From 8e3dfb4888192e8cdaf6113afc5cec7794cfc471 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 4 Apr 2024 17:24:27 -0400
Subject: [PATCH 01/25] Implemented new stuff

Co-authored-by: Alyssa Dai <alyssa.ydai@gmail.com>
Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>
---
 dev/add_data_to_graph.sh          | 244 ++++++++++++++++++++++
 dev/data-config.ttl               |  49 +++++
 dev/data-config_template.ttl      |  49 +++++
 dev/data/example_synthetic.jsonld | 331 ++++++++++++++++++++++++++++++
 dev/docker-compose.yml            |  42 ++++
 dev/graphdb_setup.sh              | 200 ++++++++++++++++++
 dev/local_nb_nodes.json           |  10 +
 dev/setup.sh                      |  23 +++
 8 files changed, 948 insertions(+)
 create mode 100755 dev/add_data_to_graph.sh
 create mode 100644 dev/data-config.ttl
 create mode 100644 dev/data-config_template.ttl
 create mode 100644 dev/data/example_synthetic.jsonld
 create mode 100644 dev/docker-compose.yml
 create mode 100755 dev/graphdb_setup.sh
 create mode 100644 dev/local_nb_nodes.json
 create mode 100755 dev/setup.sh

diff --git a/dev/add_data_to_graph.sh b/dev/add_data_to_graph.sh
new file mode 100755
index 0000000..869d13b
--- /dev/null
+++ b/dev/add_data_to_graph.sh
@@ -0,0 +1,244 @@
+#!/bin/bash
+#
+# ARG_HELP([Upload JSONLD and Turtle data to a Neurobagel graph])
+# ARG_POSITIONAL_SINGLE([dir],[Path to directory containing .jsonld and/or .ttl files. ALL .jsonld and .ttl files in this directory will be uploaded.])
+# ARG_POSITIONAL_SINGLE([graph-url],[Host and port at which to access the graph database to add data to (e.g., localhost:7200)])
+# ARG_POSITIONAL_SINGLE([graph-database],[Name of graph database to add data to])
+# ARG_POSITIONAL_SINGLE([user],[Username for graph database access])
+# ARG_POSITIONAL_SINGLE([password],[Password for graph database user])
+# ARG_OPTIONAL_BOOLEAN([clear-data],[],[Whether or not to first clear all existing data from the graph database],[off])
+# ARG_OPTIONAL_BOOLEAN([use-stardog-syntax],[],[Set to use Stardog API endpoints to update the specified graph database. If unset, assumes the graph database is a GraphDB database.],[off])
+# ARG_OPTIONAL_BOOLEAN([log-output],[],[Whether or not to write the output to a log file],[off])
+# ARG_OPTIONAL_SINGLE([log-file],[],[Path to the log file],[LOG.txt])
+# ARGBASH_GO()
+# needed because of Argbash --> m4_ignore([
+### START OF CODE GENERATED BY Argbash v2.9.0 one line above ###
+# Argbash is a bash code generator used to get arguments parsing right.
+# Argbash is FREE SOFTWARE, see https://argbash.io for more info
+# Generated online by https://argbash.io/generate
+
+
+die()
+{
+	local _ret="${2:-1}"
+	test "${_PRINT_HELP:-no}" = yes && print_help >&2
+	echo "$1" >&2
+	exit "${_ret}"
+}
+
+
+begins_with_short_option()
+{
+	local first_option all_short_options='h'
+	first_option="${1:0:1}"
+	test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
+}
+
+# THE DEFAULTS INITIALIZATION - POSITIONALS
+_positionals=()
+# THE DEFAULTS INITIALIZATION - OPTIONALS
+_arg_clear_data="off"
+_arg_use_stardog_syntax="off"
+
+_arg_log_output="off"
+_arg_log_file="LOG.txt"
+
+print_help()
+{
+	printf '%s\n' "Upload JSONLD and Turtle data to a Neurobagel graph"
+	printf 'Usage: %s [-h|--help] [--(no-)clear-data] [--(no-)use-stardog-syntax] [--(no-)log-output] [--log-file <arg>] <dir> <graph-url> <graph-database> <user> <password>\n' "$0"
+	printf '\t%s\n' "<dir>: Path to directory containing .jsonld and/or .ttl files. ALL .jsonld and .ttl files in this directory will be uploaded."
+	printf '\t%s\n' "<graph-url>: Host and port at which to access the graph database to add data to (e.g., localhost:7200)"
+	printf '\t%s\n' "<graph-database>: Name of graph database to add data to"
+	printf '\t%s\n' "<user>: Username for graph database access"
+	printf '\t%s\n' "<password>: Password for graph database user"
+	printf '\t%s\n' "-h, --help: Prints help"
+	printf '\t%s\n' "--clear-data, --no-clear-data: Whether or not to first clear all existing data from the graph database (off by default)"
+	printf '\t%s\n' "--use-stardog-syntax, --no-use-stardog-syntax: Set to use Stardog API endpoints to update the specified graph database. If unset, assumes the graph database is a GraphDB database. (off by default)"
+  	printf '\t%s\n' "--log-output, --no-log-output: Whether or not to write the output to a log file (off by default)"
+    printf '\t%s\n' "--log-file: Path to the log file (default: 'LOG.txt')"
+}
+
+
+parse_commandline()
+{
+	_positionals_count=0
+	while test $# -gt 0
+	do
+		_key="$1"
+		case "$_key" in
+			-h|--help)
+				print_help
+				exit 0
+				;;
+			-h*)
+				print_help
+				exit 0
+				;;
+			--no-clear-data|--clear-data)
+				_arg_clear_data="on"
+				test "${1:0:5}" = "--no-" && _arg_clear_data="off"
+				;;
+			--no-use-stardog-syntax|--use-stardog-syntax)
+				_arg_use_stardog_syntax="on"
+				test "${1:0:5}" = "--no-" && _arg_use_stardog_syntax="off"
+				;;
+			--no-log-output|--log-output)
+				_arg_log_output="on"
+				test "${1:0:5}" = "--no-" && _arg_log_output="off"
+				;;
+			--log-file)
+				test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+				_arg_log_file="$2"
+				shift
+				;;
+			--log-file=*)
+				_arg_log_file="${_key##--log-file=}"
+				;;
+			*)
+				_last_positional="$1"
+				_positionals+=("$_last_positional")
+				_positionals_count=$((_positionals_count + 1))
+				;;
+		esac
+		shift
+	done
+}
+
+
+handle_passed_args_count()
+{
+	local _required_args_string="'dir', 'graph-url', 'graph-database', 'user' and 'password'"
+	test "${_positionals_count}" -ge 5 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require exactly 5 (namely: $_required_args_string), but got only ${_positionals_count}." 1
+	test "${_positionals_count}" -le 5 || _PRINT_HELP=yes die "FATAL ERROR: There were spurious positional arguments --- we expect exactly 5 (namely: $_required_args_string), but got ${_positionals_count} (the last one was: '${_last_positional}')." 1
+}
+
+
+assign_positional_args()
+{
+	local _positional_name _shift_for=$1
+	_positional_names="_arg_dir _arg_graph_url _arg_graph_database _arg_user _arg_password "
+
+	shift "$_shift_for"
+	for _positional_name in ${_positional_names}
+	do
+		test $# -gt 0 || break
+		eval "$_positional_name=\${1}" || die "Error during argument parsing, possibly an Argbash bug." 1
+		shift
+	done
+}
+
+parse_commandline "$@"
+handle_passed_args_count
+assign_positional_args 1 "${_positionals[@]}"
+
+# OTHER STUFF GENERATED BY Argbash
+
+### END OF CODE GENERATED BY Argbash (sortof) ### ])
+# [ <-- needed because of Argbash
+
+
+# Reassign positional args to more readable named variables (https://argbash.readthedocs.io/en/latest/guide.html#using-parsing-results)
+jsonld_dir=$_arg_dir
+user=$_arg_user
+password=$_arg_password
+graph_db=$_arg_graph_database
+graph_url=$_arg_graph_url
+clear_data=$_arg_clear_data  # value is either on or off (https://argbash.readthedocs.io/en/stable/guide.html#optional-arguments)
+use_stardog_syntax=$_arg_use_stardog_syntax
+
+log_output=$_arg_log_output
+log_file=$_arg_log_file
+
+DELETE_TRIPLES_QUERY="
+DELETE {
+	?s ?p ?o .
+} WHERE {
+	?s ?p ?o .
+}"
+
+# Depending on the graph backend used, set URLs for uploading data to and clearing data in graph database
+base_url="http://${graph_url}/${graph_db}"
+if [ "$use_stardog_syntax" = "on" ]; then
+	upload_data_url=$base_url
+	clear_data_url="${base_url}/update"
+else
+	upload_data_url="${base_url}/statements"
+	clear_data_url=$upload_data_url
+fi
+
+# Main logic
+main() {
+    # Clear existing data in graph database if requested
+    if [ "$clear_data" = "on" ]; then
+        echo -e "\nCLEARING EXISTING DATA FROM ${graph_db}..."
+
+        response=$(curl -u "${user}:${password}" -s -S -i -w "\n%{http_code}\n" \
+            -X POST $clear_data_url \
+            -H "Content-Type: application/sparql-update" \
+            --data-binary "${DELETE_TRIPLES_QUERY}")
+
+        # Extract and check status code outputted as final line of response
+        httpcode=$(tail -n1 <<< "$response")
+        if (( $httpcode < 200 || $httpcode >= 300 )); then
