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[REF] Switch to opt-in Stardog syntax #13

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Feb 6, 2024
Merged

[REF] Switch to opt-in Stardog syntax #13

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29 changes: 15 additions & 14 deletions scripts/add_data_to_graph.sh
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
# 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-graphdb-syntax],[],[Whether or not to use GraphDB API endpoints to update the specified graph database. If off, assumes the graph database is a Stardog 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])
# ARGBASH_GO()
# needed because of Argbash --> m4_ignore([
### START OF CODE GENERATED BY Argbash v2.9.0 one line above ###
Expand Down Expand Up @@ -36,21 +36,21 @@ begins_with_short_option()
_positionals=()
# THE DEFAULTS INITIALIZATION - OPTIONALS
_arg_clear_data="off"
_arg_use_graphdb_syntax="off"
_arg_use_stardog_syntax="off"


print_help()
{
printf '%s\n' "Upload JSONLD and Turtle data to a Neurobagel graph"
printf 'Usage: %s [-h|--help] [--(no-)clear-data] [--(no-)use-graphdb-syntax] <dir> <graph-url> <graph-database> <user> <password>\n' "$0"
printf 'Usage: %s [-h|--help] [--(no-)clear-data] [--(no-)use-stardog-syntax] <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-graphdb-syntax, --no-use-graphdb-syntax: Whether or not to use GraphDB API endpoints to update the specified graph database. If off, assumes the graph database is a Stardog 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)"
}


Expand All @@ -73,9 +73,9 @@ parse_commandline()
_arg_clear_data="on"
test "${1:0:5}" = "--no-" && _arg_clear_data="off"
;;
--no-use-graphdb-syntax|--use-graphdb-syntax)
_arg_use_graphdb_syntax="on"
test "${1:0:5}" = "--no-" && _arg_use_graphdb_syntax="off"
--no-use-stardog-syntax|--use-stardog-syntax)
_arg_use_stardog_syntax="on"
test "${1:0:5}" = "--no-" && _arg_use_stardog_syntax="off"
;;
*)
_last_positional="$1"
Expand Down Expand Up @@ -119,30 +119,31 @@ assign_positional_args 1 "${_positionals[@]}"
### 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_graphdb_syntax=$_arg_use_graphdb_syntax
use_stardog_syntax=$_arg_use_stardog_syntax

DELETE_TRIPLES_QUERY="
DELETE {
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 [ "$use_graphdb_syntax" = "on" ]; then
upload_data_url="${base_url}/statements"
clear_data_url=$upload_data_url
else
if [ "$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


Expand Down Expand Up @@ -212,4 +213,4 @@ if (( ${#upload_failed[@]} != 0 )); then
printf '%s\n' "${upload_failed[@]}"
fi

# ] <-- needed because of Argbash
# ] <-- needed because of Argbash