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willirathIngmarIngmarEissfeldt
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Restructure completely (#6)
This complete re-builds the app, splitting it into three components (database, api, frontend). Individual commit messages: * current state * current state * fix display of hex grid from geojson * fix display of hex grid from geojson * data no longer in .gitignore * small fix for app.tsx * app.tsx error resolved * DB architecture * Updated dependencies (not fully functional yet) * Same functionality as before the incident * Basic hover and on click functions * api supports connectivity, frontend doesn't * Frontend properly fetches connectivity (took way too long) * Hexagons properly color based on connectivity and changed geojson to match the connectivity * Connectivity now updates properly * Updated ControlPanel * New database * inter container comms now work over the docker compose and not over local network * Batch processing of PQ file to DB * Much faster db lookup * Now refetches on parameter change * Hover tooltips added * Hover tool tip actually works now * Light mode support * api and frontend now support checkbox functionality in the control panel * Can now process multiple selected hexagons (and button to reset selection) * added buttons * fixed layering bugs * different aspect ratios * fixed scrolling issue * added readme * added readme * added readme * removed redundant comments * Move requirements and adapt instructions * Create LICENSE * Typo * Update path to datasets * Use username and password from env * Typo * Fix env file reading * Typo --------- Co-authored-by: Ingmar <ieissfeldt@geomar.de> Co-authored-by: Ingmar Eissfeldt <eissfeldt.ingmar@gmail.com>
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‎.env‎

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POSTGRES_USER: user
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POSTGRES_PASSWORD: password
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POSTGRES_DB: db

‎.gitignore‎

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node_modules
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node_modules
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db-data

‎LICENSE‎

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MIT License
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Copyright (c) 2025 GEOMAR OD
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# OYSTERS
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Visualization of simulated Oyster pathogen dispersal in the North Sea.
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## Table of Contents
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- [Installation](#installation)
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- [Usage](#usage)
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- [Configuration](#configuration)
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- [License](#license)
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## Installation
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### Prerequisites
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1. Ensure that Docker is installed, e.g., by installing [Docker Desktop](https://docs.docker.com/desktop/setup/install/linux/).
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2. Ensure you have a Python installation (e.g. via Micromamba or via the OS). In Ubuntu Linux, you can run
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```bash
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sudo apt update
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sudo apt install -y python3 python3-pip
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```
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### Getting the app code and starting the app
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Make sure the docker engine is running, e.g., through your app browser (the desktop UI can be closed).
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```bash
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# Clone the repo and change to dir
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git clone https://github.com/geomar-od-lagrange/2024_hex_dashboard.git
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cd 2024_hex_dashboard
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# Start the containers
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docker compose build
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docker compose up
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```
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### Fill up the database
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```bash
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# change to database dir
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cd database
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pip install -r requirements.txt
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# insert the data
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python metadata_to_db.py
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python geojson_to_db.py
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python connectivity_to_db.py # (might take a few minutes)
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```
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### Using the app
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Connect to http://localhost:5173/ in the browser of your choice.
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### Shutting down and restarting
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Stop the app with:
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```bash
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# from within the main project directory
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docker compose down
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```
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Apply code changes and restart:
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```bash
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# from within the main project directory
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docker compose build
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docker compose up
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```
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## License
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Distributed under the MIT License. See [LICENSE](LICENSE) for more information.
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## Credits / Acknowledgements
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- See [database/requirements.txt](database/requirements.txt) for used python libraries. Deckgl and maplibre for the frondend.
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- Contributors: Ingmar Eissfeldt (@IngmarEissfeldt), Willi Rath (@willirath), Felix Kirch (@felixkirch)

‎api/._geojsons‎

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‎api/._node_modules‎

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‎api/Dockerfile‎

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FROM node:18-alpine
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WORKDIR /app
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COPY package*.json ./
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RUN npm install
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COPY . .
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EXPOSE 3000
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CMD ["node", "server.js"]
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‎api/mydatabase_dump.sql‎

