Merge branch 'dev' into new_docmap_queries

.env.example

@@ -5,7 +5,6 @@ NEO4J_AUTH=neo4j/sourcedata
 NEO4J_dbms_memory_pagecache_size=16G
 NEO4J_dbms_memory_heap_max__size=8G
 NEO4J_dbms_security_procedures_unrestricted=gds.*
-NEO4J_dbms_unmanaged__extension__classes=n10s.endpoint=/rdf
 
 SD_API_URL=https://api.sourcedata.io/
 SD_API_USERNAME=

deploy/db

@@ -36,7 +36,7 @@ trap 'on_exit $?' EXIT
 
 log(){
   local timestamp=$(date +%Y-%m-%d\ %H:%M:%S)
-  echo "[deply/db $STAGE_NAME $PERIODICITY $timestamp] $1"
+  echo "[deploy/db $STAGE_NAME $PERIODICITY $timestamp] $1"
 }
 
 load_dotenv(){
@@ -135,10 +135,22 @@ update_local_neo4j() {
     cat sdg/update_close.cql | docker-compose -f docker-compose.deploy.yml run --rm neo4j cypher-shell -a bolt://neo4j:7687 -u neo4j -p $NEO_PASSWORD
   }
 
+  wait_for_neo4j() {
+    log "Waiting for neo4j to become available..."
+    docker-compose -f docker-compose.deploy.yml exec flask dockerize -wait tcp://neo4j:7687 -timeout 360s
+    if [ $? -ne 0 ]; then
+        log "neo4j probably failed to start, check the neo4j log for details. Aborting"
+        exit 1
+    fi
+    log "neo4j is available"
+  }
+
 
   log "starting docker"
   docker-compose -f docker-compose.deploy.yml build
   docker-compose -f docker-compose.deploy.yml up -d
+  wait_for_neo4j
+
 
   local PERIODICITY=$1
   case $PERIODICITY in

docker-compose.deploy.yml

@@ -26,7 +26,7 @@ services:
   neo4j:
     image: neo4j:4.1
     environment:
-      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]  #, "n10s"]
+      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]
     ulimits:
       nofile:
         soft: 40000

docker-compose.yml

@@ -33,7 +33,7 @@ services:
   neo4j:
     image: neo4j:4.1
     environment:
-      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science", "n10s"]
+      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]
     ulimits:
       nofile:
         soft: 40000

production.yml

@@ -24,7 +24,7 @@ services:
   neo4j:
     image: neo4j:4.1
     environment:
-      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]  #, "n10s"]
+      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]
     ulimits:
       nofile:
         soft: 40000

sdg/SD-prepare-docmap.cql

@@ -162,31 +162,6 @@ MERGE (reply_action)<-[:participants]-(person:Person {
 RETURN COUNT(person) AS `authors linked to replies`;
 :commit
 
-
-// :begin
-// // setup for semantic mapping
-
-// CALL n10s.graphconfig.init({handleVocabUris: 'MAP'});
-// :commit
-
-// :begin
-// CREATE CONSTRAINT n10s_unique_uri IF NOT EXISTS ON (r:Resource)
-// ASSERT r.uri IS UNIQUE;
-// :commit
-
-// :begin
-// // prefixes
-// CALL n10s.nsprefixes.add("dct", "http://purl.org/dc/terms/");
-// CALL n10s.nsprefixes.add("foaf", "http://xmlns.com/foaf/0.1/");
-// CALL n10s.nsprefixes.add("part", "http://www.ontologydesignpatterns.org/cp/owl/participation.owl#");
-// CALL n10s.nsprefixes.add("fabio", "http://purl.org/spar/fabio/");
-// CALL n10s.nsprefixes.add("pso", "http://purl.org/spar/pso/");
-// CALL n10s.nsprefixes.add("pwo", "http://purl.org/spar/pwo/");
-// CALL n10s.nsprefixes.add("xsd", "http://www.w3.org/2001/XMLSchema#");
-// CALL n10s.nsprefixes.add("prism", "http://prismstandard.org/namespaces/basic/2.0/");
-// :commit
-
-
 // :begin
 // // mappings
 // WITH [
@@ -215,12 +190,6 @@ RETURN COUNT(person) AS `authors linked to replies`;
 //     { internal: "hasUrl", uri: "http://purl.org/spar/fabio/", pub: "hasURL" }
 // ] as mappings
 
-// UNWIND mappings as m
-//     CALL n10s.mapping.add(m.uri + m.pub, m.internal) YIELD schemaElement
-// RETURN
-//     count(schemaElement) AS mappingsDefined;
-// :commit
-
 //try 
 // :POST /rdf/neo4j/cypher
 // {"cypher": "MATCH path=(preprint:Preprint)-[:inputs]->(action1:Action)<-[:outputs]-(ref:RefereeReport)-[:inputs]->(actions2:Action)<-[:outputs]-(reply:AuthorReply), (docmap)<-[:actions]-(action_1) RETURN path LIMIT 1", "format": "JSON-LD"}