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| -rw-r--r-- | README.md | 27 |
1 files changed, 23 insertions, 4 deletions
@@ -74,16 +74,35 @@ Here's a sample *conn.scm*. ## Transform the database -Then, to transform the database to into ttl files, \~/data/dump, run inside the shell: +Example: Transform the phenotype from SQL to Terse RDF Triple Language (TTL) ```sh -./pre-inst-env ./examples/dump-species-metadata.scm ../conn.scm ~/tmp +guile -s examples/phenotype.scm \ + --settings=conn.scm \ + --output=tmp/phenotype.ttl \ + --documentation=tmp/phenotype.ttl.md ``` -``` shell -$ guix shell -m manifest.scm -- ./pre-inst-env ./examples/dump-dataset-metadata.scm ../conn.scm ~/tmp +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 |