diff --git a/helm/plater/non-itrb-values/cebs/values-data.yaml b/helm/plater/non-itrb-values/cebs/values-data.yaml new file mode 100644 index 000000000..a337767a1 --- /dev/null +++ b/helm/plater/non-itrb-values/cebs/values-data.yaml @@ -0,0 +1,10 @@ +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.6/CEBS_Automat/6a77f858e1b9852c/graph_6a77f858e1b9852c.db.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" +metadataUrl: https://stars.renci.org/var/plater/bl-4.2.6/CEBS_Automat/6a77f858e1b9852c/CEBS_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.6/CEBS_Automat/6a77f858e1b9852c/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.6/CEBS_Automat/6a77f858e1b9852c/testing_data.json \ No newline at end of file diff --git a/helm/plater/non-itrb-values/cebs/values-populated.yaml b/helm/plater/non-itrb-values/cebs/values-populated.yaml new file mode 100644 index 000000000..227338c75 Binary files /dev/null and b/helm/plater/non-itrb-values/cebs/values-populated.yaml differ diff --git a/helm/plater/non-itrb-values/clinical-trials-kp/values-data.yaml b/helm/plater/non-itrb-values/clinical-trials-kp/values-data.yaml index b95776020..099761f2b 100644 --- a/helm/plater/non-itrb-values/clinical-trials-kp/values-data.yaml +++ b/helm/plater/non-itrb-values/clinical-trials-kp/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/neo4j.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/neo4j.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/CTKP_Automat.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/testing_data.json \ No newline at end of file +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/testing_data.json diff --git a/helm/plater/non-itrb-values/ehr-clinical-connections-kp/values-data.yaml b/helm/plater/non-itrb-values/ehr-clinical-connections-kp/values-data.yaml index 4de6e84df..eae5cead2 100644 --- a/helm/plater/non-itrb-values/ehr-clinical-connections-kp/values-data.yaml +++ b/helm/plater/non-itrb-values/ehr-clinical-connections-kp/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/neo4j.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/neo4j.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/EHR_Clinical_Connections_Automat.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/testing_data.json \ No newline at end of file +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/testing_data.json diff --git a/helm/plater/non-itrb-values/ehr-may-treat-kp/values-data.yaml b/helm/plater/non-itrb-values/ehr-may-treat-kp/values-data.yaml index 3eded8e21..2e3c4e4b6 100644 --- a/helm/plater/non-itrb-values/ehr-may-treat-kp/values-data.yaml +++ b/helm/plater/non-itrb-values/ehr-may-treat-kp/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/graph_e8ecb00fe2898f82.db.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/graph_e8ecb00fe2898f82.db.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/MayTreatKP_Automat.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/testing_data.json \ No newline at end of file +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/testing_data.json diff --git a/helm/plater/non-itrb-values/molepro/values-data.yaml b/helm/plater/non-itrb-values/molepro/values-data.yaml index 949fac7fa..48f125ac3 100644 --- a/helm/plater/non-itrb-values/molepro/values-data.yaml +++ b/helm/plater/non-itrb-values/molepro/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MolePro_Automat/c8f64284fbeb81a9/graph_c8f64284fbeb81a9.db.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MolePro_Automat/c8f64284fbeb81a9/graph_c8f64284fbeb81a9.db.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MolePro_Automat/c8f64284fbeb81a9/MolePro_Automat.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/MolePro_Automat/c8f64284fbeb81a9/meta_knowledge_graph.json testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MolePro_Automat/c8f64284fbeb81a9/testing_data.json diff --git a/helm/plater/non-itrb-values/textminingkp/values-data.yaml b/helm/plater/non-itrb-values/textminingkp/values-data.yaml index 86d7ef00f..d3c88f494 100644 --- a/helm/plater/non-itrb-values/textminingkp/values-data.yaml +++ b/helm/plater/non-itrb-values/textminingkp/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/graph_2ae17047aa1b5f3c.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/TMKP_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/TMKP_Automat/2ae17047aa1b5f3c/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/TMKP_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/TMKP_Automat/c6e319504bba0301/testing_data.json diff --git a/helm/plater/non-itrb-values/textminingkp/values-populated.yaml b/helm/plater/non-itrb-values/textminingkp/values-populated.yaml index 4890dec32..26fb90c22 100644 Binary files a/helm/plater/non-itrb-values/textminingkp/values-populated.yaml and b/helm/plater/non-itrb-values/textminingkp/values-populated.yaml differ diff --git a/helm/plater/non-itrb-values/yobokop/values-data.yaml b/helm/plater/non-itrb-values/yobokop/values-data.yaml index 50c7d3d2f..c5728303f 100644 --- a/helm/plater/non-itrb-values/yobokop/values-data.yaml +++ b/helm/plater/non-itrb-values/yobokop/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/graph_40614106c036f010.db.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/graph_40614106c036f010.db.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/YobokopKG.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/testing_data.json \ No newline at end of file +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/testing_data.json diff --git a/helm/plater/templates/configmap.yaml b/helm/plater/templates/configmap.yaml index a7adef12e..51ae6eef6 100644 --- a/helm/plater/templates/configmap.yaml +++ b/helm/plater/templates/configmap.yaml @@ -20,33 +20,491 @@ data: wget -O /data/neo4j.dump ${NEO4J_DATA_URL} touch /data/done - run_memgraph.sh: |- + download_data_memgraph.sh: |- #!/bin/sh set -e + DATA_DIR="/data/memgraph" + + # If snapshot already exists, skip ingestion + if [ ! -f /data/done ]; then + echo "Downloading Memgraph ingestion files..." + curl -L -o /data/memgraph_nodes.csv ${MEMGRAPH_DATA_URL}_nodes.csv + curl -L -o /data/memgraph_indexes.cypher ${MEMGRAPH_DATA_URL}_indexes.cypher + + curl -L -o /data/edges_manifest.txt "${MEMGRAPH_DATA_URL}_edges_manifest.txt" + echo "Downloading all edge files in parallel..." + while IFS= read -r filename; do + ori_filename="$filename" + # Remove any prefix before "edges_biolink" + filename="${filename#*edges_biolink}" + filename="edges_biolink${filename}" + curl -L -o "/data/${ori_filename}" "${MEMGRAPH_DATA_URL}_${filename}" & + done < /data/edges_manifest.txt + wait + touch /data/done + else + echo "Files have been previously downloaded already" + fi + + generate_load_cypher.py: |- + #!