The only dependencies are “redis-rkt” and “threading”, and they can be installed using raco:
git clone [email protected]:chfi/gn-proxy.git
cd gn-proxy
raco pkg install
The REST server can then be started by running server/rest.rkt, while providing the SQL username and password as environment variables:
env SQL_USER=username SQL_PASSWORD=password racket server/rest.rkt
By default it listens on port 8080 and listens on 127.0.0.1, however the port can be changed with the PORT environment variable.
The Redis and MariaDB connections are handled in server/db.rkt
, and
can be configured by editing connect-redis
and connect-sql
. See the
documentation for the respective packages for more information, if needed:
- Redis: https://docs.racket-lang.org/redis@redis-doc/client.html
- SQL: https://docs.racket-lang.org/db/connect.html
Resources can be created using the constructors in Racket (e.g.
new-geno-resource
), and then serialized into stringified JSON using
serialize-resource
, which can then be inserted into Redis.
This is an example of the JSON representation of a resource. The only
fields that will differ between resource types are “type”, “data”, and
the mask fields. The “type” must be one of the keys in the resource-type
hash defined in resource.rkt, and the “data” and mask fields depend
on the resource type.
{ "name": "r1",
"owner_id": "7733c380-b83f-45de-a8b5-17e1bc3738a9",
"data": { "path": "test1.txt",
"metadata": "test1" },
"type": "dataset-file",
"default_mask" : { "metadata": "no-access",
"data": "no-access"},
"group_masks": {"0": {"metadata": "edit",
"data": "edit"}
}
}
For reference, these are the types currently defined:
data
should be a hash containing two fields, path
which is a path
to the data file, and metadata
which is a Redis key containing
some metadata.
This type was created mainly for testing, hence its simplicity.
data
should be a hash containing two fields, dataset
which is
the name of a genotype dataset, and trait
which is the name
of a trait dataset. These are dataset.name
and trait.name
in the Python query, respectively. One example is “BXDGeno”
for the dataset name, and “rs3657281” for the trait name.
Currently this only has one action branch, and really only one action, namely viewing data.
A JSON example:
{ "name": "some-resource",
"owner_id": "7733c380-b83f-45de-a8b5-17e1bc3738a9",
"data": { "dataset": "BXDGeno",
"trait": "rs365781" },
"type": "dataset-geno",
"default_mask" : { "data": "view" },
"group_masks": { "0": {"data": "view"} }
}
The query is defined in the function select-geno
, in resource.rkt
,
and the result is provided as a string-encoded JSON array, transformed
straight from the SQL result.
data
should be a hash containing two fields, dataset
and trait
.
The Python equivalents are dataset.id
and trait.name
,
respectively. The action set is essentially the same as for
dataset-geno.
A JSON example:
{ "name": "some-resource",
"owner_id": "7733c380-b83f-45de-a8b5-17e1bc3738a9",
"data": { "dataset": "1",
"trait": "17465" },
"type": "dataset-publish",
"default_mask" : { "data": "view" },
"group_masks": { "0": {"data": "view"} }
}
The query is defined in the same module as dataset-geno, as the
function select-publish
. The query result is transformed into
a JSON array, with SQL nulls replaced by JSON nulls.
To define a new resource type, the resource-types
hash in
resource.rkt
must be extended with an entry mapping the new resource
type name (as a symbol) to the corresponding action set.
An action set is a hash of action “branches”, which are alists that
map the name of each action (as a string) to the corresponding
action
. An action
is a value of the action
struct, defined in
privileges.rkt
, and is a function of two arguments, along with the
names of any additional parameters that need to be provided by the
user (e.g. in the request to the REST endpoint).
It’s probably best to just look at how one of the existing resource
types are defined, and dataset-geno
is one of the simplest, while
still querying the SQL database.
The GeneNetwork source code is released under the Affero General Public License 3 (AGPLv3). See ./LICENSE.txt.