add script to regenerate JSONLDs in neurobagel_examples submodule

generate_neurobagel_example_jsonlds.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+# Run from repository root
+
+docker build -t bagel .
+cd tests
+
+data_dir=neurobagel_examples/data-upload
+
+# Phenotypic data only JSONLD
+docker run --rm --volume=$PWD:/data/neurobagel/bagel-cli -w /data/neurobagel/bagel-cli bagel pheno \
+    --pheno "${data_dir}/example_synthetic.tsv" \
+    --dictionary "${data_dir}/example_synthetic.json" \
+    --name "BIDS synthetic" \
+    --output "${data_dir}/example_synthetic.jsonld" \
+    --overwrite
+
+# Phenotypic & BIDS data JSONLD
+docker run --rm --volume=$PWD:/data/neurobagel/bagel-cli -w /data/neurobagel/bagel-cli bagel bids \
+    --jsonld-path ${data_dir}/example_synthetic.jsonld \
+    --bids-dir bids-examples/synthetic \
+    --output ${data_dir}/pheno-bids-output/example_synthetic_pheno-bids.jsonld \
+    --overwrite
+
+# Phenotypic & derivatives data JSONLD
+docker run --rm --volume=$PWD:/data/neurobagel/bagel-cli -w /data/neurobagel/bagel-cli bagel derivatives \
+    --tabular ${data_dir}/nipoppy_proc_status_synthetic.tsv \
+    --jsonld-path ${data_dir}/example_synthetic.jsonld \
+    --output "${data_dir}/pheno-derivatives-output/example_synthetic_pheno-derivatives.jsonld" \
+    --overwrite
+
+# Phenotypic, BIDS, and derivatives data JSONLD
+docker run --rm --volume=$PWD:/data/neurobagel/bagel-cli -w /data/neurobagel/bagel-cli bagel derivatives \
+    --tabular ${data_dir}/nipoppy_proc_status_synthetic.tsv \
+    --jsonld-path "${data_dir}/pheno-bids-output/example_synthetic_pheno-bids.jsonld" \
+    --output "${data_dir}/pheno-bids-derivatives-output/example_synthetic_pheno-bids-derivatives.jsonld" \
+    --overwrite