/usr/bin/env python3 + """ + Dynamically generates Memgraph LOAD CSV Cypher queries from typed CSV headers. + + Usage: + python3 generate_load_cypher.py node + python3 generate_load_cypher.py edge + """ + import sys + + DEFAULT_ARRAY_DELIM = '\\u001f' + + def parse_header(header_line, delimiter='\t'): + """Parse typed header columns into property type lists and WITH clause mapping.""" + float_props = [] + int_props = [] + array_props = [] + bool_props = [] + string_props = [] + skip_props = set() + with_mappings = [] - echo "Starting Memgraph..." + for col in header_line.rstrip('\n').rstrip('\r').split(delimiter): + col = col.strip() + if ':' in col: + name, typ = col.rsplit(':', 1) + else: + name, typ = col, 'string' + + if typ in ('START_ID', 'END_ID', 'TYPE'): + skip_props.add(name) + # Still need these in WITH clause for edge MATCH but not SET + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ == 'ID': + string_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ == 'LABEL': + array_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ == 'float': + float_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ == 'int': + int_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ in ('string[]', 'float[]', 'int[]'): + array_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + elif typ == 'boolean': + bool_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + else: + string_props.append(name) + with_mappings.append('row.`' + col + '` AS `' + name + '`') + + return { + 'float': float_props, + 'int': int_props, + 'array': array_props, + 'bool': bool_props, + 'string': string_props, + 'skip': skip_props, + 'with_clause': ',\n '.join(with_mappings), + } + + def build_set_statements(props, array_delim, entity): + statements = [] + + for prop in props['string']: + statements.append( + 'SET ' + entity + '.`' + prop + '` = ' + 'CASE WHEN row.`' + prop + '` <> "" ' + 'THEN row.`' + prop + '` ELSE null END' + ) + + for prop in props['float']: + statements.append( + 'SET ' + entity + '.`' + prop + '` = ' + 'CASE WHEN row.`' + prop + '` <> "" ' + 'THEN toFloat(row.`' + prop + '`) ELSE null END' + ) + + for prop in props['int']: + statements.append( + 'SET ' + entity + '.`' + prop + '` = ' + 'CASE WHEN row.`' + prop + '` <> "" ' + 'THEN toInteger(row.`' + prop + '`) ELSE null END' + ) + + for prop in props['array']: + statements.append( + 'SET ' + entity + '.`' + prop + '` = ' + 'CASE WHEN trim(row.`' + prop + '`) <> "" ' + 'THEN split(row.`' + prop + '`, "' + array_delim + '") ELSE null END' + ) + + for prop in props['bool']: + statements.append( + 'SET ' + entity + '.`' + prop + '` = ' + 'CASE WHEN row.`' + prop + '` = "true" THEN true ' + 'WHEN row.`' + prop + '` = "false" THEN false ' + 'ELSE null END' + ) + + return '\n '.join(statements) + + def generate_node_cypher(csv_file, batch_size, array_delim=DEFAULT_ARRAY_DELIM): + with open(csv_file, 'r') as f: + header_line = f.readline() + + props = parse_header(header_line) + set_statements = build_set_statements(props, array_delim, entity='n') + set_statements = set_statements.replace('row.`', '`') + cypher = ( + 'CALL {\n' + ' LOAD CSV FROM "' + csv_file + '"\n' + ' WITH HEADER DELIMITER "\\t" AS row\n' + ' WITH\n ' + props['with_clause'] + '\n' + ' CREATE (n)\n' + ' ' + set_statements + '\n' + ' RETURN 1 AS _\n' + '} IN TRANSACTIONS OF ' + str(batch_size) + ' ROWS;' + ) + return cypher + + def generate_edge_cypher(csv_file, batch_size, array_delim=DEFAULT_ARRAY_DELIM, rel_type=''): + with open(csv_file, 'r') as f: + header_line = f.readline() + + props = parse_header(header_line) + + for prop_list in props.values(): + if isinstance(prop_list, list): + for skip in ('subject', 'object', 'predicate'): + if skip in prop_list: + prop_list.remove(skip) + + set_statements = build_set_statements(props, array_delim, entity='r') + set_statements = set_statements.replace('row.`', '`') + + cypher = ( + 'LOAD CSV FROM "' + csv_file + '"\n' + 'WITH HEADER DELIMITER "\\t" AS row\n' + 'CALL {\n' + ' WITH row\n' + ' WITH\n ' + props['with_clause'] + '\n' + ' MATCH (a:`biolink:NamedThing` {id: `subject`}),\n' + ' (b:`biolink:NamedThing` {id: `object`})\n' + ' CREATE (a)-[r:`' + rel_type + '`]->(b)\n' + ' ' + set_statements + '\n' + ' RETURN 1 AS _\n' + '} IN TRANSACTIONS OF ' + str(batch_size) + ' ROWS;' + ) + return cypher + + def main(): + if len(sys.argv) < 3: + print(__doc__) + sys.exit(1) + + mode = sys.argv[1] + csv_file = sys.argv[2] + batch_size = sys.argv[3] if len(sys.argv) > 3 else '200000' + array_delim = DEFAULT_ARRAY_DELIM + + if mode == 'node': + print(generate_node_cypher(csv_file, batch_size, array_delim)) + elif mode == 'edge': + if len(sys.argv) < 5: + print("Error: edge mode requires relationship_type argument") + sys.exit(1) + rel_type = sys.argv[4] + print(generate_edge_cypher(csv_file, batch_size, array_delim, rel_type)) + else: + print(f"Error: unknown mode '{mode}', use 'node' or 'edge'") + sys.exit(1) + + if __name__ == '__main__': + main() + run_memgraph.sh: |- + #!/bin/bash + set -euo pipefail + DATA_DIR="/data/memgraph" + BATCH_SIZE=${BATCH_SIZE} + QUERY_TIMEOUT=${GRAPH_QUERY_TIMEOUT} + + echo "Cleaning stream metadata directory..." + rm -rf $DATA_DIR/streams/* + + # If final snapshot exists (post-edge-loading), skip ingestion and go straight to serving mode + if [ -f "$DATA_DIR/.ingestion_complete" ]; then + echo "Existing snapshot detected. Starting Memgraph in serving mode..." + exec /usr/lib/memgraph/memgraph \ + --bolt-port=7687 \ + --bolt-address=0.0.0.0 \ + --storage-mode=IN_MEMORY_ANALYTICAL \ + --storage-wal-enabled=false \ + --log-level=ERROR \ + --storage-snapshot-interval-sec=0 \ + --query-execution-timeout-sec=$QUERY_TIMEOUT \ + --data-directory="$DATA_DIR" + fi + + # If nodes are loaded but label assignment not done, skip to label assignment + if [ -f "$DATA_DIR/.nodes_loaded" ]; then + echo "Nodes already loaded. Skipping to label assignment..." + else + echo "Starting Memgraph in BULK INGEST mode..." + /usr/lib/memgraph/memgraph \ + --bolt-port=7687 \ + --bolt-address=0.0.0.0 \ + --storage-mode=IN_MEMORY_ANALYTICAL \ + --storage-snapshot-interval-sec=0 \ + --query-execution-timeout-sec=0 \ + --storage-wal-enabled=false \ + --log-level=WARNING \ + --memory-limit=0 \ + --query-modules-directory=/usr/lib/memgraph/query_modules \ + --data-directory="$DATA_DIR" \ + >> /var/log/memgraph/memgraph_ingest.log 2>&1 & + + MEMGRAPH_PID=$! + echo "Memgraph PID: $MEMGRAPH_PID" + echo "Waiting for Memgraph to accept connections..." + until echo "RETURN 1;" | /usr/bin/mgconsole --host localhost --port 7687 >/dev/null 2>&1; do + sleep 2 + done + echo "Bolt is ready." + echo "Loading Memgraph nodes in transactions of $BATCH_SIZE..." + + python3 /generate_load_cypher.py node \ + /data/memgraph_nodes.csv \ + "$BATCH_SIZE" \ + | /usr/bin/mgconsole --host localhost --port 7687 + + echo "Loading nodes finished." + + echo "Stopping Memgraph to restart for label assignment..." + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + echo "Memgraph stopped." + # Mark nodes as loaded + touch "$DATA_DIR/.nodes_loaded" + fi + + if [ -f "$DATA_DIR/.labels_assigned" ]; then + echo "Labels already assigned. Skipping to node indexing and edge loading..." + else + # jump directly to starting memgraph for label assignment + echo "Generating label assignment cypher file..." + echo 'CALL assign_labels.from_category() YIELD processed RETURN processed;' \ + > /tmp/assign_labels.cypher + + echo "Restarting Memgraph in background to assign labels..." + /usr/lib/memgraph/memgraph \ + --bolt-port=7687 \ + --bolt-address=0.0.0.0 \ + --storage-mode=IN_MEMORY_ANALYTICAL \ + --storage-snapshot-interval-sec=0 \ + --query-execution-timeout-sec=0 \ + --storage-wal-enabled=false \ + --log-level=WARNING \ + --memory-limit=0 \ + --query-modules-directory=/usr/lib/memgraph/query_modules \ + --data-directory="$DATA_DIR" \ + --init-data-file=/tmp/assign_labels.cypher \ + >> /var/log/memgraph/memgraph_ingest.log 2>&1 & + MEMGRAPH_PID=$! + echo "Waiting for Memgraph to accept connections..." + until echo "RETURN 1;" | /usr/bin/mgconsole --host localhost --port 7687 >/dev/null 2>&1; do + sleep 2 + done + echo "Bolt is ready, label assignment via init-data-file should be complete." + + echo "Stopping Memgraph after label assignment..." + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + echo "Label assignment complete. Memgraph stopped." + touch "$DATA_DIR/.labels_assigned" + fi + echo "Restarting Memgraph in background for node indexing and edge loading..." /usr/lib/memgraph/memgraph \ --bolt-port=7687 \ --bolt-address=0.0.0.0 \ - --log-level=INFO \ - --also-log-to-stderr \ - & + --storage-mode=IN_MEMORY_ANALYTICAL \ + --storage-snapshot-interval-sec=0 \ + --query-execution-timeout-sec=0 \ + --storage-wal-enabled=false \ + --log-level=WARNING \ + --memory-limit=0 \ + --query-modules-directory=/usr/lib/memgraph/query_modules \ + --storage-snapshot-on-exit=false \ + --data-directory="$DATA_DIR" \ + >> /var/log/memgraph/memgraph_ingest.log 2>&1 & MEMGRAPH_PID=$! - - echo "Waiting for Memgraph to accept connections...${MEMGRAPH_PID}" + + echo "Waiting for Memgraph to accept connections..." until echo "RETURN 1;" | /usr/bin/mgconsole --host localhost --port 7687 >/dev/null 2>&1; do - sleep 1 + sleep 2 done - if [ -f /data/memgraph.cypher ]; then - echo "Loading Memgraph dump..." - /usr/bin/mgconsole --host localhost --port 7687 < /data/memgraph.cypher - echo "Memgraph dump loaded" + if [ -f "$DATA_DIR/.indexes_created" ]; then + echo "Indexes already created. Skipping to edge loading..." + else + echo "All nodes are loaded. Creating indexes (with retry)..." + until /usr/bin/mgconsole --host localhost --port 7687 < /data/memgraph_indexes.cypher; do + echo "Index creation failed, retrying in 5s..." + sleep 5 + done + echo "CREATE SNAPSHOT;" | /usr/bin/mgconsole --host localhost --port 7687 + touch "$DATA_DIR/.indexes_created" + fi + + load_edge_file() { + filename="$1" + batch_size="${2:-$BATCH_SIZE}" + base=$(basename "$filename" .csv) + marker="/tmp/edge_${base}" + relpart=$(echo "$base" | sed 's/_part_[a-z]*$//' | sed 's/.*\(biolink_.*\)/\1/') + reltype=$(echo "$relpart" | sed 's/_/:/') + echo "Starting $filename as relationship type $reltype" + + if python3 /generate_load_cypher.py edge \ + "/data/$filename" \ + "$batch_size" \ + "$reltype" \ + | /usr/bin/mgconsole --host localhost --port 7687 + then + echo "Finished ${filename}" + touch "${marker}.done" + else + echo "FAILED $filename" + touch "${marker}.failed" + fi + } + + LARGE_THRESHOLD=$(printf '%.0f' "${LARGE_THRESHOLD:-1000000000}") + SPLIT_LINES=$(printf '%.0f' "${SPLIT_LINES:-4000000}") + + if [ -f "$DATA_DIR/.edges_split" ]; then + echo "Large edge files already split, loading expanded manifest..." + cp /data/edges_manifest_expanded.txt /tmp/edges_manifest_expanded.txt else - echo "No memgraph.cypher found, skipping load" + echo "Checking for large edge files to split..." + rm -f /tmp/edges_manifest_expanded.txt + while IFS= read -r filename; do + filesize=$(stat -c%s "/data/$filename" 2>/dev/null || echo 0) + if [ "$filesize" -gt "$LARGE_THRESHOLD" ]; then + echo "Splitting large file: $filename" + base="${filename%.csv}" + header=$(head -1 "/data/$filename") + # Split into parts preserving header + rm -f /data/${base}_part_*.csv + tail -n +2 "/data/$filename" | split -l "$SPLIT_LINES" \ + --additional-suffix=".csv" \ + --filter="{ echo \"$header\"; cat; } > \$FILE" \ + - "/data/${base}_part_" + for part in /data/${base}_part_*.csv; do + echo "$(basename $part)" >> /tmp/edges_manifest_expanded.txt + echo " Created part: $(basename $part) ($(stat -c%s $part) bytes)" + done + else + echo "$filename" >> /tmp/edges_manifest_expanded.txt + fi + done < /data/edges_manifest.txt + echo "Expanded manifest has $(wc -l < /tmp/edges_manifest_expanded.txt) files" + # Persist to data dir so it survives pod restarts + cp /tmp/edges_manifest_expanded.txt /data/edges_manifest_expanded.txt + touch "$DATA_DIR/.edges_split" fi + + echo "Loading all edge files in parallel..." + rm -f /tmp/edge_*.done /tmp/edge_*.failed - wait ${MEMGRAPH_PID} + MAX_PARALLEL=${MAX_PARALLEL:-10} + total_count=0 + while IFS= read -r filename; do + while [ "$(jobs -rp | wc -l)" -ge "$MAX_PARALLEL" ]; do + sleep 2 + done + load_edge_file "$filename" & + total_count=$((total_count + 1)) + done < /tmp/edges_manifest_expanded.txt + + echo "Waiting for $total_count edge files to complete in parallel..." + + while true; do + done_count=$(find /tmp -maxdepth 1 -name 'edge_*.done' | wc -l) + fail_count=$(find /tmp -maxdepth 1 -name 'edge_*.failed' | wc -l) + total=$((done_count + fail_count)) + echo "Completed: $done_count, Failed: $fail_count, Total: $total / $total_count" + if [ "$total" -eq "$total_count" ]; then break; fi + sleep 5 + done + + if [ "$fail_count" -ne 0 ]; then + echo "One or more edge loads failed. Aborting." + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + exit 1 + fi + + echo "All edge loads completed successfully." + echo "Waiting for Memgraph to