Shock

To build:

Unix/Macintosh (requires nodejs, npm, postgresql >= 8.4):

./bootstrap -d <shock_data_dir> -p <shock_site_port> -N <dbname> -H <dbhost> -U <dbuser> [ -P <dbpasswd> -h <help> ]

Windows:

untested (theoretically possible)

API

Node:

id

unique identifier

file_name

file name for attached file if present

size

file size for attached file if present

checksum

file checksum for attached file if present

attributes

arbitrary json

acl

access control (in development)

node example:

{
    "id": 6775,
    "file_name": "h_sapiens_asm.tar.gz",
    "checksum": "8fd07ad670159c491eed7baefe97c16a",
    "size": 2819582549,
    "attributes": {
        "description": "tar gzip of h_sapiens_asm bowtie indexes",
        "file_list": [
            "h_sapiens_asm.1.ebwt",
            "h_sapiens_asm.2.ebwt",
            "h_sapiens_asm.3.ebwt",
            "h_sapiens_asm.4.ebwt",
            "h_sapiens_asm.rev.1.ebwt",
            "h_sapiens_asm.rev.2.ebwt"
        ],
        "source": "ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/h_sapiens_asm.ebwt.zip"
    },
    "acl": {
        "read": [],
        "write": [],
        "delete": []
    }
}

Actions

Create node:

POST /node (multipart/form-data encoded)

• to set attributes include file field named "attributes" containing a json file of attributes
• to set file include file field named "file" containing any file

example

curl -X POST [ -F "attributes=@<path_to_json>" -F "file=@<path_to_data_file>" ] <shock_url>[:<port>]/node

returns

<new_node>

### List nodes: GET /node

• by adding ?offset=N you get the nodes starting at N+1 (in development)
• by adding ?count=N you get a maximum of N nodes returned (in development)

example

curl -X GET <shock_url>[:<port>]/node/[?offset=<offset>&count=<count>]

returns

{"total_nodes":42,"offset":0,"count":4,"nodes":[<node_1>, <node_2>, <node_3>, <node_4>]}

### Get node: GET /node/

• ?download - complete file download
• ?download&index=$index&part=$part - file part download (in development)
• ?list&indexes - list available indexes (in development)
• ?list&index=$index - index parts list (in development)

example

curl -X GET <shock_url>[:<port>]/node/<nodeid>

returns

<node>