+            echo -e "\nERROR: Failed to clear ${graph_db}:"
+            echo "$(sed '$d' <<< "$response")"
+            echo -e "\nEXITING..."
+            exit 1
+        fi
+    fi
+
+    # Add data to specified graph database
+    echo -e "\nUPLOADING DATA FROM ${jsonld_dir} TO ${graph_db}...\n"
+
+    upload_failed=()
+
+    for db in ${jsonld_dir}/*.jsonld; do
+        # Prevent edge case where no matching files are present in directory and so loop executes once with glob pattern string itself
+        [ -e "$db" ] || continue
+
+        echo "$(basename ${db}):"
+        response=$(curl -u "${user}:${password}" -s -S -i -w "\n%{http_code}\n" \
+                    -X POST $upload_data_url \
+                    -H "Content-Type: application/ld+json" \
+                    --data-binary @${db})
+
+        httpcode=$(tail -n1 <<< "$response")
+        if (( $httpcode < 200 || $httpcode >= 300 )); then
+            upload_failed+=("${db}")
+        fi
+        # Print rest of response to stdout
+        echo -e "$(sed '$d' <<< "$response")\n"
+    done
+
+    for file in ${jsonld_dir}/*.ttl; do
+        [ -e "$file" ] || continue
+
+        echo "$(basename ${file}):"
+        response=$(curl -u "${user}:${password}" -s -S -i -w "\n%{http_code}\n" \
+                    -X POST $upload_data_url \
+                    -H "Content-Type: text/turtle" \
+                    --data-binary @${file})
+
+        httpcode=$(tail -n1 <<< "$response")
+        if (( $httpcode < 200 || $httpcode >= 300 )); then
+            upload_failed+=("${file}")
+        fi
+        echo -e "$(sed '$d' <<< "$response")\n"
+    done
+
+    echo "FINISHED UPLOADING DATA FROM ${jsonld_dir} TO ${graph_db}."
+
+    if (( ${#upload_failed[@]} != 0 )); then
+        echo -e "\nERROR: Upload failed for these files:"
+        printf '%s\n' "${upload_failed[@]}"
+    fi
+}
+
+# Call the main logic function with or without output redirection
+if [ "$log_output" = "on" ]; then
+    main > "$log_file"
+else
+    main
+fi
+# ] <-- needed because of Argbash
\ No newline at end of file
diff --git a/dev/data-config.ttl b/dev/data-config.ttl
new file mode 100644
index 0000000..386b706
--- /dev/null
+++ b/dev/data-config.ttl
@@ -0,0 +1,49 @@
+#
+# RDF4J configuration template for a GraphDB repository
+#
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
+@prefix rep: <http://www.openrdf.org/config/repository#>.
+@prefix sr: <http://www.openrdf.org/config/repository/sail#>.
+@prefix sail: <http://www.openrdf.org/config/sail#>.
+@prefix graphdb: <http://www.ontotext.com/config/graphdb#>.
+
+[] a rep:Repository ;
+    rep:repositoryID "my_db" ;
+    rdfs:label "" ;
+    rep:repositoryImpl [
+        rep:repositoryType "graphdb:SailRepository" ;
+        sr:sailImpl [
+            sail:sailType "graphdb:Sail" ;
+
+            graphdb:read-only "false" ;
+
+            # Inference and Validation
+            graphdb:ruleset "rdfsplus-optimized" ;
+            graphdb:disable-sameAs "true" ;
+            graphdb:check-for-inconsistencies "false" ;
+
+            # Indexing
+            graphdb:entity-id-size "32" ;
+            graphdb:enable-context-index "false" ;
+            graphdb:enablePredicateList "true" ;
+            graphdb:enable-fts-index "false" ;
+            graphdb:fts-indexes ("default" "iri") ;
+            graphdb:fts-string-literals-index "default" ;
+            graphdb:fts-iris-index "none" ;
+
+            # Queries and Updates
+            graphdb:query-timeout "0" ;
+            graphdb:throw-QueryEvaluationException-on-timeout "false" ;
+            graphdb:query-limit-results "0" ;
+
+            # Settable in the file but otherwise hidden in the UI and in the RDF4J console
+            graphdb:base-URL "http://example.org/owlim#" ;
+            graphdb:defaultNS "" ;
+            graphdb:imports "" ;
+            graphdb:repository-type "file-repository" ;
+            graphdb:storage-folder "storage" ;
+            graphdb:entity-index-size "10000000" ;
+            graphdb:in-memory-literal-properties "true" ;
+            graphdb:enable-literal-index "true" ;
+        ]
+    ].
\ No newline at end of file
diff --git a/dev/data-config_template.ttl b/dev/data-config_template.ttl
new file mode 100644
index 0000000..386b706
--- /dev/null
+++ b/dev/data-config_template.ttl
@@ -0,0 +1,49 @@
+#
+# RDF4J configuration template for a GraphDB repository
+#
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
+@prefix rep: <http://www.openrdf.org/config/repository#>.
+@prefix sr: <http://www.openrdf.org/config/repository/sail#>.
+@prefix sail: <http://www.openrdf.org/config/sail#>.
+@prefix graphdb: <http://www.ontotext.com/config/graphdb#>.
+
+[] a rep:Repository ;
+    rep:repositoryID "my_db" ;
+    rdfs:label "" ;
+    rep:repositoryImpl [
+        rep:repositoryType "graphdb:SailRepository" ;
+        sr:sailImpl [
+            sail:sailType "graphdb:Sail" ;
+
+            graphdb:read-only "false" ;
+
+            # Inference and Validation
+            graphdb:ruleset "rdfsplus-optimized" ;
+            graphdb:disable-sameAs "true" ;
+            graphdb:check-for-inconsistencies "false" ;
+
+            # Indexing
+            graphdb:entity-id-size "32" ;
+            graphdb:enable-context-index "false" ;
+            graphdb:enablePredicateList "true" ;
+            graphdb:enable-fts-index "false" ;
+            graphdb:fts-indexes ("default" "iri") ;
+            graphdb:fts-string-literals-index "default" ;
+            graphdb:fts-iris-index "none" ;
+
+            # Queries and Updates
+            graphdb:query-timeout "0" ;
+            graphdb:throw-QueryEvaluationException-on-timeout "false" ;
+            graphdb:query-limit-results "0" ;
+
+            # Settable in the file but otherwise hidden in the UI and in the RDF4J console
+            graphdb:base-URL "http://example.org/owlim#" ;
+            graphdb:defaultNS "" ;
+            graphdb:imports "" ;
+            graphdb:repository-type "file-repository" ;
+            graphdb:storage-folder "storage" ;
+            graphdb:entity-index-size "10000000" ;
+            graphdb:in-memory-literal-properties "true" ;
+            graphdb:enable-literal-index "true" ;
+        ]
+    ].
\ No newline at end of file
diff --git a/dev/data/example_synthetic.jsonld b/dev/data/example_synthetic.jsonld
new file mode 100644
index 0000000..937951b
--- /dev/null
+++ b/dev/data/example_synthetic.jsonld
@@ -0,0 +1,331 @@
+{
+  "@context": {
+    "nb": "http://neurobagel.org/vocab/",
+    "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/",
+    "nidm": "http://purl.org/nidash/nidm#",
+    "cogatlas": "https://www.cognitiveatlas.org/task/id/",
+    "ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
+    "Acquisition": "nb:Acquisition",
+    "identifier": "@id",
+    "hasContrastType": {
+      "@id": "nb:hasContrastType"
+    },
+    "schemaKey": "@type",
+    "Assessment": "nb:Assessment",
+    "Bagel": "nb:Bagel",
+    "BaseModel": "nb:BaseModel",
+    "ControlledTerm": "nb:ControlledTerm",
+    "Dataset": "nb:Dataset",
+    "hasLabel": {
+      "@id": "nb:hasLabel"
+    },
+    "hasPortalURI": {
+      "@id": "nb:hasPortalURI"
+    },
+    "hasSamples": {
+      "@id": "nb:hasSamples"
+    },
+    "Diagnosis": "nb:Diagnosis",
+    "Image": "nb:Image",
+    "ImagingSession": "nb:ImagingSession",
+    "hasFilePath": {
+      "@id": "nb:hasFilePath"
+    },
+    "hasAcquisition": {
+      "@id": "nb:hasAcquisition"
+    },
+    "PhenotypicSession": "nb:PhenotypicSession",
+    "hasAge": {
+      "@id": "nb:hasAge"
+    },
+    "hasSex": {
+      "@id": "nb:hasSex"
+    },
+    "isSubjectGroup": {
+      "@id": "nb:isSubjectGroup"
+    },
+    "hasDiagnosis": {
+      "@id": "nb:hasDiagnosis"
+    },
+    "hasAssessment": {
+      "@id": "nb:hasAssessment"
+    },
+    "Session": "nb:Session",
+    "Sex": "nb:Sex",
+    "Subject": "nb:Subject",
+    "hasSession": {
+      "@id": "nb:hasSession"
+    },
+    "SubjectGroup": "nb:SubjectGroup"
+  },
+  "identifier": "nb:e0c7d08c-edcc-4c2a-816a-306878ed7be2",
+  "hasLabel": "BIDS synthetic",
