Installation and Running

Flatmap Server

An anatomical flatmap server to provide Mapbox compatible tilesets generated by flatmap-maker. It is intended for use with a browser-based flatmap-viewer application. The server is written in Python using the Flask web framework.

Prerequisites

  • Python 3.8

  • pipenv

  • Under Ubuntu, sudo apt-get install libgl-mesa-glx

  • If the server will also generate maps, install Tippecanoe.

Installation

  1. Download the latest release and extract it to a suitable directory.

  2. Change to this directory and run pipenv install.

Running

$ pipenv run gunicorn src.server:app

  • By default, maps are stored in ./flatmaps. This can be overridden by setting the FLATMAP_ROOT environment variable to a directory path.

  • The server listens at http://localhost:8000. Change this via Gunicorn.

Web API

A description of the server’s web API is available here.

Optional map viewer

As an option, the server provides a simple flatmap viewer application. Prerequisites are node and npm. To install the viewer give the following commands from the top-level server directory:

$ git clone https://github.com/dbrnz/flatmap-server-viewer viewer
$ cd viewer
$ npm install
$ npm run build
$ cd ..

Running

To run the server with the integrated viewer:

$ pipenv run gunicorn 'src.server:viewer()'

and open http://localhost:8000/viewer in a browser.

Map generation

The flatmap server can also generate maps. To generate a map, POST a request to the /make/map end-point specifying a directory containing a map’s manifest.json. The server will respond with the id of the maker process. The /make/status/PROCESS_ID end-point allows the process’s status to be queried and /make/log/PROCESS_ID will return a log of a running process.

Authentication

Any publicly accessible map server must control who can generate maps — we use bearer tokens (RFC 6750) for this. To enable, set the BEARER_TOKENS environment variable to a space separated list of valid tokens, before starting the server. e.g:

$ export BEARER_TOKENS="token1 token2"
$ pipenv run gunicorn src.server:app

When BEARER_TOKENS have been defined, every request to a map generation endpoint must specify a valid token using the HTTP Authorization header. With curl this is done using the -H "Authorization: Bearer BEARER_TOKEN" option.

Examples

A local map source

Request generation:

$ curl -H "Content-Type: application/json" -X POST
       -d '{"source":"/Users/dave/build/Flatmaps/new-maker/tests/gradients/manifest.json"}'
       http://localhost:8000/make/map

Response:

{"maker":18259,"source":"/Users/dave//build/Flatmaps/new-maker/tests/gradients","status":"started"}

Query build status:

$ curl http://localhost:8000/make/status/18259

Response:

{"maker":18259,"status":"terminated"}

Get log of build:

$ curl http://localhost:8000/make/log/18259

Response:

2021-01-22 09:14:05,925 Mapmaker 1.0.0b1
2021-01-22 09:14:05,928 Adding details...
2021-01-22 09:14:05,928 Outputting GeoJson features...
2021-01-22 09:14:05,928 Layer:gradients
2021-01-22 09:14:05,929 Running tippecanoe...
2021-01-22 09:14:06,020 Generating background tiles (may take a while...)
2021-01-22 09:14:06,021 Tiling gradients_image...
2021-01-22 09:14:06,040 Tiling zoom level 10 for gradients_image
2021-01-22 09:14:08,811 Tiling zoom level 9 for gradients_image
2021-01-22 09:14:08,935 Tiling zoom level 8 for gradients_image
2021-01-22 09:14:08,976 Tiling zoom level 7 for gradients_image
2021-01-22 09:14:08,994 Tiling zoom level 6 for gradients_image
2021-01-22 09:14:09,005 Tiling zoom level 5 for gradients_image
2021-01-22 09:14:09,015 Tiling zoom level 4 for gradients_image
2021-01-22 09:14:09,024 Tiling zoom level 3 for gradients_image
2021-01-22 09:14:09,034 Tiling zoom level 2 for gradients_image
2021-01-22 09:14:09,063 Creating index and style files...
2021-01-22 09:14:09,065 Generated map: gradients

A remote map source

This generates a flatmap showing part of the vagus nerve, from sources held in a publicly accessible PMR workspace:

