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Memgraph values updated #1050

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Merged
hyi merged 37 commits into from
May 17, 2026
Merged

Memgraph values updated #1050

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5d8102f
updating values files for new format and new graphs
EvanDietzMorris Feb 6, 2026
91d3c62
adding graph metadata and schema files to charts
EvanDietzMorris Feb 6, 2026
920ccfe
adding ohd values
EvanDietzMorris Feb 6, 2026
28fe7a3
updating bl version
EvanDietzMorris Feb 6, 2026
4a8190c
updating robokopkg resources closer to standalone instance
EvanDietzMorris Feb 6, 2026
5a826a1
adding cebs
EvanDietzMorris Feb 6, 2026
c45fa15
adding new files to cebs
EvanDietzMorris Feb 6, 2026
5886044
fixing robokopkg memory allocation
EvanDietzMorris Feb 6, 2026
98c1456
increasing storage size for ubergraph
EvanDietzMorris Feb 6, 2026
6543d3d
increasing storage size for ubergraph (again)
EvanDietzMorris Feb 6, 2026
b69b55e
new reactome graph
EvanDietzMorris Feb 8, 2026
74ed192
graceful fallback for missing metadata files
EvanDietzMorris Feb 8, 2026
035f4bc
updated memgraph deployment to ingest 3 cypher files
hyi Feb 10, 2026
59778a0
refactored memgraph data ingestion script to work through some issues
hyi Feb 11, 2026
f84190d
updates trying to get memgraph data ingestion working
hyi Feb 13, 2026
fb78331
memgraph edge loading performance is now acceptable for large graphs
hyi Feb 16, 2026
d49f4bd
added graph query timeout for memgraph for benchmarking
hyi Feb 16, 2026
7da3cb8
fixed a few bugs with memgraph data ingestion script
hyi Feb 17, 2026
e4bb139
updated values for benchmarking neo4j vs memgraph
hyi Feb 17, 2026
073c3ff
set logging level to error for memgraph in serving mode
hyi Feb 17, 2026
af9694d
disabling default snapshotting for memgraph to save disk space
hyi Feb 17, 2026
2e5cefd
disable snapshotting for memgraph in serving mode in another condition
hyi Feb 17, 2026
1dc34a7
disabling snapshotting has to go with disabling WAL
hyi Feb 18, 2026
c3e4616
updated memgraph deployment to load nodes from csv dump
hyi Mar 6, 2026
59570f7
only creating one snapshot for memgraph
hyi Mar 6, 2026
1f79f84
run_memgraph.sh script improvement
hyi Mar 7, 2026
c3616cf
a couple of improvement to run_memgraph.sh script
hyi Mar 10, 2026
870a2d3
more memgraph script improvement
hyi Mar 10, 2026
765a580
finally get whole robokopkg loaded into memgraph
hyi Mar 11, 2026
c06fce3
verify latest snapshot is created successfully before deleting interm…
hyi Mar 11, 2026
fb402ed
avoid creating duplicate final snapshot
hyi Mar 12, 2026
e6d4b89
fix edge type issue
hyi Mar 12, 2026
d07a7cb
make LARGE_THRESHOLD and SPLIT_LINES configurable which influence mem…
hyi Mar 12, 2026
0ae4487
improved memgraph data ingestion to filter out empty properties and d…
hyi Mar 13, 2026
821815b
updating robokopkg standalone neo4j
EvanDietzMorris Mar 17, 2026
bc868f8
bumping plater version
EvanDietzMorris Mar 17, 2026
1cfdcc0
bumping plater version
EvanDietzMorris Mar 18, 2026
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10 changes: 10 additions & 0 deletions helm/plater/non-itrb-values/cebs/values-data.yaml
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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
Binary file added helm/plater/non-itrb-values/cebs/values-populated.yaml
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10 changes: 8 additions & 2 deletions helm/plater/non-itrb-values/clinical-trials-kp/values-data.yaml
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@@ -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
testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/CTKP_Automat/3a11bc62b676c6aa/testing_data.json
10 changes: 8 additions & 2 deletions helm/plater/non-itrb-values/ehr-clinical-connections-kp/values-data.yaml
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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
testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/EHR_Clinical_Connections_Automat/613242929fd651b8/testing_data.json
10 changes: 8 additions & 2 deletions helm/plater/non-itrb-values/ehr-may-treat-kp/values-data.yaml
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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
testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.1/MayTreatKP_Automat/e8ecb00fe2898f82/testing_data.json
8 changes: 7 additions & 1 deletion helm/plater/non-itrb-values/molepro/values-data.yaml
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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
14 changes: 10 additions & 4 deletions helm/plater/non-itrb-values/textminingkp/values-data.yaml
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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
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
Binary file modified helm/plater/non-itrb-values/textminingkp/values-populated.yaml
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10 changes: 8 additions & 2 deletions helm/plater/non-itrb-values/yobokop/values-data.yaml
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@@ -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
testingDataUrl: https://stars.renci.org/var/plater/bl-4.2.0/YobokopKG/40614106c036f010/testing_data.json
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