+  "hasPortalURI": "https://github.com/bids-standard/bids-examples",
+  "hasSamples": [
+    {
+      "identifier": "nb:34ec1e2d-9a81-4a50-bcd0-eb22c88d11e1",
+      "hasLabel": "sub-01",
+      "hasSession": [
+        {
+          "identifier": "nb:85c7473c-6122-4999-ad3b-5cd57a883c87",
+          "hasLabel": "ses-01",
+          "hasAge": 34.1,
+          "hasSex": {
+            "identifier": "snomed:248152002",
+            "schemaKey": "Sex"
+          },
+          "isSubjectGroup": {
+            "identifier": "ncit:C94342",
+            "schemaKey": "SubjectGroup"
+          },
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        },
+        {
+          "identifier": "nb:eb57d0c1-fb96-4c04-8c16-1f29f7f40db4",
+          "hasLabel": "ses-02",
+          "hasAge": 35.3,
+          "hasSex": {
+            "identifier": "snomed:248152002",
+            "schemaKey": "Sex"
+          },
+          "isSubjectGroup": {
+            "identifier": "ncit:C94342",
+            "schemaKey": "SubjectGroup"
+          },
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        }
+      ],
+      "schemaKey": "Subject"
+    },
+    {
+      "identifier": "nb:2de41397-805f-4059-b464-388ef501d6e5",
+      "hasLabel": "sub-02",
+      "hasSession": [
+        {
+          "identifier": "nb:0ce182f3-b47c-4b50-8b76-8f257e490cf3",
+          "hasLabel": "ses-01",
+          "hasSex": {
+            "identifier": "snomed:248153007",
+            "schemaKey": "Sex"
+          },
+          "hasDiagnosis": [
+            {
+              "identifier": "snomed:406506008",
+              "schemaKey": "Diagnosis"
+            }
+          ],
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        },
+        {
+          "identifier": "nb:4871d5c2-963f-4825-ab43-85a87edac4ce",
+          "hasLabel": "ses-02",
+          "hasAge": 39.0,
+          "hasSex": {
+            "identifier": "snomed:248153007",
+            "schemaKey": "Sex"
+          },
+          "hasDiagnosis": [
+            {
+              "identifier": "snomed:406506008",
+              "schemaKey": "Diagnosis"
+            }
+          ],
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        }
+      ],
+      "schemaKey": "Subject"
+    },
+    {
+      "identifier": "nb:d4258426-2971-43ff-92fa-4b20bd21c31f",
+      "hasLabel": "sub-03",
+      "hasSession": [
+        {
+          "identifier": "nb:3f9c82d5-6648-4b9b-8f86-195ee9283875",
+          "hasLabel": "ses-01",
+          "hasAge": 22.1,
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        },
+        {
+          "identifier": "nb:0f7fe93b-13b1-4ca7-9e58-b997a18ec9b9",
+          "hasLabel": "ses-02",
+          "hasAge": 23.2,
+          "hasDiagnosis": [
+            {
+              "identifier": "snomed:406506008",
+              "schemaKey": "Diagnosis"
+            }
+          ],
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        }
+      ],
+      "schemaKey": "Subject"
+    },
+    {
+      "identifier": "nb:73193f71-cd19-4b8c-ae73-abc882e9b688",
+      "hasLabel": "sub-04",
+      "hasSession": [
+        {
+          "identifier": "nb:962aa986-dbd7-4412-a180-49c0a24c9f87",
+          "hasLabel": "ses-01",
+          "hasAge": 21.1,
+          "hasSex": {
+            "identifier": "snomed:248152002",
+            "schemaKey": "Sex"
+          },
+          "isSubjectGroup": {
+            "identifier": "ncit:C94342",
+            "schemaKey": "SubjectGroup"
+          },
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        },
+        {
+          "identifier": "nb:8622fc66-013d-4675-a328-fdcccd4616b0",
+          "hasLabel": "ses-02",
+          "hasAge": 22.3,
+          "hasSex": {
+            "identifier": "snomed:248152002",
+            "schemaKey": "Sex"
+          },
+          "isSubjectGroup": {
+            "identifier": "ncit:C94342",
+            "schemaKey": "SubjectGroup"
+          },
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        }
+      ],
+      "schemaKey": "Subject"
+    },
+    {
+      "identifier": "nb:cb8d7a96-fdec-425c-b0b5-9e9ac3c70e8c",
+      "hasLabel": "sub-05",
+      "hasSession": [
+        {
+          "identifier": "nb:1d7c30f5-cae9-43c9-a154-26dbe0029594",
+          "hasLabel": "ses-01",
+          "hasAge": 42.5,
+          "hasSex": {
+            "identifier": "snomed:248153007",
+            "schemaKey": "Sex"
+          },
+          "hasDiagnosis": [
+            {
+              "identifier": "snomed:406506008",
+              "schemaKey": "Diagnosis"
+            }
+          ],
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        },
+        {
+          "identifier": "nb:2401e418-6f9b-4113-9511-b1b9a332a5d0",
+          "hasLabel": "ses-02",
+          "hasAge": 43.2,
+          "hasSex": {
+            "identifier": "snomed:248153007",
+            "schemaKey": "Sex"
+          },
+          "hasDiagnosis": [
+            {
+              "identifier": "snomed:406506008",
+              "schemaKey": "Diagnosis"
+            }
+          ],
+          "hasAssessment": [
+            {
+              "identifier": "cogatlas:trm_57964b8a66aed",
+              "schemaKey": "Assessment"
+            },
+            {
+              "identifier": "cogatlas:tsk_4a57abb949ece",
+              "schemaKey": "Assessment"
+            }
+          ],
+          "schemaKey": "PhenotypicSession"
+        }
+      ],
+      "schemaKey": "Subject"
+    }
+  ],
+  "schemaKey": "Dataset"
+}
\ No newline at end of file
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
new file mode 100644
index 0000000..0394707
--- /dev/null
+++ b/dev/docker-compose.yml
@@ -0,0 +1,42 @@
+version: "3.8"
+
+services:
+  api:
+    image: "neurobagel/api:${NB_NAPI_TAG:-latest}"
+    ports:
+      - "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
+    environment:
+      NB_GRAPH_USERNAME: ${NB_GRAPH_USERNAME}
+      NB_GRAPH_PASSWORD: ${NB_GRAPH_PASSWORD}
+      NB_GRAPH_ADDRESS: ${NB_GRAPH_ADDRESS:-graph}
+      NB_GRAPH_PORT: ${NB_GRAPH_PORT:-7200}
+      NB_GRAPH_DB: ${NB_GRAPH_DB:-repositories/my_db}
+      NB_RETURN_AGG: ${NB_RETURN_AGG:-true}
+      NB_API_PORT: ${NB_NAPI_PORT:-8000}
+      NB_API_ALLOWED_ORIGINS: ${NB_NAPI_ALLOWED_ORIGINS}
+  graph:
+    image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
+    volumes:
+      - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
+      - "${PWD}:/usr/src"
+    ports:
+      - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
+    entrypoint:
+      - "/usr/src/setup.sh"
+    working_dir: "/usr/src"
+  federation:
+    image: "neurobagel/federation_api:${NB_FAPI_TAG:-latest}"
+    ports:
+      - "${NB_FAPI_PORT_HOST:-8080}:${NB_FAPI_PORT:-8000}"
+    volumes:
+      - "${PWD}/local_nb_nodes.json:/usr/src/local_nb_nodes.json:ro"
+    environment:
+      NB_API_PORT: ${NB_FAPI_PORT:-8000}
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+  query:
+    image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
+    ports:
+      - "${NB_QUERY_PORT_HOST:-3000}:5173"
+    environment:
+      NB_API_QUERY_URL: ${NB_API_QUERY_URL:-http://localhost:8000/}
\ No newline at end of file
diff --git a/dev/graphdb_setup.sh b/dev/graphdb_setup.sh
new file mode 100755
index 0000000..62a16f5
--- /dev/null
+++ b/dev/graphdb_setup.sh
@@ -0,0 +1,200 @@
+#!/bin/bash
+#
+# ARG_POSITIONAL_SINGLE([admin-pass],[Password for the "admin" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users.])
+# ARG_OPTIONAL_SINGLE([env-file-path],[],[Path to a .env file containing environment variables for Neurobagel node configuration.],[.env])
+# ARG_OPTIONAL_BOOLEAN([run-user-setup],[],[Whether or not to run the first-time GraphDB setup steps, including changing the admin password and creating a new database user.],[on])
+# ARG_HELP([Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/.])
+# ARGBASH_GO()
+# needed because of Argbash --> m4_ignore([
+### START OF CODE GENERATED BY Argbash v2.9.0 one line above ###
+# Argbash is a bash code generator used to get arguments parsing right.
+# Argbash is FREE SOFTWARE, see https://argbash.io for more info
+# Generated online by https://argbash.io/generate
