Building Brassica-Premium v61-RC1

Author: holegar

rres-endpoints/config/datasets/brassicaceae-premium-61-cfg.sh

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+. "$KETL_HOME/config/datasets/${KETL_DATASET_ID}-common.sh"

rres-endpoints/config/datasets/brassicaceae-premium-61-metadata-descriptor.properties

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+# 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 = brassicaceae
+datasetAccession = KnetMiner:Brassicaceae-premium
+datasetTitle = Knetminer's knowledge graph about brassicaceae
+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 Arabidopsis, Brassica_napus, Brassica_oleracea, Brassica_rapa_ro18, Camelina_sativa, Brassica_juncea.
+datasetVersion = 61
+# TODO: better URLs
+datasetURL = https://knetminer.com/about
+datasetNeo4jBrowserURL = <http://knetminer-wheat.cyverseuk.org:7474>
+datasetNeo4jBOLTURL = <bolt://knetminer-neo4j.cyverseuk.org:7687>

rres-endpoints/config/datasets/brassicaceae-premium-common.sh

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+# The OXL is somewhere like:
+#   /home/data/knetminer/etl-test/brassicaceae-premium/61/generic/knowledge-network.oxl
+# Unfortunately, there isn't consistence, so we need the following
+
+oxl_home="$KNET_HOME/etl-test/$KETL_DATASET_ID/$KETL_DATASET_VERSION_NUM"
+
+export KETL_SRC_OXL="$oxl_home/generic/knowledge-network.oxl"
+
+export KETL_OUT="$KETL_OUT_HOME/$KETL_DATASET_ID/$KETL_DATASET_VERSION"
+
+## Neo 
+#
+export KETL_HAS_NEO4J=true
+export KETL_NEO_VERSION='5.26.0'
+export NEO4J_HOME="$KNET_SOFTWARE/neo4j-community-$KETL_NEO_VERSION-etl"
+
+
+# TODO: to be remove, we don't deploy on RRes anymore
+
+##### 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/brassicaceae-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"

rres-endpoints/config/datasets/brassicaceae-premium-v61-RC1-cfg.sh

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+. "$KETL_HOME/config/datasets/${KETL_DATASET_ID}-${KETL_DATASET_VERSION_NUM}-cfg.sh"

rres-endpoints/config/datasets/vegetables-premium-61-metadata-descriptor.properties

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+# 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 = vegetables-premium
+datasetAccession = KnetMiner:Vegetables-premium
+datasetTitle = Knetminer's knowledge graph about Vegetables
+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 solanaceae dataset contains information about the 5 gramineae species, which is also linked \
+	to embedded data about the Arabidopsis model organism.\n\
+	This edition includes Arabidopsis, Asparagus officinalis, Arabidopsis thaliana, Beta vulgaris, Capsicum annuum, Cucumis sativus, Daucus carota, Lactuca sativa, Nicotiana attenuata, Solanum lycopersicum, Solanum tuberosum.
+datasetVersion = 61
+# TODO: better URLs
+datasetURL = https://knetminer.com/about
+datasetNeo4jBrowserURL = <http://knetminer-wheat.cyverseuk.org:7474>
+datasetNeo4jBOLTURL = <bolt://knetminer-neo4j.cyverseuk.org:7687>