$ curl -H "Content-Type: application/json"
       -X POST
       -d '{"source":"https://models.physiomeproject.org/workspace/693/rawfile/aa83dc1b19c03101d6a5306c77d144823fd59ea5/vagus_test.manifest.json"}'
       http://localhost:8000/make/map

Response:

{"map":"83f6c97d571b67fb4c273e20287b53b4f0a1f70780d3d6a2a282e66cef5f9473","process":57906,"source":"https://models.physiomeproject.org/workspace/693/rawfile/aa83dc1b19c03101d6a5306c77d144823fd59ea5/vagus_test.manifest.json","status":"started"}

Query build status:

$  curl http://localhost:8000/make/status/57906

Response shows running:

{"process":57906,"status":"running"}

Get log showing progress:

$ curl http://localhost:8000/make/log/57906

Response:

2021-06-11 13:46:17,386 INFO: Mapmaker 1.2.0b3
2021-06-11 13:46:17,903 INFO: Making map: 83f6c97d571b67fb4c273e20287b53b4f0a1f70780d3d6a2a282e66cef5f9473
2021-06-11 13:46:20,148 WARNING: Unknown anatomical entity: SAO:1770195789
2021-06-11 13:46:20,724 INFO: Adding details...
2021-06-11 13:46:20,728 INFO: Routing paths...
2021-06-11 13:46:20,728 INFO: Outputting GeoJson features...
2021-06-11 13:46:20,728 INFO: Layer: vagus_test
2021-06-11 13:46:20,800 INFO: Layer: vagus_test_routes
2021-06-11 13:46:20,800 INFO: Running tippecanoe...
2021-06-11 13:46:20,996 INFO: Generating background tiles (may take a while...)
2021-06-11 13:46:20,998 INFO: Tiling vagus_test_image...
2021-06-11 13:46:21,019 INFO: Tiling zoom level 10 for vagus_test_image

Check status

$  curl http://localhost:8000/make/status/57906

Response shows terminated:

{"process":57906,"status":"terminated"}

Get full log:

$ curl http://localhost:8000/make/log/57906

Response:

2021-06-11 13:46:17,386 INFO: Mapmaker 1.2.0b3
2021-06-11 13:46:17,903 INFO: Making map: 83f6c97d571b67fb4c273e20287b53b4f0a1f70780d3d6a2a282e66cef5f9473
2021-06-11 13:46:20,148 WARNING: Unknown anatomical entity: SAO:1770195789
2021-06-11 13:46:20,724 INFO: Adding details...
2021-06-11 13:46:20,728 INFO: Routing paths...
2021-06-11 13:46:20,728 INFO: Outputting GeoJson features...
2021-06-11 13:46:20,728 INFO: Layer: vagus_test
2021-06-11 13:46:20,800 INFO: Layer: vagus_test_routes
2021-06-11 13:46:20,800 INFO: Running tippecanoe...
2021-06-11 13:46:20,996 INFO: Generating background tiles (may take a while...)
2021-06-11 13:46:20,998 INFO: Tiling vagus_test_image...
2021-06-11 13:46:21,019 INFO: Tiling zoom level 10 for vagus_test_image
2021-06-11 13:46:23,802 INFO: Tiling zoom level 9 for vagus_test_image
2021-06-11 13:46:23,969 INFO: Tiling zoom level 8 for vagus_test_image
2021-06-11 13:46:24,034 INFO: Tiling zoom level 7 for vagus_test_image
2021-06-11 13:46:24,062 INFO: Tiling zoom level 6 for vagus_test_image
2021-06-11 13:46:24,079 INFO: Tiling zoom level 5 for vagus_test_image
2021-06-11 13:46:24,097 INFO: Tiling zoom level 4 for vagus_test_image
2021-06-11 13:46:24,116 INFO: Tiling zoom level 3 for vagus_test_image
2021-06-11 13:46:24,136 INFO: Tiling zoom level 2 for vagus_test_image
2021-06-11 13:46:24,188 INFO: Creating index and style files...
2021-06-11 13:46:24,195 INFO: Generated map: 83f6c97d571b67fb4c273e20287b53b4f0a1f70780d3d6a2a282e66cef5f9473