+
+
+die()
+{
+	local _ret="${2:-1}"
+	test "${_PRINT_HELP:-no}" = yes && print_help >&2
+	echo "$1" >&2
+	exit "${_ret}"
+}
+
+
+begins_with_short_option()
+{
+	local first_option all_short_options='h'
+	first_option="${1:0:1}"
+	test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
+}
+
+# THE DEFAULTS INITIALIZATION - POSITIONALS
+_positionals=()
+# THE DEFAULTS INITIALIZATION - OPTIONALS
+_arg_env_file_path=".env"
+_arg_run_user_setup="on"
+
+
+print_help()
+{
+	printf '%s\n' "Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/."
+	printf 'Usage: %s [--env-file-path <arg>] [--(no-)run-user-setup] [-h|--help] <admin-pass>\n' "$0"
+	printf '\t%s\n' "<admin-pass>: Password for the \"admin\" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users."
+	printf '\t%s\n' "--env-file-path: Path to a .env file containing environment variables for Neurobagel node configuration. (default: '.env')"
+	printf '\t%s\n' "--run-user-setup, --no-run-user-setup: Whether or not to run the first-time GraphDB setup steps, including changing the admin password and creating a new database user. (on by default)"
+	printf '\t%s\n' "-h, --help: Prints help"
+}
+
+
+parse_commandline()
+{
+	_positionals_count=0
+	while test $# -gt 0
+	do
+		_key="$1"
+		case "$_key" in
+			--env-file-path)
+				test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+				_arg_env_file_path="$2"
+				shift
+				;;
+			--env-file-path=*)
+				_arg_env_file_path="${_key##--env-file-path=}"
+				;;
+			--no-run-user-setup|--run-user-setup)
+				_arg_run_user_setup="on"
+				test "${1:0:5}" = "--no-" && _arg_run_user_setup="off"
+				;;
+			-h|--help)
+				print_help
+				exit 0
+				;;
+			-h*)
+				print_help
+				exit 0
+				;;
+			*)
+				_last_positional="$1"
+				_positionals+=("$_last_positional")
+				_positionals_count=$((_positionals_count + 1))
+				;;
+		esac
+		shift
+	done
+}
+
+
+handle_passed_args_count()
+{
+	local _required_args_string="'admin-pass'"
+	test "${_positionals_count}" -ge 1 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require exactly 1 (namely: $_required_args_string), but got only ${_positionals_count}." 1
+	test "${_positionals_count}" -le 1 || _PRINT_HELP=yes die "FATAL ERROR: There were spurious positional arguments --- we expect exactly 1 (namely: $_required_args_string), but got ${_positionals_count} (the last one was: '${_last_positional}')." 1
+}
+
+
+assign_positional_args()
+{
+	local _positional_name _shift_for=$1
+	_positional_names="_arg_admin_pass "
+
+	shift "$_shift_for"
+	for _positional_name in ${_positional_names}
+	do
+		test $# -gt 0 || break
+		eval "$_positional_name=\${1}" || die "Error during argument parsing, possibly an Argbash bug." 1
+		shift
+	done
+}
+
+parse_commandline "$@"
+handle_passed_args_count
+assign_positional_args 1 "${_positionals[@]}"
+
+# OTHER STUFF GENERATED BY Argbash
+
+### END OF CODE GENERATED BY Argbash (sortof) ### ])
+# [ <-- needed because of Argbash
+
+set -euo pipefail
+
+# Reassign command line args to more readable named variables
+ENV_FILE_PATH=$_arg_env_file_path
+ADMIN_PASS=$_arg_admin_pass
+RUN_USER_SETUP=$_arg_run_user_setup
+
+# Set the environment variables in the shell, to use in the script
+source "${ENV_FILE_PATH}"
+echo "Environment variables have been set from ${ENV_FILE_PATH}."
+
+# Extract just the database name
+DB_NAME="${NB_GRAPH_DB#repositories/}"
+NB_GRAPH_PORT_HOST=${NB_GRAPH_PORT_HOST:-7200}
+
+# Get the directory of this script to be able to find the data-config_template.ttl file
+SCRIPT_DIR=$(dirname "$0")
+
+echo "The GraphDB server is being accessed at http://localhost:${NB_GRAPH_PORT_HOST}."
+
+##### First time GraphDB setup #####
+
+if [ "${RUN_USER_SETUP}" = "on" ]; then
+    echo "First time GraphDB user setup enabled."
+
+    # 1. Change database admin password
+    echo "Changing the admin password (note: if you have previously set the admin password, this has no effect)..."
+	# TODO: To change a *previously set* admin password, we need to also provide the current password via -u
+    curl -X PATCH --header 'Content-Type: application/json' http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/admin -d "{\"password\": \""${ADMIN_PASS}"\"}"
+    
+	# 2. If security is not enabled, enable it (i.e. allow only authenticated users access)
+	is_security_enabled=$(curl -s -X GET http://localhost:${NB_GRAPH_PORT_HOST}/rest/security)
+	if [ "${is_security_enabled}" = "false" ]; then
+		echo "Enabling password-based access control to all databases ..."
+		# NOTE: This command fails without credentials once security is enabled
+		curl -X POST --header 'Content-Type: application/json' -d true http://localhost:${NB_GRAPH_PORT_HOST}/rest/security
+	else
+		echo "Password-based access control has already been enabled."
+	fi
+
+    # 3. Create a new database user
+	# TODO: Separate this out from the first-time setup? As this can technically be run at any time to create additional users.
+	# NOTE: If user already exists, response will be "An account with the given username already exists." OK for script.
+	echo "Creating a new database user ${NB_GRAPH_USERNAME}..."
+    curl -X POST --header 'Content-Type: application/json' -u "admin:${ADMIN_PASS}" -d @- http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/${NB_GRAPH_USERNAME} <<EOF
+    {
+        "username": "${NB_GRAPH_USERNAME}",
+        "password": "${NB_GRAPH_PASSWORD}"
+    } 
+EOF
+fi
+
+
+##### Database setup #####
+
+# 4. Create and save custom configuration file for the new database
+# TODO: Should we add a suffix to data-config.ttl for the db name?
+echo "Creating a GraphDB configuration file (./data-config.ttl) for the new database ${DB_NAME}..."
+sed 's/rep:repositoryID "my_db" ;/rep:repositoryID "'"${DB_NAME}"'" ;/' ${SCRIPT_DIR}/data-config_template.ttl > data-config.ttl
+
+# 5. Create a new database
+# Assumes data-config.ttl is in the same directory as this script!
+echo "Creating the GraphDB database ${DB_NAME}..."
+curl -X PUT -u "admin:${ADMIN_PASS}" http://localhost:${NB_GRAPH_PORT_HOST}/${NB_GRAPH_DB} --data-binary "@data-config.ttl" -H "Content-Type: application/x-turtle"
+
+# 6. Grant newly created user access permission to the database
+# Confirm user wants to proceed with changing user permissions
+# while true; do
+# 	read -p "WARNING: We will now give ${NB_GRAPH_USERNAME} read/write access to ${NB_GRAPH_DB}. This operation will REPLACE any existing permissions you have granted to user ${NB_GRAPH_USERNAME}, including any access to other databases. ${NB_GRAPH_USERNAME} may lose access to other databases as a result. Proceed? (y/n) " yn
+# 	case $yn in
+# 		[Yy]* ) break;;
+# 		[Nn]* ) echo "Exiting..."; exit;;
+# 		* ) echo "Please answer y or n.";;
+# 	esac
+# done
+
+echo "Granting user ${NB_GRAPH_USERNAME} read/write permissions to database ${DB_NAME}..."
+curl -X PUT --header 'Content-Type: application/json' -d "
+{\"grantedAuthorities\": [\"WRITE_REPO_${DB_NAME}\",\"READ_REPO_${DB_NAME}\"]}" http://localhost:${NB_GRAPH_PORT_HOST}/rest/security/users/${NB_GRAPH_USERNAME} -u "admin:${ADMIN_PASS}"
+
+echo "Done."
+
+# ] <-- needed because of Argbash
diff --git a/dev/local_nb_nodes.json b/dev/local_nb_nodes.json
new file mode 100644
index 0000000..9a07778
--- /dev/null
+++ b/dev/local_nb_nodes.json
@@ -0,0 +1,10 @@
+[
+    {
+        "NodeName": "Local graph 1",
+        "ApiURL": "http://host.docker.internal:8000"
+    },
+    {
+        "NodeName": "Local graph 2",
+        "ApiURL": "http://192.168.0.1"
+    }
+]
diff --git a/dev/setup.sh b/dev/setup.sh
new file mode 100755
index 0000000..78ee08b
--- /dev/null
+++ b/dev/setup.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+echo "The script is running..."
+
+/opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/ &
+
+# Waiting for GraphDB to start
+while ! curl --silent "localhost:7200/rest/repositories" | grep '\[\]'; do
+    :
+done
+
+echo "Running GraphDB setup..."
+
+./graphdb_setup.sh apple
+
+echo "GraphDB set up complete."
+
+echo "Adding data to databases..."
+./add_data_to_graph.sh ./data localhost:7200 repositories/my_db DBUSER DBPASSWORD
+
+
+tail -f /dev/null
+

