Creating Fungi-lite. Updating Ascomycota 58RC3

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="[email protected] [email protected]"

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 [email protected]
+#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="[email protected] [email protected]"

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 = <http://knetminer-wheat.cyverseuk.org:7474>
+datasetNeo4jBOLTURL = <bolt://knetminer-neo4j.cyverseuk.org:7687>

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}\"
 });