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--
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-- PostgreSQL database dump
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--
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-- Dumped from database version 15.4 (Debian 15.4-1.pgdg110+1)
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-- Dumped by pg_dump version 15.4 (Debian 15.4-1.pgdg110+1)
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SET statement_timeout = 0;
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SET lock_timeout = 0;
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SET idle_in_transaction_session_timeout = 0;
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SET client_encoding = 'UTF8';
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SET standard_conforming_strings = on;
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SELECT pg_catalog.set_config('search_path', '', false);
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SET check_function_bodies = false;
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SET xmloption = content;
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SET client_min_messages = warning;
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SET row_security = off;
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--
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-- Name: tiger; Type: SCHEMA; Schema: -; Owner: myuser
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--
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CREATE SCHEMA tiger;
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ALTER SCHEMA tiger OWNER TO myuser;
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--
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-- Name: tiger_data; Type: SCHEMA; Schema: -; Owner: myuser
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--
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CREATE SCHEMA tiger_data;
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ALTER SCHEMA tiger_data OWNER TO myuser;
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--
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-- Name: topology; Type: SCHEMA; Schema: -; Owner: myuser
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--
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CREATE SCHEMA topology;
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ALTER SCHEMA topology OWNER TO myuser;
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--
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-- Name: SCHEMA topology; Type: COMMENT; Schema: -; Owner: myuser
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--
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COMMENT ON SCHEMA topology IS 'PostGIS Topology schema';
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--
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-- Name: fuzzystrmatch; Type: EXTENSION; Schema: -; Owner: -
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--
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CREATE EXTENSION IF NOT EXISTS fuzzystrmatch WITH SCHEMA public;
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--
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-- Name: EXTENSION fuzzystrmatch; Type: COMMENT; Schema: -; Owner:
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--
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COMMENT ON EXTENSION fuzzystrmatch IS 'determine similarities and distance between strings';
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--
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-- Name: postgis; Type: EXTENSION; Schema: -; Owner: -
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--
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CREATE EXTENSION IF NOT EXISTS postgis WITH SCHEMA public;
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--
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-- Name: EXTENSION postgis; Type: COMMENT; Schema: -; Owner:
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--
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COMMENT ON EXTENSION postgis IS 'PostGIS geometry and geography spatial types and functions';
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--
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-- Name: postgis_tiger_geocoder; Type: EXTENSION; Schema: -; Owner: -
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--
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CREATE EXTENSION IF NOT EXISTS postgis_tiger_geocoder WITH SCHEMA tiger;
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--
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-- Name: EXTENSION postgis_tiger_geocoder; Type: COMMENT; Schema: -; Owner:
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--
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COMMENT ON EXTENSION postgis_tiger_geocoder IS 'PostGIS tiger geocoder and reverse geocoder';
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--
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-- Name: postgis_topology; Type: EXTENSION; Schema: -; Owner: -
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--
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CREATE EXTENSION IF NOT EXISTS postgis_topology WITH SCHEMA topology;
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--
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-- Name: EXTENSION postgis_topology; Type: COMMENT; Schema: -; Owner:
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--
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COMMENT ON EXTENSION postgis_topology IS 'PostGIS topology spatial types and functions';
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--
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-- Data for Name: spatial_ref_sys; Type: TABLE DATA; Schema: public; Owner: myuser
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--
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COPY public.spatial_ref_sys (srid, auth_name, auth_srid, srtext, proj4text) FROM stdin;
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\.
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--
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-- Data for Name: geocode_settings; Type: TABLE DATA; Schema: tiger; Owner: myuser
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--
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COPY tiger.geocode_settings (name, setting, unit, category, short_desc) FROM stdin;
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\.
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--
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-- Data for Name: pagc_gaz; Type: TABLE DATA; Schema: tiger; Owner: myuser
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--
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COPY tiger.pagc_gaz (id, seq, word, stdword, token, is_custom) FROM stdin;
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\.
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--
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-- Data for Name: pagc_lex; Type: TABLE DATA; Schema: tiger; Owner: myuser
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--
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COPY tiger.pagc_lex (id, seq, word, stdword, token, is_custom) FROM stdin;
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\.
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--
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-- Data for Name: pagc_rules; Type: TABLE DATA; Schema: tiger; Owner: myuser
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--
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COPY tiger.pagc_rules (id, rule, is_custom) FROM stdin;
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\.
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--
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-- Data for Name: topology; Type: TABLE DATA; Schema: topology; Owner: myuser
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--
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COPY topology.topology (id, name, srid, "precision", hasz) FROM stdin;
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\.
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--
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-- Data for Name: layer; Type: TABLE DATA; Schema: topology; Owner: myuser
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--
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COPY topology.layer (topology_id, layer_id, schema_name, table_name, feature_column, feature_type, level, child_id) FROM stdin;
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\.
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--
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-- Name: topology_id_seq; Type: SEQUENCE SET; Schema: topology; Owner: myuser
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--
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SELECT pg_catalog.setval('topology.topology_id_seq', 1, false);
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--
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-- PostgreSQL database dump complete
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--
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