From 090e73c49a950b58985e38edaf2481358be5f7d4 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 4 Apr 2024 17:29:58 -0400
Subject: [PATCH 02/25] Added `template.env` file

---
 dev/template.env | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 dev/template.env

diff --git a/dev/template.env b/dev/template.env
new file mode 100644
index 0000000..08aed56
--- /dev/null
+++ b/dev/template.env
@@ -0,0 +1,40 @@
+# THIS IS A TEMPLATE .env FILE. MAKE A COPY OF THIS FILE NAMED .env 
+# AND MODIFY THE VALUES AS DESCRIBED IN THE DOCUMENTATION.
+
+# ---- CONFIGURATION FOR graph ----
+NB_GRAPH_USERNAME=DBUSER  # REPLACE DBUSER WITH YOUR GRAPH DATABASE USERNAME
+NB_GRAPH_PASSWORD=DBPASSWORD  # REPLACE DBPASSWORD WITH YOUR GRAPH DATABASE PASSWORD
+NB_GRAPH_DB=repositories/my_db
+NB_RETURN_AGG=true
+NB_NAPI_TAG=latest
+NB_GRAPH_IMG=ontotext/graphdb:10.3.1
+
+
+# ---- CONFIGURATION FOR n-API ----
+## ADDITIONAL CONFIGURABLE PARAMETERS: Uncomment and modify values of the below variables as needed to use non-default values.
+NB_NAPI_ALLOWED_ORIGINS=""  # Allow multiple origins of requests. e.g. For a query tool deployed locally using default ports, use: NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
+NB_NAPI_PORT_HOST=8000
+NB_NAPI_PORT=8000
+NB_GRAPH_ROOT_HOST=~/graphdb-home
+NB_GRAPH_ROOT_CONT=/opt/graphdb/home
+NB_GRAPH_ADDRESS=graph
+NB_GRAPH_PORT_HOST=7200
+NB_GRAPH_PORT=7200
+NB_QUERY_TAG=latest
+NB_QUERY_PORT_HOST=3000
+
+# ---- CONFIGURATION FOR f-API ----
+# Port that the f-API will run on INSIDE the docker container (default 8000)
+NB_FAPI_PORT=8000
+# Port that the f-API will be exposed on to the host computer (and likely the outside network)
+NB_FAPI_PORT_HOST=8080
+# Docker image tag of the f-API (default latest)
+NB_FAPI_TAG=latest
+
+# ---- CONFIGURATION FOR QUERY TOOL ----
+# URL of the f-API as it will appear to a user
+NB_API_QUERY_URL=http://localhost:8080
+# Docker image tag of the query tool (default latest)
+NB_QUERY_TAG=latest
+# Port that the query tool will be exposed on the host and likely the network (default 3000)
+NB_QUERY_PORT_HOST=3000
\ No newline at end of file

From 508902dee6cd0923424acb9e0822610257bafc49 Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Thu, 4 Apr 2024 19:37:40 -0400
Subject: [PATCH 03/25] Added vocab file and renamed .env

.env is ignored by default
---
 dev/{template.env => .env} |  2 +-
 dev/data/nb_vocab.ttl      | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 1 deletion(-)
 rename dev/{template.env => .env} (87%)
 create mode 100644 dev/data/nb_vocab.ttl

diff --git a/dev/template.env b/dev/.env
similarity index 87%
rename from dev/template.env
rename to dev/.env
index 08aed56..f2435de 100644
--- a/dev/template.env
+++ b/dev/.env
@@ -12,7 +12,7 @@ NB_GRAPH_IMG=ontotext/graphdb:10.3.1
 
 # ---- CONFIGURATION FOR n-API ----
 ## ADDITIONAL CONFIGURABLE PARAMETERS: Uncomment and modify values of the below variables as needed to use non-default values.
-NB_NAPI_ALLOWED_ORIGINS=""  # Allow multiple origins of requests. e.g. For a query tool deployed locally using default ports, use: NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
+NB_NAPI_ALLOWED_ORIGINS="*"  # Allow multiple origins of requests. e.g. For a query tool deployed locally using default ports, use: NB_API_ALLOWED_ORIGINS="http://localhost:3000 http://127.0.0.1:3000"
 NB_NAPI_PORT_HOST=8000
 NB_NAPI_PORT=8000
 NB_GRAPH_ROOT_HOST=~/graphdb-home
diff --git a/dev/data/nb_vocab.ttl b/dev/data/nb_vocab.ttl
new file mode 100644
index 0000000..2dd308b
--- /dev/null
+++ b/dev/data/nb_vocab.ttl
@@ -0,0 +1,37 @@
+@prefix nb: <http://neurobagel.org/vocab/> . 
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+nb:Acquisition
+    a rdfs:Class.
+
+nb:Age
+    a rdfs:Class.
+
+nb:Assessment 
+    a rdfs:Class ;
+    rdfs:subClassOf nb:ControlledTerm .
+
+nb:ControlledTerm
+    a rdfs:Class.
+
+nb:Diagnosis
+    a rdfs:Class ;
+    rdfs:subClassOf nb:ControlledTerm .
+
+nb:Image
+    a rdfs:Class ;
+    rdfs:subClassOf nb:ControlledTerm .
+
+nb:Session
+    a rdfs:Class.
+
+nb:Sex
+    a rdfs:Class ;
+    rdfs:subClassOf nb:ControlledTerm .
+
+nb:Subject 
+    a rdfs:Class.
+
+nb:SubjectGroup
+    a rdfs:Class ;
+    rdfs:subClassOf nb:ControlledTerm .

From 95db818859afe39819945787f3159a0a78f9ab9c Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Thu, 4 Apr 2024 20:11:43 -0400
Subject: [PATCH 04/25] Wait specifically for the graphDB process ID

---
 dev/setup.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/dev/setup.sh b/dev/setup.sh
index 78ee08b..4990eae 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -3,6 +3,7 @@
 echo "The script is running..."
 
 /opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/ &
+GRAPHDB_PID=$!
 
 # Waiting for GraphDB to start
 while ! curl --silent "localhost:7200/rest/repositories" | grep '\[\]'; do
@@ -19,5 +20,7 @@ echo "Adding data to databases..."
 ./add_data_to_graph.sh ./data localhost:7200 repositories/my_db DBUSER DBPASSWORD
 
 
-tail -f /dev/null
+# We don't have jobcontrol here, so can't bring graphdb back to foreground
+# instead we'll wait
+wait $GRAPHDB_PID
 

From c94bf0bae4c4cab431cb47ef9cbe6cd241987e85 Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Thu, 4 Apr 2024 20:24:20 -0400
Subject: [PATCH 05/25] Use Docker service name for local node

---
 dev/docker-compose.yml  | 4 ++++
 dev/local_nb_nodes.json | 6 +-----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index 0394707..5dbf898 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -1,6 +1,7 @@
 version: "3.8"
 
 services:
+
   api:
     image: "neurobagel/api:${NB_NAPI_TAG:-latest}"
     ports:
@@ -14,6 +15,7 @@ services:
       NB_RETURN_AGG: ${NB_RETURN_AGG:-true}
       NB_API_PORT: ${NB_NAPI_PORT:-8000}
       NB_API_ALLOWED_ORIGINS: ${NB_NAPI_ALLOWED_ORIGINS}
+  
   graph:
     image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
     volumes:
@@ -24,6 +26,7 @@ services:
     entrypoint:
       - "/usr/src/setup.sh"
     working_dir: "/usr/src"
+
   federation:
     image: "neurobagel/federation_api:${NB_FAPI_TAG:-latest}"
     ports:
@@ -34,6 +37,7 @@ services:
       NB_API_PORT: ${NB_FAPI_PORT:-8000}
     extra_hosts:
       - "host.docker.internal:host-gateway"
+
   query:
     image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
     ports:
diff --git a/dev/local_nb_nodes.json b/dev/local_nb_nodes.json
index 9a07778..bc5fea7 100644
--- a/dev/local_nb_nodes.json
+++ b/dev/local_nb_nodes.json
@@ -1,10 +1,6 @@
 [
     {
         "NodeName": "Local graph 1",
-        "ApiURL": "http://host.docker.internal:8000"
-    },
-    {
-        "NodeName": "Local graph 2",
-        "ApiURL": "http://192.168.0.1"
+        "ApiURL": "http://api:8000"
     }
 ]

