Update requests to work with current versions of fuseki

.gitignore

@@ -0,0 +1,3 @@
+# Fuseki related
+**/run/*
+**/fuseki.out

bin/esteemer.sh

@@ -1,19 +1,46 @@
 #!/usr/bin/env bash
 
+# Requires fuseki-server to be installed
+command -v robot 1> /dev/null 2>&1 || \
+  { echo >&2 "fuseki-server required but it's not in PATH.  Aborting."; exit 1; }
+
 # Usage message
 read -r -d '' USE_MSG <<'HEREDOC'
 Usage:
+  esteemer.sh
   esteemer.sh -h
-  esteemer.sh -p causal_pathway.json
   esteemer.sh -s spek.json  
 
-Esteemer reads a spek from stdin or provided file path.  
+Esteemer is currently a rubber stamp that adds 'promoted by' predicate to approved candidates.
 
 Options:
   -h | --help   print help and exit
   -s | --spek   path to spek file (default to stdin)
 HEREDOC
 
+# From Chris Down https://gist.github.com/cdown/1163649
+urlencode() {
+    # urlencode <string>
+    old_lc_collate=$LC_COLLATE
+    LC_COLLATE=C
+    local length="${#1}"
+    for (( i = 0; i < length; i++ )); do
+        local c="${1:$i:1}"
+        case $c in
+            [a-zA-Z0-9.~_-]) printf '%s' "$c" ;;
+            *) printf '%%%02X' "'$c" ;;
+        esac
+    done
+    LC_COLLATE=$old_lc_collate
+}
+
+# From Chris Down https://gist.github.com/cdown/1163649
+urldecode() {
+    # urldecode <string>
+    local url_encoded="${1//+/ }"
+    printf '%b' "${url_encoded//%/\\x}"
+}
+
 # Parse args
 PARAMS=()
 while (( "$#" )); do
@@ -52,17 +79,23 @@ if [[ -z ${FUSEKI_PING}} || ${FUSEKI_PING} -ne 200 ]]; then
   echo >&2 "Fuseki not running locally."; 
 
   # Try to start custom fuseki locally
-  FUSEKI_DIR=/opt/fuseki/apache-jena-fuseki-3.10.0
-  ${FUSEKI_DIR}/fuseki-server --mem --update /ds 1> fuseki.out 2>&1 &
-
-  exit 1;
+  fuseki-server --mem --update /ds 1> fuseki.out 2>&1 &
+  read -p "Waiting five secs for Fuseki to start..." -t 5
 fi
 
-# Define SPARQL Queries for updates and results
+# Define,url encode, and create param string for fully qualified graph iris.
+VAL_SPEK="http://localhost:3030/ds/spek"
+ENC_SPEK=$(urlencode "${VAL_SPEK}")
+PARAM_SPEK="graph=${ENC_SPEK}"
+
+VAL_SEEPS="http://localhost:3030/ds/seeps"
+ENC_SEEPS=$(urlencode "${VAL_SEEPS}")
+PARAM_SEEPS="graph=${ENC_SEEPS}"
+
+# Define SPARQL Query for updating spek
 read -r -d '' UPD_SPARQL <<'SPARQL'
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX cpo: <http://example.com/cpo#>
 PREFIX slowmo: <http://example.com/slowmo#>
 
 INSERT {
@@ -72,29 +105,27 @@ INSERT {
 }
 USING <http://localhost:3030/ds/spek>
 WHERE {
-  ?candi a cpo:cpo_0000053 .
+  ?candi a obo:cpo_0000053 .
   ?candi slowmo:acceptable_by ?o
 }
 SPARQL
 
 
-# Read from SPEK_FILE or pipe from stdin
-#   Use '-' to instruct curl to read from stdin
-if [[ -z ${SPEK_FILE} ]]; then
-  SPEK_FILE="-"
+# If spek file is not empty, load into fuseki  
+#  Otherwise assume it's loaded into fuseki already.
+if [[ ! -z ${SPEK_FILE} ]]; then
+  # Load in spek
+  curl --silent -X PUT --data-binary "@${SPEK_FILE}" \
+    --header 'Content-type: application/ld+json' \
+    "http://localhost:3030/ds?${PARAM_SPEK}" >&2
 fi
 
-# Load spek into fuseki
-curl --silent -X PUT --data-binary "@${SPEK_FILE}" \
-  --header 'Content-type: application/ld+json' \
-  'http://localhost:3030/ds?graph=spek' >&2
-
 # run update sparql
 curl --silent -X POST --data-binary "${UPD_SPARQL}" \
   --header 'Content-type: application/sparql-update' \
   'http://localhost:3030/ds/update' >&2
 
 # get updated spek
-curl --silent -X GET --header 'Accept: application/ld+json' \
-  'http://localhost:3030/ds?graph=spek'
-
+curl --silent -G --header 'Accept: application/ld+json' \
+    --data-urlencode "graph=http://localhost:3030/ds/spek" \
+    'http://localhost:3030/ds'

test/alice.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+
+# Start by assuming it was the path invoked.
+THIS_SCRIPT="$0"
+
+# Handle resolving symlinks to this script.
+# Using ls instead of readlink, because bsd and gnu flavors
+# have different behavior.
+while [ -h "$THIS_SCRIPT" ] ; do
+  ls=`ls -ld "$THIS_SCRIPT"`
+  # Drop everything prior to ->
+  link=`expr "$ls" : '.*-> \(.*\)$'`
+  if expr "$link" : '/.*' > /dev/null; then
+    THIS_SCRIPT="$link"
+  else
+    THIS_SCRIPT=`dirname "$THIS_SCRIPT"`/"$link"
+  fi
+done
+
+# Get path to the scripts directory.
+SCRIPT_DIR=$(dirname "${THIS_SCRIPT}")
+
+ESTEEMER="${SCRIPT_DIR}/../bin/esteemer.sh"
+TEST_SPEK="${SCRIPT_DIR}/alice_spek.json"
+
+
+CANDIDATE_TYPE="http://purl.obolibrary.org/obo/cpo_0000053"
+
+${ESTEEMER} -s ${TEST_SPEK} |\
+  jq --arg t "$CANDIDATE_TYPE" '."@graph"[] | select(."@type" == $t and ."AncestorPerformer" == "_:pAlice")' |\
+  grep --color -E '"promoted_by.*"|^'
+