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[](https://ci.genenetwork.org/jobs/dump-genenetwork-database-tests)
[](https://ci.genenetwork.org/jobs/dump-genenetwork-database)
This repository contains code to dump the metadata in the GeneNetwork relational database to RDF. It requires a connection to a SQL server.
# Using
Drop into a development environment with
``` shell
$ guix shell -m manifest.scm
```
If the path is not picked up add
```
export PATH=$GUIX_ENVIRONMENT/bin:$PATH
```
Build the sources.
``` shell
$ make
```
or for a container
```shell
mkdir ./tmp
guix shell -C --network --share=/run/mysqld/ --manifest=manifest.scm
export GUILE_LOAD_PATH=.:$GUILE_LOAD_PATH
guile json-to-ttl.scm etc/sample.json tmp/
```
That reads the `etc/sample.json` file included in this repository and converts it to an RDF representation that is stored in a file `./tmp/sampledata.ttl`.
## Set up connection parameters
Describe the database connection parameters in a file *conn.scm* file as
shown below. Take care to replace the placeholders within angle brackets
with the appropriate values.
``` scheme
((sql-username . "<sql-username-here>")
(sql-password . "<sql-password-here>")
(sql-database . "<sql-database-name-here>")
(sql-host . "<sql-hostname-here>")
(sql-port . <sql-port-here>)
(virtuoso-port . <virtuoso-port-here>)
(virtuoso-username . "<virtuoso-username-here>")
(virtuoso-password . "<virtuoso-password-here>")
(sparql-scheme . <sparql-endpoint-scheme-here>)
(sparql-host . "<sparql-endpoint-hostname-here>")
(sparql-port . <sparql-endpoint-port-here>))
```
Here's a sample *conn.scm*.
``` scheme
((sql-username . "webqtlout")
(sql-password . "my-secret-password")
(sql-database . "db_webqtl")
(sql-host . "localhost")
(sql-port . 3306)
(virtuoso-port . 9081)
(virtuoso-username . "dba")
(virtuoso-password . "my-secret-virtuoso-password")
(sparql-scheme . http)
(sparql-host . "localhost")
(sparql-port . 9082))
```
## Transform the database
Example: Transform the phenotype from SQL to Terse RDF Triple Language (TTL)
```sh
guile -s examples/phenotype.scm \
--settings=conn.scm \
--output=tmp/phenotype.ttl \
--documentation=tmp/phenotype.ttl.md
```
the `-s` option to *guile* runs the `examples/phenotype.scm` file as a script. Everything else on the command line is passed onto the script as command-line arguments.
This should create the files:
- `tmp/phenotype.ttl`: will contain the data in the database in TTL format
- `tmp/phenotype.ttl.md`: will contain a short documentation on the data in the file above.
**Note to Devs**: The current `pre-inst-env` script will not work within containers since it assumes the existence of `/usr/bin/env`. We need to fix that if we intend to keep using that.
There is a shorter form of the command above:
```sh
guile -s examples/phenotype.scm \
-s conn.scm \
-o tmp/phenotype.ttl \
-d tmp/phenotype.ttl.md
```
which does the same thing, but has the potential to be confusing due to the two `-s` options: the first `-s` option is to guile while the second is to the script itself.
## Validate and load dump
Then, validate the dumped RDF using `rapper` and load it into
virtuoso. This will load the dumped RDF into the
`http://genenetwork.org` graph, and will delete all pre-existing data
in that graph (FIXME)
``` shell
$ guix shell -m manifest.scm -- rapper --input turtle --count ~/data/dump/dump.ttl
$ guix shell -m manifest.scm -- ./pre-inst-env ./load-rdf.scm conn.scm ~/data/dump/dump.ttl
```
## Upload data to virtuoso
See https://issues.genenetwork.org/topics/systems/virtuoso
## Visualize schema
Now, you may query virtuoso to visualize the SQL and RDF schema.
``` shell
$ guix shell -m manifest.scm -- ./pre-inst-env ./visualize-schema.scm conn.scm
```
This will output graphviz dot files `sql.dot` and `rdf.dot` describing
the schema. Render them into SVG images like so.
``` shell
$ dot -Tsvg -osql.svg sql.dot
$ dot -Tsvg -ordf.svg rdf.dot
```
Or, peruse them interactively with `xdot`.
``` shell
$ xdot sql.dot
$ xdot rdf.dot
```
The
[dump-genenetwork-database](https://ci.genenetwork.org/jobs/dump-genenetwork-database)
continuous integration job runs these steps on every commit and
publishes its version of
[sql.svg](https://ci.genenetwork.org/archive/dump-genenetwork-database/latest/sql.svg)
and
[rdf.svg](https://ci.genenetwork.org/archive/dump-genenetwork-database/latest/rdf.svg).
# LICENSE
AGPLv3. See LICENSE.txt
# Contributing
The main code tree is hosted at https://git.genenetwork.org/.
```sh
git remote add gn git.genenetwork.org:/home/git/public/gn-transform-databases
```
See bugs and tasks in BUGS.org.
|