From af42e5f0e906a02b82c5f5740cda5135021f84f2 Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Thu, 4 Apr 2024 20:34:03 -0400
Subject: [PATCH 06/25] Add profiles

- "dev" replaces the old behaviour
- other profile names replace the files in the other subdirectories
- start with `docker compose --profile <NAME> up`
---
 dev/docker-compose.yml | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index 5dbf898..53e0755 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -4,6 +4,10 @@ services:
 
   api:
     image: "neurobagel/api:${NB_NAPI_TAG:-latest}"
+    profiles:
+      - "local_node"
+      - "local_node_query"
+      - "dev"
     ports:
       - "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
     environment:
@@ -18,6 +22,10 @@ services:
   
   graph:
     image: "${NB_GRAPH_IMG:-ontotext/graphdb:10.3.1}"
+    profiles:
+      - "local_node"
+      - "local_node_query"
+      - "dev"
     volumes:
       - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
       - "${PWD}:/usr/src"
@@ -29,17 +37,22 @@ services:
 
   federation:
     image: "neurobagel/federation_api:${NB_FAPI_TAG:-latest}"
+    profiles:
+      - "local_federation"
+      - "dev"
     ports:
       - "${NB_FAPI_PORT_HOST:-8080}:${NB_FAPI_PORT:-8000}"
     volumes:
       - "${PWD}/local_nb_nodes.json:/usr/src/local_nb_nodes.json:ro"
     environment:
       NB_API_PORT: ${NB_FAPI_PORT:-8000}
-    extra_hosts:
-      - "host.docker.internal:host-gateway"
 
   query:
     image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
+    profiles:
+      - "local_federation"
+      - "local_node_query"
+      - "dev"
     ports:
       - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:

From 83fae936de3b38014ebf7771da46296d29aae80f Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Thu, 4 Apr 2024 21:01:17 -0400
Subject: [PATCH 07/25] Make the local data directory configurable

---
 dev/.env               | 1 +
 dev/docker-compose.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/dev/.env b/dev/.env
index f2435de..427e848 100644
--- a/dev/.env
+++ b/dev/.env
@@ -9,6 +9,7 @@ NB_RETURN_AGG=true
 NB_NAPI_TAG=latest
 NB_GRAPH_IMG=ontotext/graphdb:10.3.1
 
+LOCAL_GRAPH_DATA=./data
 
 # ---- CONFIGURATION FOR n-API ----
 ## ADDITIONAL CONFIGURABLE PARAMETERS: Uncomment and modify values of the below variables as needed to use non-default values.
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index 53e0755..93b1e5c 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -29,6 +29,7 @@ services:
     volumes:
       - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
       - "${PWD}:/usr/src"
+      - "${LOCAL_GRAPH_DATA}:/data"
     ports:
       - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
     entrypoint:

From 1143a4f5961f05b68157f7f7df1f518291010418 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Tue, 9 Apr 2024 22:41:13 -0400
Subject: [PATCH 08/25] upload vocab from separate directory + more progress
 messages

---
 dev/setup.sh                     | 19 +++++++++++--------
 dev/{data => vocab}/nb_vocab.ttl |  0
 2 files changed, 11 insertions(+), 8 deletions(-)
 rename dev/{data => vocab}/nb_vocab.ttl (100%)

diff --git a/dev/setup.sh b/dev/setup.sh
index 4990eae..7b168eb 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-echo "The script is running..."
+echo "Setting up a Neurobagel graph backend..."
 
 /opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/ &
 GRAPHDB_PID=$!
@@ -10,17 +10,20 @@ while ! curl --silent "localhost:7200/rest/repositories" | grep '\[\]'; do
     :
 done
 
-echo "Running GraphDB setup..."
-
+echo "Running GraphDB server setup..."
 ./graphdb_setup.sh apple
+echo "Finished server setup."
 
-echo "GraphDB set up complete."
-
-echo "Adding data to databases..."
+echo "Adding datasets to the database..."
 ./add_data_to_graph.sh ./data localhost:7200 repositories/my_db DBUSER DBPASSWORD
+echo "Finished adding datasets to databases."
 
+echo "Adding Neurobagel vocabulary to the database"
+./add_data_to_graph.sh ./vocab localhost:7200 repositories/my_db DBUSER DBPASSWORD
+echo "Finished adding the Neurobagel vocabulary to the database."
 
-# We don't have jobcontrol here, so can't bring graphdb back to foreground
+echo "Finished setting up the Neurobagel graph backend."
+
+# We don't have jobcontrol here, so can't bring GraphDB back to foreground
 # instead we'll wait
 wait $GRAPHDB_PID
-
diff --git a/dev/data/nb_vocab.ttl b/dev/vocab/nb_vocab.ttl
similarity index 100%
rename from dev/data/nb_vocab.ttl
rename to dev/vocab/nb_vocab.ttl

From 30561d320b62ba60d00924dfc2e40879fdb9dce9 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Tue, 9 Apr 2024 22:42:18 -0400
Subject: [PATCH 09/25] remove non-template data-config.ttl (auto-created
 during setup)

---
 dev/data-config.ttl | 49 ---------------------------------------------
 1 file changed, 49 deletions(-)
 delete mode 100644 dev/data-config.ttl

diff --git a/dev/data-config.ttl b/dev/data-config.ttl
deleted file mode 100644
index 386b706..0000000
--- a/dev/data-config.ttl
+++ /dev/null
@@ -1,49 +0,0 @@
-#
-# RDF4J configuration template for a GraphDB repository
-#
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
-@prefix rep: <http://www.openrdf.org/config/repository#>.
-@prefix sr: <http://www.openrdf.org/config/repository/sail#>.
-@prefix sail: <http://www.openrdf.org/config/sail#>.
-@prefix graphdb: <http://www.ontotext.com/config/graphdb#>.
-
-[] a rep:Repository ;
-    rep:repositoryID "my_db" ;
-    rdfs:label "" ;
-    rep:repositoryImpl [
-        rep:repositoryType "graphdb:SailRepository" ;
-        sr:sailImpl [
-            sail:sailType "graphdb:Sail" ;
-
-            graphdb:read-only "false" ;
-
-            # Inference and Validation
-            graphdb:ruleset "rdfsplus-optimized" ;
-            graphdb:disable-sameAs "true" ;
-            graphdb:check-for-inconsistencies "false" ;
-
-            # Indexing
-            graphdb:entity-id-size "32" ;
-            graphdb:enable-context-index "false" ;
-            graphdb:enablePredicateList "true" ;
-            graphdb:enable-fts-index "false" ;
-            graphdb:fts-indexes ("default" "iri") ;
-            graphdb:fts-string-literals-index "default" ;
-            graphdb:fts-iris-index "none" ;
-
-            # Queries and Updates
-            graphdb:query-timeout "0" ;
-            graphdb:throw-QueryEvaluationException-on-timeout "false" ;
-            graphdb:query-limit-results "0" ;
-
-            # Settable in the file but otherwise hidden in the UI and in the RDF4J console
-            graphdb:base-URL "http://example.org/owlim#" ;
-            graphdb:defaultNS "" ;
-            graphdb:imports "" ;
-            graphdb:repository-type "file-repository" ;
-            graphdb:storage-folder "storage" ;
-            graphdb:entity-index-size "10000000" ;
-            graphdb:in-memory-literal-properties "true" ;
-            graphdb:enable-literal-index "true" ;
-        ]
-    ].
\ No newline at end of file

From 205b1864743a6f37742f71094a707b63ae7bbc9b Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Tue, 9 Apr 2024 22:47:41 -0400
Subject: [PATCH 10/25] add data-config.ttl to gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 0afcf87..8810f99 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,6 +143,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# Neurobagel
+data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
+
 # Pyre type checker
 .pyre/
 

From b5b97951074f8a0100ca21f468bba036526b7c44 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Tue, 9 Apr 2024 23:11:23 -0400
Subject: [PATCH 11/25] fix default value and mounting of data/

---
 dev/.env               | 1 -
 dev/docker-compose.yml | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/dev/.env b/dev/.env
index 427e848..6302bf7 100644
--- a/dev/.env
+++ b/dev/.env
@@ -8,7 +8,6 @@ NB_GRAPH_DB=repositories/my_db
 NB_RETURN_AGG=true
 NB_NAPI_TAG=latest
 NB_GRAPH_IMG=ontotext/graphdb:10.3.1
-
 LOCAL_GRAPH_DATA=./data
 
 # ---- CONFIGURATION FOR n-API ----
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index 93b1e5c..ae9aa95 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -29,7 +29,7 @@ services:
     volumes:
       - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
       - "${PWD}:/usr/src"
-      - "${LOCAL_GRAPH_DATA}:/data"
+      - "${LOCAL_GRAPH_DATA:-./data}:/usr/src/data"
     ports:
       - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
     entrypoint:

From b71cc6d8d275c4389ba7d6d4bc036215704bfb9f Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 11:40:13 -0400
Subject: [PATCH 12/25] replace hardcoded params inside setup.sh with env vars

---
 dev/.env               | 1 +
 dev/docker-compose.yml | 1 +
 dev/setup.sh           | 8 ++++----
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/dev/.env b/dev/.env
index 6302bf7..61d057e 100644
--- a/dev/.env
+++ b/dev/.env
@@ -2,6 +2,7 @@
 # AND MODIFY THE VALUES AS DESCRIBED IN THE DOCUMENTATION.
 