finish ingestion transactions..." + while true; do + active=$(echo "SHOW TRANSACTIONS;" | \ + /usr/bin/mgconsole --host localhost --port 7687 | \ + grep -c "transaction_id") + if [ "$active" -le 1 ]; then break; fi + echo "Still $active active transactions..." + sleep 5 + done + echo "Checking for active transactions..." + echo "SHOW TRANSACTIONS;" | /usr/bin/mgconsole --host localhost --port 7687 + + echo "Checking storage info before snapshot..." + echo "SHOW STORAGE INFO;" | /usr/bin/mgconsole --host localhost --port 7687 + + echo "Creating persistent snapshot (this may take a while for large graph)..." + echo "CREATE SNAPSHOT;" | /usr/bin/mgconsole --host localhost --port 7687 + + SNAP_STATUS=$? + + if [ "$SNAP_STATUS" -ne 0 ]; then + echo "Snapshot failed!" + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + exit 1 + fi + + # Verify snapshot is not empty before deleting old ones + SNAP_FILE=$(ls -t "$DATA_DIR/snapshots/" | head -1) + SNAP_SIZE=$(stat -c%s "$DATA_DIR/snapshots/$SNAP_FILE") + if [ "$SNAP_SIZE" -lt 2000000 ]; then + echo "ERROR: New snapshot appears empty (${SNAP_SIZE} bytes), aborting!" + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + exit 1 + fi + echo "Snapshot verified: $SNAP_FILE (${SNAP_SIZE} bytes)" + echo "Cleaning up intermediate snapshots (keeping newest)..." + # Keep only the most recent snapshot + ls -t "$DATA_DIR/snapshots/" | tail -n +2 | xargs -I{} rm -f "$DATA_DIR/snapshots/{}" + + echo "Switching to serving mode..." + + kill -TERM "$MEMGRAPH_PID" + wait "$MEMGRAPH_PID" + touch "$DATA_DIR/.ingestion_complete" + exec /usr/lib/memgraph/memgraph \ + --bolt-port=7687 \ + --bolt-address=0.0.0.0 \ + --storage-mode=IN_MEMORY_ANALYTICAL \ + --storage-wal-enabled=false \ + --storage-snapshot-interval-sec=0 \ + --log-level=ERROR \ + --query-execution-timeout-sec=$QUERY_TIMEOUT \ + --data-directory="$DATA_DIR" health_check.sh: |- #!/usr/bin/env bash @@ -66,6 +524,11 @@ data: RC=0 function download() { + if [ -z "$2" ]; then + echo "SKIPPING $1 (no URL provided), writing empty JSON file" + echo '{}' > "$LOCAL_DESTINATION/$1" + return 0 + fi CMD="wget -O $LOCAL_DESTINATION/$1 $2" echo "RUNNING: $CMD" $CMD @@ -76,7 +539,9 @@ data: download metadata.json ${PLATER_METADATA_URL} && \ download meta_knowledge_graph.json ${PLATER_METAKG_URL} && \ - download sri_testing_data.json ${PLATER_TEST_DATA_URL} + download sri_testing_data.json ${PLATER_TEST_DATA_URL} && \ + download graph_metadata.json ${PLATER_GRAPH_METADATA_URL} && \ + download schema.json ${PLATER_SCHEMA_URL} RC=$? if [[ $RC == 0 ]]; then break; @@ -120,4 +585,4 @@ data: openapi-config.yaml: |- {{ tpl $open_api_config . | indent 4 }} skip-attr.json: | - {{ .Values.skipAttributes | toJson }} \ No newline at end of file + {{ .Values.skipAttributes | toJson }} diff --git a/helm/plater/templates/env-config-map.yaml b/helm/plater/templates/env-config-map.yaml index 199549265..18e99fc72 100644 --- a/helm/plater/templates/env-config-map.yaml +++ b/helm/plater/templates/env-config-map.yaml @@ -30,6 +30,10 @@ data: {{- else }} MEMGRAPH_HOST: {{ include "plater.fullname" . }}-memgraph-service MEMGRAPH_BOLT_PORT: "{{ .Values.app.memgraph.boltPort }}" + BATCH_SIZE: "{{ .Values.app.memgraph.BATCH_SIZE }}" + MAX_PARALLEL: "{{ .Values.app.memgraph.MAX_PARALLEL }}" + LARGE_THRESHOLD: "{{ .Values.app.memgraph.LARGE_THRESHOLD }}" + SPLIT_LINES: "{{ .Values.app.memgraph.SPLIT_LINES }}" {{- end }} {{- end }} @@ -38,6 +42,8 @@ data: PLATER_TITLE: {{ .Release.Name }} PLATER_VERSION: {{ .Values.image.plater.tag }} PLATER_METADATA_URL: "{{ .Values.metadataUrl }}" + PLATER_GRAPH_METADATA_URL: "{{ .Values.graphMetadataUrl }}" + PLATER_SCHEMA_URL: "{{ .Values.schemaUrl }}" PLATER_METAKG_URL: "{{ .Values.metaKGUrl }}" PLATER_TEST_DATA_URL: "{{ .Values.testingDataUrl }}" PROVENANCE_TAG: "{{ .Values.datasetDesc.provenanceTag }}" diff --git a/helm/plater/templates/memgraph-deployment.yaml b/helm/plater/templates/memgraph-deployment.yaml index 053a39e54..f7e5a5ade 100644 --- a/helm/plater/templates/memgraph-deployment.yaml +++ b/helm/plater/templates/memgraph-deployment.yaml @@ -22,15 +22,18 @@ spec: - name: {{ include "plater.fullname" . }}-memgraph-download-container image: curlimages/curl:8.16.0 command: - - sh - - -c - - | - echo "Downloading Memgraph dump..." - curl -L -o /data/memgraph.cypher {{ .Values.app.memgraph.dataUrl }} + - '/download_data_memgraph.sh' + env: + - name: MEMGRAPH_DATA_URL + value: {{ .Values.app.memgraph.dataUrl }} + volumeMounts: - name: {{ include "plater.fullname" . }}-memgraph-pvc mountPath: /data subPath: memgraph_data + - name: {{ include "plater.fullname" . }}-scripts + mountPath: /download_data_memgraph.sh + subPath: download_data_memgraph.sh resources: {{- toYaml .Values.app.memgraph.initresources | nindent 12 }} {{- end }} @@ -39,12 +42,23 @@ spec: - name: {{ include "plater.fullname" . }}-memgraph-container image: "{{ .Values.image.memgraph.repository }}:{{ .Values.image.memgraph.tag }}" imagePullPolicy: {{ .Values.image.memgraph.imagePullPolicy }} + command: + - '/run_memgraph.sh' + env: + - name: GRAPH_QUERY_TIMEOUT + value: "{{ .Values.app.GRAPH_QUERY_TIMEOUT }}" + - name: BATCH_SIZE + value: "{{ .Values.app.memgraph.BATCH_SIZE }}" + - name: MAX_PARALLEL + value: "{{ .Values.app.memgraph.MAX_PARALLEL }}" + - name: LARGE_THRESHOLD + value: "{{ .Values.app.memgraph.LARGE_THRESHOLD }}" + - name: SPLIT_LINES + value: "{{ .Values.app.memgraph.SPLIT_LINES }}" ports: - name: memgraph-bolt containerPort: {{ .Values.app.memgraph.boltPort }} protocol: TCP - command: - - '/run_memgraph.sh' {{- with .Values.app.memgraph.resources }} resources: {{- toYaml . | nindent 12 }} @@ -56,12 +70,15 @@ spec: - name: {{ include "plater.fullname" . }}-scripts mountPath: /run_memgraph.sh subPath: run_memgraph.sh + - name: {{ include "plater.fullname" . }}-scripts + mountPath: /generate_load_cypher.py + subPath: generate_load_cypher.py startupProbe: -{{ toYaml .Values.app.memgraph.startupProbe | indent 12 }} +{{ toYaml .Values.memgraph.startupProbe | indent 12 }} readinessProbe: -{{ toYaml .Values.app.memgraph.readinessProbe | indent 12 }} +{{ toYaml .Values.memgraph.readinessProbe | indent 12 }} livenessProbe: -{{ toYaml .Values.app.memgraph.livenessProbe | indent 12 }} +{{ toYaml .Values.memgraph.livenessProbe | indent 12 }} restartPolicy: Always {{ with .Values.app.memgraph.nodeSelector }} diff --git a/helm/plater/templates/neo4j-deployment.yaml b/helm/plater/templates/neo4j-deployment.yaml index 71eb52626..9384084bf 100644 --- a/helm/plater/templates/neo4j-deployment.yaml +++ b/helm/plater/templates/neo4j-deployment.yaml @@ -17,7 +17,7 @@ spec: {{- include "plater.selectorLabels" . | nindent 8 }} service-type: neo4j-database spec: - {{- if .Values.dataUrl }} + {{- if .Values.app.neo4j.dataUrl }} initContainers: - name: {{ include "plater.fullname" . }}-neo4j-download-container image: {{ .Values.image.neo4j.repository }}:{{ .Values.image.neo4j.tag }} @@ -25,7 +25,7 @@ spec: - '/download_data_neo4j.sh' env: - name: NEO4J_DATA_URL - value: {{ .Values.dataUrl }} + value: {{ .Values.app.neo4j.dataUrl }} resources: {{- toYaml .Values.app.neo4j.initresources | nindent 12 }} volumeMounts: diff --git a/helm/plater/values.yaml b/helm/plater/values.yaml index b9388a3ea..0eff2cc7b 100644 --- a/helm/plater/values.yaml +++ b/helm/plater/values.yaml @@ -21,15 +21,15 @@ bash: image: plater: repository: ghcr.io/translatorsri/plater-clustered - tag: "v2.3.0" + tag: "v2.3.3" imagePullPolicy: Always neo4j: repository: ghcr.io/translatorsri/plater-neo4j tag: "neo4j-5.26" imagePullPolicy: Always memgraph: - repository: memgraph/memgraph - tag: "3.5.1" + repository: renci/memgraph + tag: "3.5.2" pullPolicy: Always nameOverride: "" @@ -78,6 +78,29 @@ neo4j: tolerations: [] nodeSelector: {} +memgraph: + readinessProbe: + tcpSocket: + port: 7687 + initialDelaySeconds: 30 + periodSeconds: 5 + failureThreshold: 3 + timeoutSeconds: 10 + + livenessProbe: + tcpSocket: + port: 7687 + initialDelaySeconds: 60 + periodSeconds: 30 + failureThreshold: 720 + timeoutSeconds: 10 + + startupProbe: + tcpSocket: + port: 7687 + failureThreshold: 720 + periodSeconds: 10 + timeoutSeconds: 10 service: type: ClusterIP @@ -88,11 +111,11 @@ app: jaegerPort: "4317" profiler_on: "False" gunicorn: - worker_timeout: 3600 + worker_timeout: 10800 num_workers: 4 # this is the timeout used for the http request made to neo4j # and also controls the https://neo4j.com/docs/operations-manual/4.2/reference/configuration-settings/#config_dbms.transaction.timeout - GRAPH_QUERY_TIMEOUT: 1600 + GRAPH_QUERY_TIMEOUT: 10800 web: resources: requests: @@ -106,6 +129,7 @@ app: automatAddress: http://automat bl_version: 4.2.1 neo4j: + dataUrl: "" # URL to neo4j data dump, if deploying internally protocol: bolt httpPort: 7474 boltPort: 7687 @@ -173,14 +197,25 @@ app: service: type: ClusterIP boltPort: 7687 - dataUrl: "" # URL to memgraph cypher file to populate the database, if deploying internally + # dataUrl is the base URL with _nodes.cypher, _edges.cypher, and _indexes.cypher to be appended + # to point to three required memgraph cypher files to populate the database, if deploying internally + dataUrl: "" + # BATCH_SIZE controls how many CSV edge rows are processed per transaction + # MAX_PARALLEL controls how many parallel jobs to run simultaneously for edge ingestion + # LARGE_THRESHOLD serves as the file size threshold which determines which large csv edge files get split. + # SPLIT_LINES determines split file size. + # All these four values influence memory usage: reduce these values will reduce total memory usage. + BATCH_SIZE: 2000 + MAX_PARALLEL: 10 + LARGE_THRESHOLD: 1000000000 + SPLIT_LINES: 4000000 initresources: requests: memory: 1Gi cpu: 500m limits: memory: 1Gi - cpu: 1000m + cpu: 3000m resources: requests: memory: 5Gi @@ -206,7 +241,8 @@ externalMemgraph: boltPort: 7687 skipAttributes: -dataUrl: "" # this dataUrl is for neo4j data dump. Although it is better to move it to app.neo4j block, it could introduce breaking changes, so keep it here for now. +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: "" metaKGUrl: "" testingDataUrl: "" diff --git a/helm/plater/values/binding-db/values-data.yaml b/helm/plater/values/binding-db/values-data.yaml index 31b0aecfd..221666175 100644 --- a/helm/plater/values/binding-db/values-data.yaml +++ b/helm/plater/values/binding-db/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/graph_9164067231dc9b8c.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/BINDING_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/BINDING_Automat/9164067231dc9b8c/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/BINDING_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/BINDING_Automat/91b19a479da83ddb/testing_data.json diff --git a/helm/plater/values/binding-db/values-populated.yaml b/helm/plater/values/binding-db/values-populated.yaml index e8e3261c0..8290f3523 100644 Binary files a/helm/plater/values/binding-db/values-populated.yaml and b/helm/plater/values/binding-db/values-populated.yaml differ diff --git a/helm/plater/values/cam-kp/values-data.yaml b/helm/plater/values/cam-kp/values-data.yaml index e2e9775cc..a6bf89e4e 100644 --- a/helm/plater/values/cam-kp/values-data.yaml +++ b/helm/plater/values/cam-kp/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/graph_e92bd7b217535f2d.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/CAMKP_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CAMKP_Automat/e92bd7b217535f2d/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/CAMKP_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/CAMKP_Automat/349f328cbccbb78f/testing_data.json diff --git a/helm/plater/values/cam-kp/values-populated.yaml b/helm/plater/values/cam-kp/values-populated.yaml index 4fd6f2c24..4d3172665 100644 Binary files a/helm/plater/values/cam-kp/values-populated.yaml and b/helm/plater/values/cam-kp/values-populated.yaml differ diff --git a/helm/plater/values/cohd/values-data.yaml b/helm/plater/values/cohd/values-data.yaml index e8a3961d0..94e827d42 100644 --- a/helm/plater/values/cohd/values-data.yaml +++ b/helm/plater/values/cohd/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/COHD_Automat/8ebe848c557cff42/neo4j.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/COHD_Automat/8ebe848c557cff42/COHD_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/COHD_Automat/8ebe848c557cff42/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/COHD_Automat/8ebe848c557cff42/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/COHD_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/COHD_Automat/c5dbcc677cd94de2/testing_data.json diff --git a/helm/plater/values/cohd/values-populated.yaml b/helm/plater/values/cohd/values-populated.yaml index 5cba0dca8..09358e195 100644 Binary files a/helm/plater/values/cohd/values-populated.yaml and b/helm/plater/values/cohd/values-populated.yaml differ diff --git a/helm/plater/values/ctd/values-data.yaml b/helm/plater/values/ctd/values-data.yaml index 1dc86639a..8bf1f59fc 100644 --- a/helm/plater/values/ctd/values-data.yaml +++ b/helm/plater/values/ctd/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/graph_f92c663160ec5e36.