
- && ls -alh /usr/share/postgresql/*/extension/*.control | sort \
- && echo "include_dir='./conf.d'" >> /var/lib/postgresql/data/postgresql.conf \
+ ## Hack: fix system python / conda python
+ && cp -rf /opt/conda/lib/python3.11/platform.py.bak /opt/conda/lib/python3.11/platform.py \
  && echo "Clean up" && list_installed_packages && install__clean
 
 USER postgres

diff --git a/docker_postgres/rootfs/docker-entrypoint-initdb.d/00-extensions-prepare.sql b/docker_postgres/rootfs/docker-entrypoint-initdb.d/00-extensions-prepare.sql
@@ -0,0 +1,23 @@
+CREATE OR REPLACE PROCEDURE enable_all_extensions()
+LANGUAGE plpgsql
+AS $$
+DECLARE
+    extension_name TEXT;
+BEGIN
+    FOR extension_name IN
+        SELECT name FROM pg_available_extensions
+        WHERE name NOT IN (SELECT extname AS name FROM pg_extension)
+        ORDER BY name
+    LOOP
+        BEGIN
+            EXECUTE format('CREATE EXTENSION IF NOT EXISTS %I', extension_name);
+        EXCEPTION WHEN OTHERS THEN
+            -- Optionally log the error or do nothing to continue with the next extension
+            RAISE NOTICE 'Failed to create extension %: %', extension_name, SQLERRM;
+        END;
+    END LOOP;
+END;
+$$;
+
+CREATE EXTENSION "hstore";
+-- CALL enable_all_extensions();
diff --git a/docker_postgres/rootfs/docker-entrypoint-initdb.d/01-init-db.sh b/docker_postgres/rootfs/docker-entrypoint-initdb.d/01-init-db.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+set -Eeo pipefail
+
+printenv | sort
+
+ls -alh /usr/share/postgresql/${PG_MAJOR}/extension/*.control
+
+mkdir -pv ${PGDATA}/conf.d
+echo "include_dir='./conf.d'" >> ${PGDATA}/postgresql.conf
+sudo mv /opt/utils/pg-ext.conf ${PGDATA}/conf.d/
+
+cat ${PGDATA}/conf.d/*
+tail ${PGDATA}/postgresql.conf
+
+
+# https://github.com/docker-library/postgres/blob/master/docker-entrypoint.sh
+# form: docker-entrypoint.sh
+docker_temp_server_stop
+docker_temp_server_start
+
+psql -v ON_ERROR_STOP=0 --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
+    CALL enable_all_extensions();
+    SELECT extname AS name, extversion AS ver FROM pg_extension ORDER BY extname;
+EOSQL