 # ---- CONFIGURATION FOR graph ----
+NB_GRAPH_ADMIN_PASSWORD=ADMINPASSWORD
 NB_GRAPH_USERNAME=DBUSER  # REPLACE DBUSER WITH YOUR GRAPH DATABASE USERNAME
 NB_GRAPH_PASSWORD=DBPASSWORD  # REPLACE DBPASSWORD WITH YOUR GRAPH DATABASE PASSWORD
 NB_GRAPH_DB=repositories/my_db
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index ae9aa95..86c48ee 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -32,6 +32,7 @@ services:
       - "${LOCAL_GRAPH_DATA:-./data}:/usr/src/data"
     ports:
       - "${NB_GRAPH_PORT_HOST:-7200}:${NB_GRAPH_PORT:-7200}"
+    env_file: .env    
     entrypoint:
       - "/usr/src/setup.sh"
     working_dir: "/usr/src"
diff --git a/dev/setup.sh b/dev/setup.sh
index 7b168eb..63d2c93 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -6,20 +6,20 @@ echo "Setting up a Neurobagel graph backend..."
 GRAPHDB_PID=$!
 
 # Waiting for GraphDB to start
-while ! curl --silent "localhost:7200/rest/repositories" | grep '\[\]'; do
+while ! curl --silent "localhost:${NB_GRAPH_PORT_HOST}/rest/repositories" | grep '\[\]'; do
     :
 done
 
 echo "Running GraphDB server setup..."
-./graphdb_setup.sh apple
+./graphdb_setup.sh "${NB_GRAPH_ADMIN_PASSWORD}"
 echo "Finished server setup."
 
 echo "Adding datasets to the database..."
-./add_data_to_graph.sh ./data localhost:7200 repositories/my_db DBUSER DBPASSWORD
+./add_data_to_graph.sh ./data localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
 echo "Finished adding datasets to databases."
 
 echo "Adding Neurobagel vocabulary to the database"
-./add_data_to_graph.sh ./vocab localhost:7200 repositories/my_db DBUSER DBPASSWORD
+./add_data_to_graph.sh ./vocab localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
 echo "Finished adding the Neurobagel vocabulary to the database."
 
 echo "Finished setting up the Neurobagel graph backend."

From f34d6231062c61f99de0cd11e14e775db5c57e63 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 13:25:25 -0400
Subject: [PATCH 13/25] update gitignore

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 8810f99..32d85ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -144,7 +144,7 @@ venv.bak/
 dmypy.json
 
 # Neurobagel
-data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
+**/data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
 
 # Pyre type checker
 .pyre/

From 59807cbd01c35b9122919e02e54c1bbd255abc36 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 14:18:58 -0400
Subject: [PATCH 14/25] set default profile in .env

---
 dev/.env | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/dev/.env b/dev/.env
index 61d057e..caad55a 100644
--- a/dev/.env
+++ b/dev/.env
@@ -1,6 +1,9 @@
 # THIS IS A TEMPLATE .env FILE. MAKE A COPY OF THIS FILE NAMED .env 
 # AND MODIFY THE VALUES AS DESCRIBED IN THE DOCUMENTATION.
 
+# ---- CONFIGURATION FOR docker compose ----
+COMPOSE_PROFILES=local_node
+
 # ---- CONFIGURATION FOR graph ----
 NB_GRAPH_ADMIN_PASSWORD=ADMINPASSWORD
 NB_GRAPH_USERNAME=DBUSER  # REPLACE DBUSER WITH YOUR GRAPH DATABASE USERNAME

From 812ec5a0656f34ddafff4a4ea7a9bcf8c05dccd5 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 14:23:01 -0400
Subject: [PATCH 15/25] update gitignore again

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 32d85ac..8810f99 100644
--- a/.gitignore
+++ b/.gitignore
@@ -144,7 +144,7 @@ venv.bak/
 dmypy.json
 
 # Neurobagel
-**/data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
+data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
 
 # Pyre type checker
 .pyre/

From 5cbc922670d1aba4e2e3fe84aa054eeb9cf89d47 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 14:58:55 -0400
Subject: [PATCH 16/25] write output of setup.sh to log

---
 dev/setup.sh | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/dev/setup.sh b/dev/setup.sh
index 63d2c93..4a9d919 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -1,7 +1,5 @@
 #!/bin/bash
 
-echo "Setting up a Neurobagel graph backend..."
-
 /opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/ &
 GRAPHDB_PID=$!
 
@@ -10,19 +8,26 @@ while ! curl --silent "localhost:${NB_GRAPH_PORT_HOST}/rest/repositories" | grep
     :
 done
 
-echo "Running GraphDB server setup..."
-./graphdb_setup.sh "${NB_GRAPH_ADMIN_PASSWORD}"
-echo "Finished server setup."
+# Logic for main setup
+main() {
+    echo -e "Setting up a Neurobagel graph backend...\n"
+
+    echo "Setting up GraphDB server..."
+    ./graphdb_setup.sh "${NB_GRAPH_ADMIN_PASSWORD}"
+    echo "Finished server setup."
+
+    echo "Adding datasets to the database..."
+    ./add_data_to_graph.sh ./data localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
+    echo "Finished adding datasets to databases."
 
-echo "Adding datasets to the database..."
-./add_data_to_graph.sh ./data localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
-echo "Finished adding datasets to databases."
+    echo "Adding Neurobagel vocabulary to the database"
+    ./add_data_to_graph.sh ./vocab localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
+    echo "Finished adding the Neurobagel vocabulary to the database."
 
-echo "Adding Neurobagel vocabulary to the database"
-./add_data_to_graph.sh ./vocab localhost:${NB_GRAPH_PORT_HOST} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
-echo "Finished adding the Neurobagel vocabulary to the database."
+    echo "Finished setting up the Neurobagel graph backend."
+}
 
-echo "Finished setting up the Neurobagel graph backend."
+main 2>&1 | tee -a ./NEUROBAGEL_SETUP_LOG.txt
 
 # We don't have jobcontrol here, so can't bring GraphDB back to foreground
 # instead we'll wait

From 35a45d3f32a82350ff03f4766ae0b000fe6dbcf1 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 14:25:08 -0400
Subject: [PATCH 17/25] update .gitignore again :(

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 8810f99..3ab2e7c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -144,7 +144,8 @@ venv.bak/
 dmypy.json
 
 # Neurobagel
-data-config.ttl  # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
+# RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
+data-config.ttl
 
 # Pyre type checker
 .pyre/

From 2a93b408d2255c6ff53ed6db742a0a019e384a2c Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Fri, 5 Apr 2024 11:46:43 -0400
Subject: [PATCH 18/25] switch query tool port to default used by Vite (#31)

---
 local_federation/docker-compose.yml           | 2 +-
 local_node_with_query_tool/docker-compose.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/local_federation/docker-compose.yml b/local_federation/docker-compose.yml
index a4e9762..32d32dd 100644
--- a/local_federation/docker-compose.yml
+++ b/local_federation/docker-compose.yml
@@ -14,6 +14,6 @@ services:
   query:
     image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
     ports:
-      - "${NB_QUERY_PORT_HOST:-3000}:3000"
+      - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:
       - NB_API_QUERY_URL=${NB_API_QUERY_URL:-http://localhost:8000/}
\ No newline at end of file
diff --git a/local_node_with_query_tool/docker-compose.yml b/local_node_with_query_tool/docker-compose.yml
index 188f814..c622c27 100644
--- a/local_node_with_query_tool/docker-compose.yml
+++ b/local_node_with_query_tool/docker-compose.yml
@@ -23,6 +23,6 @@ services:
   query:
     image: "neurobagel/query_tool:${NB_QUERY_TAG:-latest}"
     ports:
-      - "${NB_QUERY_PORT_HOST:-3000}:3000"
+      - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:
       NB_API_QUERY_URL: "${NB_API_QUERY_URL:-http://localhost:8000/}"
\ No newline at end of file

From 9f4a89f3d23a2c5aa7dad6576c36d7f224fa7d82 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 15:07:22 -0400
Subject: [PATCH 19/25] change log file name

---
 dev/setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/setup.sh b/dev/setup.sh
index 4a9d919..a327419 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -27,7 +27,7 @@ main() {
     echo "Finished setting up the Neurobagel graph backend."
 }
 
