isanwong/madeline

Madeline Pedigree Drawing Engine Web Service (https://madeline.med.umich.edu/madeline/)

Madeline Pedigree Drawing Engine Web Service

Web service to generate pedigree diagrams utilizing the Madeline 2.0 Pedigree Drawing Engine (http://madeline.med.umich.edu/madeline).

Build

• 1. Install docker-engine (https://docs.docker.com/engine/installation/)
• 2. Install docker-compose (https://docs.docker.com/compose/install/)
• 3. Execute ./bin/test running steps:
  • a. Build a docker image of madeline tagged test-madeline:latest
  • b. Run docker-compose up using base image madeline to start containers:
    • test-madeline-app
    • test-madeline-client
  • c. Run docker exec test-madeline-client ./test.sh to run the test suite

API

Submit

Submit data and command line arguments to render a pedigree diagram.

Arguments may be provided other than --outputprefix', --outputext, or the path to the input file which are provided internally to the madeline2` binary by the service.

URL

http://<app>/submit

Methods

POST

JSON Parameters:

{
  'data': <text>,            # Tab-separated/XML data
  'args': [<arg>, <arg...>]  # Madeline PDE command line arguments
}

Response (Success):

{
  'status': 'success',
  'data': <svg_xml>,
  'command': <command>,
  'output': <command_output>
}

Response (Error):

{
  'status': 'error',
  'data': <error_information>,
  'command': <command>,
  'output': <command_output>
}

Examples

Note: Test data available at: http://madeline.med.umich.edu/madeline/testdata/

$ cat madeline/data/cs_001.data

Individualid	Familyid	Gender	Mother	Father
m100	cs_001	m	.	.
m101	cs_001	f	.	.
m102	cs_001	m	m101	m100
m103	cs_001	f	m101	m100
m104	cs_001	m	.	.
m105	cs_001	f	m101	m100
m106	cs_001	m	.	.
m107	cs_001	m	m101	m100
m109	cs_001	m	m103	m104
m108	cs_001	m	m103	m104
m110	cs_001	m	m114	m108
m111	cs_001	m	m114	m108
m114	cs_001	f	m105	m106
m112	cs_001	m	m105	m106

$ cat madeline/tests/data/request-with-tsv.json
{
  "args": [ "--color", "--noiconlabels" ],
  "data": "Individualid\tFamilyid\tGender\tMother\tFather\nm100\tcs_001\tm\t.\t.\nm101\tcs_001\tf\t...etc."
}

$ curl -X POST -d @madeline/tests/data/request-with-tsv.json http://localhost:5000/submit
{
  "status": "success",
  "svg": "<?xml version=\"1.0\" standalone=\"no\"?>\n <svg version=\"1.1\"  id=\"svgDC\" xmlns=...etc.",
  "command": [
    "madeline2",
    "--color",
    "--noiconlabels",
    "--outputprefix",
    "tmp/2ff66bac-07d8-41d2-a7c2-ae3d194840f6/output",
    "tmp/2ff66bac-07d8-41d2-a7c2-ae3d194840f6/2ff66bac-07d8-41d2-a7c2-ae3d194840f6.txt"
  ],
  "output": "┌────────────────────┐\n│ Welcome to Madeline 2.0 PDE │\n└──────────────────...etc."
}

Version

Returns version (Github Commit SHA and Date) of compiled madeline PDE binary.

The madeline PDE binary is compiled from the Madeline PDE source code located at https://github.com/piratical/Madeline_2.0_PDE.

URL

http://<app>/version

Methods

GET

Parameters:

None

Response:

<git_url> - <datestamp_of_commit>

Examples

$ curl http://<app>/version

https://github.com/piratical/Madeline_2.0_PDE/tree/8ab82ad - 2016-12-21 00:38:52 -0500

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