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[REF] update syntax for data upload script (#160)
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Because of neurobagel/recipes#13
we now default to using graphDB syntax. This updates
the docs to show the new behaviour
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surchs authored Feb 6, 2024
1 parent 128ac46 commit 6a46e21
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10 changes: 5 additions & 5 deletions docs/infrastructure.md
Original file line number Diff line number Diff line change
Expand Up @@ -497,14 +497,14 @@ Next, upload the `.jsonld` file in the directory `neurobagel_examples/data-uploa
``` bash
./add_data_to_graph.sh PATH/TO/neurobagel_examples/data-upload/pheno-bids-output \
localhost:7200 repositories/my_db DBUSER DBPASSWORD \
--clear-data --use-graphdb-syntax
--clear-data
```

=== "Stardog"
``` bash
./add_data_to_graph.sh PATH/TO/neurobagel_examples/data-upload/pheno-bids-output \
localhost:5820 test_data DBUSER DBPASSWORD \
--clear-data
--clear-data --use-stardog-syntax
```

**Note:** Here we added the `--clear-data` flag to remove any existing data in the database (if the database is empty, the flag has no effect).
Expand Down Expand Up @@ -543,14 +543,14 @@ Run the following code (assumes you are in the `scripts` subdirectory inside the
=== "GraphDB"
``` bash
./add_data_to_graph.sh ../vocab \
localhost:7200 repositories/my_db DBUSER DBPASSWORD \
--use-graphdb-syntax
localhost:7200 repositories/my_db DBUSER DBPASSWORD
```

=== "Stardog"
``` bash
./add_data_to_graph.sh ../vocab \
localhost:5820 test_data DBUSER DBPASSWORD
localhost:5820 test_data DBUSER DBPASSWORD \
--use-stardog-syntax
```

### Updating a dataset in the graph database
Expand Down

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