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createSets.sh
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#! /bin/bash
##
## Optionally specify the backend as argument, e.g.
## ./createSets.sh http://10.22.13.12:6081/oai-backend
##
BACKEND="${1:-http://localhost:8081/oai-backend}"
## STN: I used plural for the set name and description
## and singular for the tags
## The first tag is the Bioschemas profile,
## and the second a custom combination of MassBank and content
##
## Create Sets for schema.org types
##
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Datacatalogs", "spec": "DataCatalog", "description": "All items of schema.org type DataCatalog, usually describing repositories", "tags": ["DataCatalog"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Projects", "spec": "Project", "description": "All items of schema.org type Project, usually containing a number of studies", "tags": ["Project"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Studies", "spec": "Study", "description": "All items of schema.org type Study, usually containing a number of Datasets", "tags": ["Study"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Datasets", "spec": "Dataset", "description": "All items of schema.org type Dataset, describing e.g. simulated or measured chemical data", "tags": ["Dataset"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "MolecularEntities", "spec": "MolecularEntity", "description": "All items of schema.org type MolecularEntity, describing the notion and often structure of a molecule", "tags": ["MolecularEntity"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "ChemicalSubstances", "spec": "ChemicalSubstance", "description": "All items of schema.org type ChemicalSubstance, describing a specific aliquot or sample of a chemical substance", "tags": ["ChemicalSubstance"]}'
##
## Create Sets for MassBank
##
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "MassBank items", "spec": "MassBank", "description": "All items in MassBank", "tags": ["MassBank"]}'
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "MassBank Molecules", "spec": "MassBank:MolecularEntity", "description": "All molecules known in MassBank", "tags": ["MassBank:MolecularEntity"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "MassBank Molecules", "spec": "MassBank:ChemicalSubstance", "description": "All chemical substances known in MassBank", "tags": ["MassBank:ChemicalSubstance"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "MassBank Spectra", "spec": "MassBank:Dataset", "description": "All MassBank Spectra", "tags": ["MassBank:Dataset"]}'
##
## Create Sets for RADAR4Chem
##
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "RADAR4Chem items", "spec": "RADAR4Chem", "description": "All items in RADAR4Chem", "tags": ["RADAR4Chem"]}'
#
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "RADAR4Chem Datasets", "spec": "RADAR4Chem:Dataset", "description": "All RADAR4Chem datasets", "tags": ["RADAR4Chem:Dataset"]}'
##
## Create Sets for nmrXiv
##
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "nmrXiv items", "spec": "nmrXiv", "description": "All items in nmrXiv", "tags": ["nmrXiv"]}'
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "nmrXiv Molecules", "spec": "nmrXiv:MolecularEntity", "description": "All molecules known in MassBank", "tags": ["nmrXiv:MolecularEntity"]}'
#
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "nmrXiv Spectra", "spec": "nmrXiv:Dataset", "description": "All nmrXiv Spectra", "tags": ["nmrXiv:Dataset"]}'
##
## Create Sets for Chemotion
##
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "Chemotion items", "spec": "Chemotion", "description": "All items in Chemotion", "tags": ["Chemotion"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Chemotion Studies", "spec": "Chemotion:Study", "description": "All chemical studies (samples) known in Chemotion", "tags": ["Chemotion:Study"]}'
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "Chemotion Samples", "spec": "Chemotion:ChemicalSubstance", "description": "All chemical substances known in Chemotion", "tags": ["Chemotion:ChemicalSubstance"]}'
#curl -X POST -H 'Content-Type: application/json' \
# -i "$BACKEND/set" \
# --data '{"name": "Chemotion Reactions", "spec": "Chemotion:Reaction", "description": "All reactions known in Chemotion", "tags": ["Chemotion:Reaction"]}'
curl -X POST -H 'Content-Type: application/json' \
-i "$BACKEND/set" \
--data '{"name": "Chemotion Datasets", "spec": "Chemotion:Dataset", "description": "All Chemotion Datasets", "tags": ["Chemotion:Dataset"]}'