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Makefile
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all: convert
# TODO Implement analysis on data model changes
analyze:
@echo "Analyzing data model..."
convert:
bb ./retold/retold as-jsonld --dir modules --out NF.jsonld
# Recompile certain json schemas with LinkML with selective import of props, enums, and template
# LinkML output needs to be dereferenced bc Synapse doesn't suppport full specs such as $defs
PortalDataset:
yq '.slots |= with_entries(select(.value.in_subset[] == "portal"))' modules/props.yaml > relevant_props.yaml
yq ea '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/Assay/Assay.yaml modules/Sample/Species.yaml modules/DCC/Portal.yaml > relevant_enums.yaml
cat header.yaml relevant_props.yaml relevant_enums.yaml modules/Template/PortalDataset.yaml > temp.yaml
gen-json-schema --inline --no-metadata --title-from=title --not-closed temp.yaml > tmp.json
json-dereference -s tmp.json -o tmp.json
jq '."$$defs".PortalDataset | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portaldataset"' tmp.json > registered-json-schemas/PortalDataset.json
rm -f relevant_props.yaml relevant_enums.yaml temp.yaml tmp.json
@echo "--- Saved registered-json-schemas/PortalDataset.json ---"
# yq '.slots |= with_entries(select(.value.in_subset[] == "portal"))' modules/props.yaml > relevant_props.yaml
PortalStudy:
yq eval-all '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/DCC/Portal.yaml modules/Other/Organization.yaml > relevant_enums.yaml
cat header.yaml relevant_enums.yaml modules/Template/PortalStudy.yaml > temp.yaml
gen-json-schema --inline --no-metadata --not-closed temp.yaml > tmp.json
json-dereference -s tmp.json -o tmp.json
jq '."$$defs".PortalStudy | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalstudy"' tmp.json > registered-json-schemas/PortalStudy.json
rm -f relevant_enums.yaml temp.yaml tmp.json
@echo "--- Saved registered-json-schemas/PortalStudy.json ---"
Protocol:
yq '.slots |= with_entries(select(.value.in_subset[] == "portal" or .value.in_subset[] == "registered"))' modules/props.yaml > relevant_props.yaml
yq ea '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/DCC/Portal.yaml modules/Assay/Assay.yaml > relevant_enums.yaml
cat header.yaml relevant_props.yaml relevant_enums.yaml modules/Template/Protocol.yaml > temp.yaml
gen-json-schema --inline --no-metadata --not-closed --title-from=title temp.yaml > tmp.json
json-dereference -s tmp.json -o tmp.json
jq '."$$defs".Protocol | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-protocol"' tmp.json > registered-json-schemas/Protocol.json
rm -f relevant_props.yaml relevant_enums.yaml temp.yaml tmp.json
@echo "--- Saved registered-json-schemas/Protocol.json ---"
Superdataset:
jq '. += input | del(.required) | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-superdataset"' registered-json-schemas/PortalDataset.json registered-json-schemas/super_rules.json > registered-json-schemas/Superdataset.json
@echo "--- Saved registered-json-schemas/Superdataset.json ---"
PortalPublication:
yq ea '. as $$item ireduce ({}; . * $$item )' modules/DCC/Portal.yaml modules/Other/PublicationEnum.yaml > relevant_enums.yaml
cat header.yaml modules/Template/PortalPublication.yaml relevant_enums.yaml > temp.yaml
gen-json-schema --top-class=PortalPublication --no-metadata --not-closed --title-from=title temp.yaml > tmp.json
json-dereference -s tmp.json -o tmp.json
jq '."$$defs".PortalPublication | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalpublication"' tmp.json > registered-json-schemas/PortalPublication.json
rm -f tmp.json temp.yaml relevant_enums.yaml
@echo "--- Saved registered-json-schemas/PortalPublication.json ---"
PortalPublication:
yq ea '. as $$item ireduce ({}; . * $$item )' modules/DCC/Portal.yaml modules/Other/PublicationEnum.yaml > relevant_enums.yaml
cat header.yaml modules/Template/PortalPublication.yaml relevant_enums.yaml > temp.yaml
gen-json-schema --top-class=PortalPublication --no-metadata --not-closed --title-from=title temp.yaml > tmp.json
json-dereference -s tmp.json -o tmp.json
jq '."$$defs".PortalPublication | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalpublication"' tmp.json > registered-json-schemas/PortalPublication.json
rm -f tmp.json temp.yaml relevant_enums.yaml
@echo "--- Saved registered-json-schemas/PortalPublication.json ---"