-main 2>&1 | tee -a ./NEUROBAGEL_SETUP_LOG.txt
+main 2>&1 | tee -a ./DEPLOY.log
 
 # We don't have jobcontrol here, so can't bring GraphDB back to foreground
 # instead we'll wait

From fa172292365835e1877fe0a0d072097cde00f8cf Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 15:21:56 -0400
Subject: [PATCH 20/25] bring back template configs

---
 .gitignore                                                | 1 +
 dev/{local_nb_nodes.json => local_nb_nodes.template.json} | 0
 dev/{.env => template.env}                                | 1 +
 3 files changed, 2 insertions(+)
 rename dev/{local_nb_nodes.json => local_nb_nodes.template.json} (100%)
 rename dev/{.env => template.env} (94%)

diff --git a/.gitignore b/.gitignore
index 3ab2e7c..1c3aece 100644
--- a/.gitignore
+++ b/.gitignore
@@ -146,6 +146,7 @@ dmypy.json
 # Neurobagel
 # RDF data configuration file, created automatically during setup from data-config_template.ttl based on .env values
 data-config.ttl
+local_nb_nodes.json
 
 # Pyre type checker
 .pyre/
diff --git a/dev/local_nb_nodes.json b/dev/local_nb_nodes.template.json
similarity index 100%
rename from dev/local_nb_nodes.json
rename to dev/local_nb_nodes.template.json
diff --git a/dev/.env b/dev/template.env
similarity index 94%
rename from dev/.env
rename to dev/template.env
index caad55a..1d84693 100644
--- a/dev/.env
+++ b/dev/template.env
@@ -2,6 +2,7 @@
 # AND MODIFY THE VALUES AS DESCRIBED IN THE DOCUMENTATION.
 
 # ---- CONFIGURATION FOR docker compose ----
+# Default service profile (deployment "flavour") when none are provided to the `docker compose` command
 COMPOSE_PROFILES=local_node
 
 # ---- CONFIGURATION FOR graph ----

From a7a2f3991ecad311f2be9ab786e12c3baa08b0ca Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 17:08:19 -0400
Subject: [PATCH 21/25] rename dev profile and update README

---
 README.md              | 49 ++++++++++++++++++++++++++++++++++++++++++
 dev/docker-compose.yml |  8 +++----
 2 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 08ab50f..4d21144 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,55 @@ Configuration files for a Neurobagel deployment.
 ## How to use
 For detailed instructions on the deployment options for Neurobagel, see the official Neurobagel documentation on [setting up a local knowledge graph (node)](https://neurobagel.org/infrastructure/) and [local query federation](https://neurobagel.org/federate/).
 
+### Using the full-stack Docker Compose file
+
+1. Clone the repository
+```bash
+git clone https://github.com/neurobagel/recipes.git
+```
+
+2. `cd` into the directory containing the Neurobagel deployment recipe
+<!---
+TODO: Change once we rename this directory for production!
+-->
+```bash
+cd recipes/dev
+```
+
+3. Copy and rename template files in the directory
+```bash
+cp template.env .env
+
+# if also setting up local federation
+cp local_nb_nodes.template.json local_nb_nodes.json
+```
+Ensure to edit the file(s) according to your deployment.
+
+4. Start the Docker Compose stack and specify your desired deployment profile
+
+**To set up only a local node:**
+```bash
+docker compose up -d
+```
+or
+```bash
+docker compose --profile local_node up -d
+```
+
+**To set up a local node with a graphical query tool:**
+```bash
+docker compose --profile local_node_query up -d
+```
+
+**To set up a local node and local federation (including a graphical query tool):**
+```bash
+docker compose --profile full_stack up -d
+```
+
+### Using deployment type-specific Docker Compose files
+
+**Note: These instructions will soon be superceded by the full-stack Docker Compose file instructions.**
+
 1. Clone the repository
 ```bash
 git clone https://github.com/neurobagel/recipes.git
diff --git a/dev/docker-compose.yml b/dev/docker-compose.yml
index 86c48ee..394e282 100644
--- a/dev/docker-compose.yml
+++ b/dev/docker-compose.yml
@@ -7,7 +7,7 @@ services:
     profiles:
       - "local_node"
       - "local_node_query"
-      - "dev"
+      - "full_stack"
     ports:
       - "${NB_NAPI_PORT_HOST:-8000}:${NB_NAPI_PORT:-8000}"
     environment:
@@ -25,7 +25,7 @@ services:
     profiles:
       - "local_node"
       - "local_node_query"
-      - "dev"
+      - "full_stack"
     volumes:
       - "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"
       - "${PWD}:/usr/src"
@@ -41,7 +41,7 @@ services:
     image: "neurobagel/federation_api:${NB_FAPI_TAG:-latest}"
     profiles:
       - "local_federation"
-      - "dev"
+      - "full_stack"
     ports:
       - "${NB_FAPI_PORT_HOST:-8080}:${NB_FAPI_PORT:-8000}"
     volumes:
@@ -54,7 +54,7 @@ services:
     profiles:
       - "local_federation"
       - "local_node_query"
-      - "dev"
+      - "full_stack"
     ports:
       - "${NB_QUERY_PORT_HOST:-3000}:5173"
     environment:

From 7f8fe7b1424da4c4dce4cef20cfa7d026c812e19 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 17:11:12 -0400
Subject: [PATCH 22/25] clean up README indentation

---
 README.md | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index 4d21144..2996743 100644
--- a/README.md
+++ b/README.md
@@ -30,24 +30,24 @@ Ensure to edit the file(s) according to your deployment.
 
 4. Start the Docker Compose stack and specify your desired deployment profile
 
-**To set up only a local node:**
-```bash
-docker compose up -d
-```
-or
-```bash
-docker compose --profile local_node up -d
-```
-
-**To set up a local node with a graphical query tool:**
-```bash
-docker compose --profile local_node_query up -d
-```
-
-**To set up a local node and local federation (including a graphical query tool):**
-```bash
-docker compose --profile full_stack up -d
-```
+    **To set up only a local node:**
+    ```bash
+    docker compose up -d
+    ```
+    or
+    ```bash
+    docker compose --profile local_node up -d
+    ```
+
+    **To set up a local node with a graphical query tool:**
+    ```bash
+    docker compose --profile local_node_query up -d
+    ```
+
+    **To set up a local node and local federation (including a graphical query tool):**
+    ```bash
+    docker compose --profile full_stack up -d
+    ```
 
 ### Using deployment type-specific Docker Compose files
 

From 10ae958f18be2d7ce2ca478563a9b322ae3a2662 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 10 Apr 2024 17:13:58 -0400
Subject: [PATCH 23/25] mention log file

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 2996743..29446eb 100644
--- a/README.md
+++ b/README.md
@@ -48,6 +48,7 @@ Ensure to edit the file(s) according to your deployment.
     ```bash
     docker compose --profile full_stack up -d
     ```
+A log file `DEPLOY.log` will be automatically created in the current directory with a copy of the STDOUT from the automatic deployment process.
 
 ### Using deployment type-specific Docker Compose files
 

From ed6caa3a29a18090fa69d9df0a4f9a81ebb01dff Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Thu, 11 Apr 2024 10:58:27 -0400
Subject: [PATCH 24/25] write log to script dir rather than working dir

---
 dev/setup.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/dev/setup.sh b/dev/setup.sh
index a327419..80e467d 100755
--- a/dev/setup.sh
+++ b/dev/setup.sh
@@ -8,6 +8,9 @@ while ! curl --silent "localhost:${NB_GRAPH_PORT_HOST}/rest/repositories" | grep
     :
 done
 
+# TODO: Do we also want to use this elsewhere in the script or stick to ./<some_path>?
+SCRIPT_DIR=$(dirname "$0")
+
 # Logic for main setup
 main() {
     echo -e "Setting up a Neurobagel graph backend...\n"
@@ -27,7 +30,7 @@ main() {
     echo "Finished setting up the Neurobagel graph backend."
 }
 
-main 2>&1 | tee -a ./DEPLOY.log
+main 2>&1 | tee -a ${SCRIPT_DIR}/DEPLOY.log
 
 # We don't have jobcontrol here, so can't bring GraphDB back to foreground
 # instead we'll wait

From 3dbdded67a0995b2c704fc9ba196c06eedd3ff80 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Thu, 11 Apr 2024 11:01:50 -0400
Subject: [PATCH 25/25] add comment about data path

---
 dev/template.env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/template.env b/dev/template.env
index 1d84693..47070ad 100644
--- a/dev/template.env
+++ b/dev/template.env
@@ -13,7 +13,7 @@ NB_GRAPH_DB=repositories/my_db
 NB_RETURN_AGG=true
 NB_NAPI_TAG=latest
 NB_GRAPH_IMG=ontotext/graphdb:10.3.1
-LOCAL_GRAPH_DATA=./data
+LOCAL_GRAPH_DATA=./data  # REPLACE WITH PATH TO YOUR JSONLD FILES
 
 # ---- CONFIGURATION FOR n-API ----
 ## ADDITIONAL CONFIGURABLE PARAMETERS: Uncomment and modify values of the below variables as needed to use non-default values.