diff --git a/rres-endpoints/config/datasets/ascomycota-premium-58-cfg.sh b/rres-endpoints/config/datasets/ascomycota-premium-58-cfg.sh index ae20c58..e8f366b 100644 --- a/rres-endpoints/config/datasets/ascomycota-premium-58-cfg.sh +++ b/rres-endpoints/config/datasets/ascomycota-premium-58-cfg.sh @@ -5,7 +5,8 @@ oxl_home="$KNET_HOME/etl-test/ascomycota-premium/$KETL_DATASET_VERSION" export KETL_SRC_OXL="$oxl_home/generic/knowledge-network.oxl" -export KETL_OUT="$KETL_OUT_HOME/$KETL_DATASET_ID/$KETL_DATASET_VERSION" +# Sam 20240909 - New versioning convention +export KETL_OUT="$KETL_OUT_HOME/$KETL_DATASET_ID/v$KETL_DATASET_VERSION-RC3" ## Neo  # @@ -32,7 +33,7 @@ export KNET_INIT_DATASET_ID="ascomycota-premium" # # Test servers like babvs73 -export KNET_TESTINST_DATA_PATH=/opt/data/knetminer-datasets/brassica +export KNET_TESTINST_DATA_PATH=/opt/data/knetminer-datasets/ascomycota-premium # babvs73: based on old Traverser, available at knetminer.com/ci-test # babvs72: based on Neo4j+OXL Traverser, available at knetminer.com/ci-test-cypher export KNET_TESTINST_SSH="brandizim@babvs73.rothamsted.ac.uk brandizim@babvs72.rothamsted.ac.uk" diff --git a/rres-endpoints/config/datasets/fungi-lite-60-cfg.sh b/rres-endpoints/config/datasets/fungi-lite-60-cfg.sh new file mode 100644 index 0000000..ef5cfaf --- /dev/null +++ b/rres-endpoints/config/datasets/fungi-lite-60-cfg.sh @@ -0,0 +1,39 @@ +# /home/data/knetminer/etl-test/fungi-lite/60/generic/knowledge-network.oxl + +# Unfortunately, there isn't consistence, so we can use KETL_DATASET_ID here +oxl_home="$KNET_HOME/etl-test/fungi-lite/$KETL_DATASET_VERSION" + +export KETL_SRC_OXL="$oxl_home/generic/knowledge-network.oxl" + +# Sam 20240909 - New versioning convention +export KETL_OUT="$KETL_OUT_HOME/$KETL_DATASET_ID/v$KETL_DATASET_VERSION-RC1" + +## Neo  +# +export KETL_HAS_NEO4J=true +export KETL_NEO_VERSION='5.23.0' +export NEO4J_HOME="$KNET_SOFTWARE/neo4j-community-$KETL_NEO_VERSION-etl" + +## Knet Initialiser +# +# The name within the code base, which identifies the config dir to be +# used for the KnetMiner initialiser +export KNET_INIT_DATASET_ID="fungi-lite" + + +##### Values for server-sync.sh +# + +## RRes Neo server +#export KNET_NEO_SSH=neo4j@babvs65.rothamsted.ac.uk +#export KNET_NEO_DATA=/opt/data + + +## RRes Test instances for Knetminer +# + +# Test servers like babvs73 +export KNET_TESTINST_DATA_PATH=/opt/data/knetminer-datasets/fungi-lite +# babvs73: based on old Traverser, available at knetminer.com/ci-test +# babvs72: based on Neo4j+OXL Traverser, available at knetminer.com/ci-test-cypher +# export KNET_TESTINST_SSH="brandizim@babvs73.rothamsted.ac.uk brandizim@babvs72.rothamsted.ac.uk" diff --git a/rres-endpoints/config/datasets/fungi-lite-60-metadata-descriptor.properties b/rres-endpoints/config/datasets/fungi-lite-60-metadata-descriptor.properties new file mode 100644 index 0000000..1b532fc --- /dev/null +++ b/rres-endpoints/config/datasets/fungi-lite-60-metadata-descriptor.properties @@ -0,0 +1,17 @@ +# These files are passed to the Ondex Metadata descriptor tool. +# https://github.com/Rothamsted/knetbuilder/tree/master/ondex-knet-builder/modules/rdf-export-2 +# +datasetId = fungi-lite +datasetAccession = KnetMiner:Fungi-lite +datasetTitle = Knetminer's knowledge graph about fungi +datasetDescription = \ + Knetminer is a gene discovery platform, which allows for exploring knwoledge graphs computed \ + from common plant biology data, such as ENSEMBL, UniProt, TAIR, PUBMED and more.\n\ + The brassica dataset contains information about the 5 gramineae species, which is also linked \ + to embedded data about the Arabidopsis model organism.\n\ + This edition includes Saccharomyces cerevisiae, Fusarium_culmorum, Fusarium_graminearum, Schizosaccharomyces_pombe, Zymoseptoria_tritici. +datasetVersion = 58 +# TODO: better URLs +datasetURL = https://knetminer.com/about +datasetNeo4jBrowserURL = +datasetNeo4jBOLTURL = diff --git a/rres-endpoints/utils/neo4j/neo-stats.sh b/rres-endpoints/utils/neo4j/neo-stats.sh index d63f793..ac0d138 100644 --- a/rres-endpoints/utils/neo4j/neo-stats.sh +++ b/rres-endpoints/utils/neo4j/neo-stats.sh @@ -11,7 +11,7 @@ CREATE (s:Metadata { nodeCount: nodeCount, edgeCount: edgeCount, version: \"${KETL_DATASET_VERSION}\", - fileLocation: \"s3://knet-data-store/${KETL_DATASET_ID}/v${KETL_DATASET_VERSION}-RC2\", + fileLocation: \"s3://knet-data-store/${KETL_DATASET_ID}/v${KETL_DATASET_VERSION}-RC1\", date: \"${current_date}\" });