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/CTD_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/CTD_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/CTD_Automat/501d914abb7c8d45/testing_data.json diff --git a/helm/plater/values/ctd/values-populated.yaml b/helm/plater/values/ctd/values-populated.yaml index e45591e3e..e25d55360 100644 Binary files a/helm/plater/values/ctd/values-populated.yaml and b/helm/plater/values/ctd/values-populated.yaml differ diff --git a/helm/plater/values/drugcentral/values-data.yaml b/helm/plater/values/drugcentral/values-data.yaml index aa855db41..7c95b6f4f 100644 --- a/helm/plater/values/drugcentral/values-data.yaml +++ b/helm/plater/values/drugcentral/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/graph_dec0617490b49c7a.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/DrugCentral_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/DrugCentral_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/DrugCentral_Automat/4d492047aa51f86f/testing_data.json diff --git a/helm/plater/values/drugcentral/values-populated.yaml b/helm/plater/values/drugcentral/values-populated.yaml index c02f5ff89..17d4a0449 100644 Binary files a/helm/plater/values/drugcentral/values-populated.yaml and b/helm/plater/values/drugcentral/values-populated.yaml differ diff --git a/helm/plater/values/genome-alliance/values-data.yaml b/helm/plater/values/genome-alliance/values-data.yaml index 89f3c345a..8ed1ad7ff 100644 --- a/helm/plater/values/genome-alliance/values-data.yaml +++ b/helm/plater/values/genome-alliance/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/graph_06e2a3c1eeea5251.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/GenomeAllianceOrthologs_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GenomeAllianceOrthologs_Automat/06e2a3c1eeea5251/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/GenomeAllianceOrthologs_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/GenomeAllianceOrthologs_Automat/72d362eb2cdea697/testing_data.json diff --git a/helm/plater/values/genome-alliance/values-populated.yaml b/helm/plater/values/genome-alliance/values-populated.yaml index a91d36998..14d264e36 100644 Binary files a/helm/plater/values/genome-alliance/values-populated.yaml and b/helm/plater/values/genome-alliance/values-populated.yaml differ diff --git a/helm/plater/values/gtex/values-data.yaml b/helm/plater/values/gtex/values-data.yaml index 6f157a308..5be45b51c 100644 --- a/helm/plater/values/gtex/values-data.yaml +++ b/helm/plater/values/gtex/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/graph_a6448b9092bb81a1.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/GTEx_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/GTEx_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/GTEx_Automat/2ad22865c5fb3c6a/testing_data.json diff --git a/helm/plater/values/gtex/values-populated.yaml b/helm/plater/values/gtex/values-populated.yaml index 6151026e3..579201254 100644 Binary files a/helm/plater/values/gtex/values-populated.yaml and b/helm/plater/values/gtex/values-populated.yaml differ diff --git a/helm/plater/values/gtopdb/values-data.yaml b/helm/plater/values/gtopdb/values-data.yaml index eb298a3c1..0990ffb51 100644 --- a/helm/plater/values/gtopdb/values-data.yaml +++ b/helm/plater/values/gtopdb/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/graph_0ea6074c824c2236.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/GtoPdb_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/GtoPdb_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/GtoPdb_Automat/09ba5a16136b957c/testing_data.json diff --git a/helm/plater/values/gtopdb/values-populated.yaml b/helm/plater/values/gtopdb/values-populated.yaml index 49bd01ed2..5092de75a 100644 Binary files a/helm/plater/values/gtopdb/values-populated.yaml and b/helm/plater/values/gtopdb/values-populated.yaml differ diff --git a/helm/plater/values/gwas-catalog/values-data.yaml b/helm/plater/values/gwas-catalog/values-data.yaml index aa7866c19..f97d4a9ad 100644 --- a/helm/plater/values/gwas-catalog/values-data.yaml +++ b/helm/plater/values/gwas-catalog/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/graph_e30aceb322a33462.db.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/graph_e30aceb322a33462.db.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/GWASCatalog_Automat.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/testing_data.json \ No newline at end of file +testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/testing_data.json diff --git a/helm/plater/values/gwas-catalog/values-populated.yaml b/helm/plater/values/gwas-catalog/values-populated.yaml index 48d76e11c..796ce43f6 100644 Binary files a/helm/plater/values/gwas-catalog/values-populated.yaml and b/helm/plater/values/gwas-catalog/values-populated.yaml differ diff --git a/helm/plater/values/hetio/values-data.yaml b/helm/plater/values/hetio/values-data.yaml index 95c531abc..aaec290c8 100644 --- a/helm/plater/values/hetio/values-data.yaml +++ b/helm/plater/values/hetio/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/graph_85a5f53e63150e1e.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/Hetio_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/Hetio_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/Hetio_Automat/3f3cddfca8a4691c/testing_data.json diff --git a/helm/plater/values/hetio/values-populated.yaml b/helm/plater/values/hetio/values-populated.yaml index e1418f08f..72db11470 100644 Binary files a/helm/plater/values/hetio/values-populated.yaml and b/helm/plater/values/hetio/values-populated.yaml differ diff --git a/helm/plater/values/hgnc/values-data.yaml b/helm/plater/values/hgnc/values-data.yaml index e4cf672b8..37728d8b1 100644 --- a/helm/plater/values/hgnc/values-data.yaml +++ b/helm/plater/values/hgnc/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/graph_dee31cfce74e5944.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/HGNC_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/HGNC_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/HGNC_Automat/18d7d0e936fac5fe/testing_data.json diff --git a/helm/plater/values/hgnc/values-populated.yaml b/helm/plater/values/hgnc/values-populated.yaml index 84391f6ea..2cbee2d57 100644 Binary files a/helm/plater/values/hgnc/values-populated.yaml and b/helm/plater/values/hgnc/values-populated.yaml differ diff --git a/helm/plater/values/hmdb/values-data.yaml b/helm/plater/values/hmdb/values-data.yaml index 9db07f0fe..7b3e59ee9 100644 --- a/helm/plater/values/hmdb/values-data.yaml +++ b/helm/plater/values/hmdb/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/graph_6715124699b6dbf0.