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sumatra-server 0.2.0

Sumatra Server is a Django app that implements an HTTP-based store for records of computational experiments.

Sumatra Server is a Django app that implements an HTTP-based store for records of computational experiments (e.g. simulations, scripted analyses), with the goal of supporting reproducible research.

In particular, it implements the server-side counterpart to the HttpRecordStore client in Sumatra.

It is based on the Piston framework.

Getting started

The following assumes that you already have a Django project to which you wish to add a record store for computational experiments. If you don’t, you can download an example project here.

You will need to have installed Sumatra Server, Sumatra, Piston and django-tagging. Add the following lines to the INSTALLED_APPS tuple in your settings.py:

'sumatra_server',
'sumatra.web',
'sumatra.recordstore.django_store',
'tagging',

Your INSTALLED_APPS should also contain 'django.contrib.auth' and 'django.contrib.contenttypes'.

Now decide where in your URL structure the record store will live and edit your urls.py accordingly, e.g.:

urlpatterns = patterns('',
    # other url mappings
    (r'^records/', include('sumatra_server.urls')),
)

Now update your database by running syncdb:

$ python manage.py syncdb
Creating tables ...
Creating table sumatra_server_projectpermission
Creating table django_store_project
Creating table django_store_executable
Creating table django_store_dependency
Creating table django_store_repository
Creating table django_store_parameterset
Creating table django_store_launchmode
Creating table django_store_datastore
Creating table django_store_platforminformation
Creating table django_store_record_platforms
Creating table django_store_record_dependencies
Creating table django_store_record
Creating table tagging_tag
Creating table tagging_taggeditem

If you would like to load some test data to try it out, run:

$ python manage.py loaddata haggling permissions

This will populate the record store with some simulation records, owned by a user “testuser” with password “abc123”.

API

Sumatra server implements a RESTful API, which returns either HTML or JSON, depending on the Accept header in the HTTP request. Normally, if you access the page through a web browser you should get the HTML version, while Sumatra or compatible tools will receive the JSON version. You can also override the Accept header by explicitly adding ?format=html or ?format=json to the end of the URL.

<caption>Table showing the operations that can be performed on the record store.</caption>
URL GET POST PUT DELETE
/ Return a list of projects . . .
/<project_name>/ Return a list of records for the given project. May add a querystring ?tags=tag1,tag2 to show only records that have one of the supplied tags . Create a new project and give the current user permission to access the project .
/<project_name>/permissions/ Return a list of users who can access this project Give a user permission to access this project . .
/<project_name>/<record_label>/ Return the record with the given label . Create or update a record with the given label Delete the record with the given label
/<project_name>/tagged/<tag>/ Return a list of records with the given tag (not yet implemented) . . Delete all records having the given tag (not yet implemented)

JSON format

Here is an example of a simulation record encoded using JSON. This is the format that must be used to PUT a new record into the store:

{
    "user": "testuser",
    "project_id": "TestProject",
    "label": "20100709-154255",
    "reason": "Simulation to test the HttpRecordStore with Sumatra Server",
    "outcome": "Eureka! Nobel prize here we come.",
    "executable": {
        "path": "/usr/local/bin/python",
        "version": "2.5.2",
        "name": "Python",
        "options": ""
    },
    "repository": {
        "url": "/Users/andrew/tmp/SumatraTest",
        "type": "MercurialRepository"
    },
    "version": "396c2020ca50",
    "diff": "",
    "main_file": "main.py",
    "parameters": {
        "content": "seed = 65785 # seed for random number generator\ndistr = \"uniform\" # statistical distribution to draw values from \nn = 100 # number of values to draw",
        "type": "SimpleParameterSet"
    },
    "launch_mode": {
        "type": "SerialLaunchMode",
        "parameters": "{}"
    },
    "timestamp": "2010-07-09 15:42:55",
    "duration": 0.58756184577941895,
    "datastore": {
        "type": "FileSystemDataStore",
        "parameters": "{'root': '/Users/andrew/tmp/SumatraTest/Data'}"
    },
    "output_data": [
        {
            "path": "output.dat",
            "digest": 'a39100d5130f613b96c9fcf605b68d53d60f6fdb',
            "metadata": "",
        } for key in record.output_data],
    "input_datastore": {
        "type": "FileSystemDataStore", ,
        "parameters": "{'root': '/'}",
    },
    "input_data": [],
    "dependencies": [
        {
            "path": "/Library/Frameworks/Python.framework/Versions/4.0.30002/lib/python2.5/site-packages/matplotlib-0.98.3.0001-py2.5-macosx-10.3-fat.egg/matplotlib",
            "version": "0.98.3",
            "name": "matplotlib",
            "module": "python",
            "diff": ""
        },
        {
            "path": "/Library/Frameworks/Python.framework/Versions/4.0.30002/lib/python2.5/site-packages/numpy-1.1.1.0001-py2.5-macosx-10.3-fat.egg/numpy",
            "version": "1.1.1",
            "name": "numpy",
            "module": "python",
            "diff": ""
        },
    ],
    "platforms": [
        {
            "system_name": "Darwin",
            "ip_addr": "127.0.0.1",
            "architecture_bits": "32bit",
            "machine": "i386",
            "architecture_linkage": "",
            "version": "Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386",
            "release": "9.8.0",
            "network_name": "localhost",
            "processor": "i386"
        }
    ],
    "tags": ""
}

Most of these fields are write-once, i.e. if you PUT another record to the same URL, only changes in “reason”, “outcome” and “tags” will be taken into account.

Authentication

Sumatra Server uses HTTP Basic authentication, and validates against the user database of your Django project.

 
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