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/HMDB_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/HMDB_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/HMDB_Automat/1ffe388752ed4727/testing_data.json diff --git a/helm/plater/values/hmdb/values-populated.yaml b/helm/plater/values/hmdb/values-populated.yaml index 8af17afef..112794ab5 100644 Binary files a/helm/plater/values/hmdb/values-populated.yaml and b/helm/plater/values/hmdb/values-populated.yaml differ diff --git a/helm/plater/values/human-goa/values-data.yaml b/helm/plater/values/human-goa/values-data.yaml index 005680ea5..261878bea 100644 --- a/helm/plater/values/human-goa/values-data.yaml +++ b/helm/plater/values/human-goa/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/graph_06f107a4e9e8e547.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/HumanGOA_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/HumanGOA_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/HumanGOA_Automat/abbe9af6ff54da74/testing_data.json diff --git a/helm/plater/values/human-goa/values-populated.yaml b/helm/plater/values/human-goa/values-populated.yaml index debf15e94..edec81122 100644 Binary files a/helm/plater/values/human-goa/values-populated.yaml and b/helm/plater/values/human-goa/values-populated.yaml differ diff --git a/helm/plater/values/icees-kg/values-data.yaml b/helm/plater/values/icees-kg/values-data.yaml index 87d1001c5..79d2c55d8 100644 --- a/helm/plater/values/icees-kg/values-data.yaml +++ b/helm/plater/values/icees-kg/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/neo4j.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/neo4j.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/icees-kg.meta.json metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/meta_knowledge_graph.json testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/testing_data.json diff --git a/helm/plater/values/icees-kg/values-populated.yaml b/helm/plater/values/icees-kg/values-populated.yaml index a62833d2a..2e8d55ca1 100644 Binary files a/helm/plater/values/icees-kg/values-populated.yaml and b/helm/plater/values/icees-kg/values-populated.yaml differ diff --git a/helm/plater/values/intact/values-data.yaml b/helm/plater/values/intact/values-data.yaml index a06d10c63..6c053c867 100644 --- a/helm/plater/values/intact/values-data.yaml +++ b/helm/plater/values/intact/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/graph_e5b936f966a02c2c.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/IntAct_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/IntAct_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/IntAct_Automat/ec42fee770b73c4c/testing_data.json diff --git a/helm/plater/values/intact/values-populated.yaml b/helm/plater/values/intact/values-populated.yaml index 76cb6791f..d4cdc1192 100644 Binary files a/helm/plater/values/intact/values-populated.yaml and b/helm/plater/values/intact/values-populated.yaml differ diff --git a/helm/plater/values/monarch-kg/values-data.yaml b/helm/plater/values/monarch-kg/values-data.yaml index a614cdad2..26458ea69 100644 --- a/helm/plater/values/monarch-kg/values-data.yaml +++ b/helm/plater/values/monarch-kg/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/monarchinitiative/2024-07-12/neo4j.dump +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/monarchinitiative/2024-07-12/neo4j.dump + memgraph: + dataUrl: "" +graphMetadataUrl: "" +schemaUrl: "" metadataUrl: https://stars.renci.org/var/plater/monarchinitiative/2024-07-12/monarchinitiative.meta.json metaKGUrl: https://stars.renci.org/var/plater/monarchinitiative/2024-07-12/meta_knowledge_graph.json testingDataUrl: https://stars.renci.org/var/plater/monarchinitiative/2024-07-12/testing_data.json diff --git a/helm/plater/values/monarch-kg/values-populated.yaml b/helm/plater/values/monarch-kg/values-populated.yaml index 91397a559..2938bdf0b 100644 Binary files a/helm/plater/values/monarch-kg/values-populated.yaml and b/helm/plater/values/monarch-kg/values-populated.yaml differ diff --git a/helm/plater/values/ohd/values-data.yaml b/helm/plater/values/ohd/values-data.yaml new file mode 100644 index 000000000..c62a6a63a --- /dev/null +++ b/helm/plater/values/ohd/values-data.yaml @@ -0,0 +1,10 @@ +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/OHD_Carolina_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/OHD_Carolina_Automat/c157584568c21397/testing_data.json diff --git a/helm/plater/values/ohd/values-populated.yaml b/helm/plater/values/ohd/values-populated.yaml new file mode 100644 index 000000000..ab1c6637e Binary files /dev/null and b/helm/plater/values/ohd/values-populated.yaml differ diff --git a/helm/plater/values/panther/values-data.yaml b/helm/plater/values/panther/values-data.yaml index 672347f18..47aa3ec2b 100644 --- a/helm/plater/values/panther/values-data.yaml +++ b/helm/plater/values/panther/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/graph_c0189f14ba41da6c.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/PANTHER_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/PANTHER_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/PANTHER_Automat/a39d2667617d6e69/testing_data.json diff --git a/helm/plater/values/panther/values-populated.yaml b/helm/plater/values/panther/values-populated.yaml index 75c43ea68..6b039fff1 100644 Binary files a/helm/plater/values/panther/values-populated.yaml and b/helm/plater/values/panther/values-populated.yaml differ diff --git a/helm/plater/values/pharos/values-data.yaml b/helm/plater/values/pharos/values-data.yaml index c3ef1fd72..a8cbe30fc 100644 --- a/helm/plater/values/pharos/values-data.yaml +++ b/helm/plater/values/pharos/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/graph_d3068b509bf17ff3.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/PHAROS_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/PHAROS_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/PHAROS_Automat/a6022ac51591a48b/testing_data.json diff --git a/helm/plater/values/pharos/values-populated.yaml b/helm/plater/values/pharos/values-populated.yaml index a5742ab63..e084b88ba 100644 Binary files a/helm/plater/values/pharos/values-populated.yaml and b/helm/plater/values/pharos/values-populated.yaml differ diff --git a/helm/plater/values/reactome/values-data.yaml b/helm/plater/values/reactome/values-data.yaml index 763b8aaf6..d98aa7c6d 100644 --- a/helm/plater/values/reactome/values-data.yaml +++ b/helm/plater/values/reactome/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Reactome_Automat/07a8dc1cac1936b5/graph_07a8dc1cac1936b5.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Reactome_Automat/07a8dc1cac1936b5/Reactome_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/Reactome_Automat/07a8dc1cac1936b5/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/Reactome_Automat/07a8dc1cac1936b5/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/Reactome_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/Reactome_Automat/daa56e23aecd8900/testing_data.json diff --git a/helm/plater/values/reactome/values-populated.yaml b/helm/plater/values/reactome/values-populated.yaml index 94002a234..31a04afdd 100644 Binary files a/helm/plater/values/reactome/values-populated.yaml and b/helm/plater/values/reactome/values-populated.yaml differ diff --git a/helm/plater/values/robokopkg/values-data.yaml b/helm/plater/values/robokopkg/values-data.yaml index 33a7bf48f..9be828ff4 100644 --- a/helm/plater/values/robokopkg/values-data.yaml +++ b/helm/plater/values/robokopkg/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/graphs/23f46efa87c2bad7/graph_23f46efa87c2bad7.db.dump -metadataUrl: https://stars.renci.org/var/plater/graphs/23f46efa87c2bad7/RobokopKG.meta.json -metaKGUrl: https://stars.renci.org/var/plater/graphs/23f46efa87c2bad7/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/graphs/23f46efa87c2bad7/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/memgraph/memgraph_graph +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/RobokopKG.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/testing_data.json diff --git a/helm/plater/values/robokopkg/values-populated.yaml b/helm/plater/values/robokopkg/values-populated.yaml index ab4a09b9e..059daf32f 100644 Binary files a/helm/plater/values/robokopkg/values-populated.yaml and b/helm/plater/values/robokopkg/values-populated.yaml differ diff --git a/helm/plater/values/string-db/values-data.yaml b/helm/plater/values/string-db/values-data.yaml index 71b3ce0b2..63456075c 100644 --- a/helm/plater/values/string-db/values-data.yaml +++ b/helm/plater/values/string-db/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/graph_4ca5a0ce557e2c18.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/STRING-DB_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/STRING-DB_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/STRING-DB_Automat/6a5d9e79a31500ec/testing_data.json diff --git a/helm/plater/values/string-db/values-populated.yaml b/helm/plater/values/string-db/values-populated.yaml index dd1071086..44c80da23 100644 Binary files a/helm/plater/values/string-db/values-populated.yaml and b/helm/plater/values/string-db/values-populated.yaml differ diff --git a/helm/plater/values/translatorkg/values-data.yaml b/helm/plater/values/translatorkg/values-data.yaml new file mode 100644 index 000000000..5f3a04502 --- /dev/null +++ b/helm/plater/values/translatorkg/values-data.yaml @@ -0,0 +1,10 @@ +app: + neo4j: + dataUrl: https://stars.renci.org/var/data_services/translator_kg/2026_02_03/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/data_services/translator_kg/2026_02_03/memgraph_output/memgraph_graph +graphMetadataUrl: https://stars.renci.org/var/data_services/translator_kg/2026_02_03/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/schema.json +metadataUrl: https://stars.renci.org/var/data_services/translator_kg/2026_02_03/merge-metadata.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/RobokopKG/f10f782cda309e98/testing_data.json diff --git a/helm/plater/values/translatorkg/values-populated.yaml b/helm/plater/values/translatorkg/values-populated.yaml new file mode 100644 index 000000000..f12fe93ed Binary files /dev/null and b/helm/plater/values/translatorkg/values-populated.yaml differ diff --git a/helm/plater/values/ubergraph/values-data.yaml b/helm/plater/values/ubergraph/values-data.yaml index 6285d6e85..5b64c445f 100644 --- a/helm/plater/values/ubergraph/values-data.yaml +++ b/helm/plater/values/ubergraph/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/graph_e6b3204fd3a04413.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/UbergraphRedundant_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/testing_data.json \ No newline at end of file +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/UbergraphRedundant_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/UbergraphRedundant_Automat/9d6f487cccc834c1/testing_data.json diff --git a/helm/plater/values/ubergraph/values-populated.yaml b/helm/plater/values/ubergraph/values-populated.yaml index c9bbbe735..41593f263 100644 Binary files a/helm/plater/values/ubergraph/values-populated.yaml and b/helm/plater/values/ubergraph/values-populated.yaml differ diff --git a/helm/plater/values/viral-proteome/values-data.yaml b/helm/plater/values/viral-proteome/values-data.yaml index a33236fb2..c6b8cbc5f 100644 --- a/helm/plater/values/viral-proteome/values-data.yaml +++ b/helm/plater/values/viral-proteome/values-data.yaml @@ -1,4 +1,10 @@ -dataUrl: https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/graph_8ca116ae0bba6945.db.dump -metadataUrl: https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/ViralProteome_Automat.meta.json -metaKGUrl: https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/meta_knowledge_graph.json -testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/ViralProteome_Automat/8ca116ae0bba6945/testing_data.json +app: + neo4j: + dataUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/neo4j.dump + memgraph: + dataUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/memgraph.cypher +graphMetadataUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/graph-metadata.json +schemaUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/schema.json +metadataUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/ViralProteome_Automat.meta.json +metaKGUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/meta_knowledge_graph.json +testingDataUrl: https://stars.renci.org/var/plater/graphs/ViralProteome_Automat/be3a42b4b9d961a6/testing_data.json diff --git a/helm/plater/values/viral-proteome/values-populated.yaml b/helm/plater/values/viral-proteome/values-populated.yaml index 56d7b2865..8b5a78e55 100644 Binary files a/helm/plater/values/viral-proteome/values-populated.yaml and b/helm/plater/values/viral-proteome/values-populated.yaml differ diff --git a/helm/robokopkg/renci-robokopkg-5-values-populated.yaml b/helm/robokopkg/renci-robokopkg-5-values-populated.yaml index ee4d6d326..6aa26f7c4 100644 Binary files a/helm/robokopkg/renci-robokopkg-5-values-populated.yaml and b/helm/robokopkg/renci-robokopkg-5-values-populated.yaml differ