datasets updated. new dedup. new partitions

master
Andrea Mannocci 2 years ago
parent 594ba0e1c7
commit abfb626faa

@ -26,8 +26,8 @@ requirements: test_environment
$(PYTHON_INTERPRETER) -m pip install -r requirements.txt
## Make Dataset
data: requirements
$(PYTHON_INTERPRETER) src/data/make_dataset.py data/raw data/processed
# data: requirements
# $(PYTHON_INTERPRETER) src/data/make_dataset.py data/raw data/processed
## Delete all compiled Python files
clean:
@ -39,20 +39,20 @@ lint:
flake8 src
## Upload Data to S3
sync_data_to_s3:
ifeq (default,$(PROFILE))
aws s3 sync data/ s3://$(BUCKET)/data/
else
aws s3 sync data/ s3://$(BUCKET)/data/ --profile $(PROFILE)
endif
# sync_data_to_s3:
# ifeq (default,$(PROFILE))
# aws s3 sync data/ s3://$(BUCKET)/data/
# else
# aws s3 sync data/ s3://$(BUCKET)/data/ --profile $(PROFILE)
# endif
## Download Data from S3
sync_data_from_s3:
ifeq (default,$(PROFILE))
aws s3 sync s3://$(BUCKET)/data/ data/
else
aws s3 sync s3://$(BUCKET)/data/ data/ --profile $(PROFILE)
endif
# sync_data_from_s3:
# ifeq (default,$(PROFILE))
# aws s3 sync s3://$(BUCKET)/data/ data/
# else
# aws s3 sync s3://$(BUCKET)/data/ data/ --profile $(PROFILE)
# endif
## Set up python interpreter environment
create_environment:

@ -0,0 +1,960 @@
{"name": "WDC Sunspot Index and Long-term Solar Observations", "originalId": "3226", "websiteurl": "http://sidc.be/silso/home", "collectedfrom": "FAIRsharing", "alternativeNames": ["WDC-SILSO"], "id": "https://fairsharing.org/10.25504/FAIRsharing.d6423b"}
{"name": "Biological Magnetic Resonance Data Bank", "originalId": "2114", "websiteurl": "https://bmrb.io/", "collectedfrom": "FAIRsharing", "alternativeNames": ["BMRB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.p06nme"}
{"name": "Fisheries and Oceans Canada Pacific Region Data Archive", "originalId": "3022", "websiteurl": "http://www.pac.dfo-mpo.gc.ca/science/oceans/data-donnees/index-eng.html", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.8b7a2f"}
{"name": "Climate Prediction Center", "originalId": "2998", "websiteurl": "https://www.cpc.ncep.noaa.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CPC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.e08886"}
{"name": "Acytostelium Gene Database", "originalId": "2301", "websiteurl": "http://cosmos.bot.kyoto-u.ac.jp/acytodb//cgi-bin/index.cgi?org=as", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.meh9wz"}
{"name": "Geochron", "originalId": "3237", "websiteurl": "https://www.geochron.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Geochron"], "id": "https://fairsharing.org/fairsharing_records/3237"}
{"name": "Taiwan Biodiversity Information Facility IPT - GBIF Taiwan", "originalId": "2475", "websiteurl": "http://ipt.taibif.tw/", "collectedfrom": "FAIRsharing", "alternativeNames": ["TaiBIF IPT - GBIF Taiwan"], "id": "https://fairsharing.org/10.25504/FAIRsharing.y2vm4r"}
{"name": "Germplasm Resources Information Network", "originalId": "2078", "websiteurl": "https://www.ars-grin.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GRIN"], "id": "https://fairsharing.org/10.25504/FAIRsharing.3axym7"}
{"name": "meereisportal.de Data Portal", "originalId": "3149", "websiteurl": "https://data.seaiceportal.de", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.bf65d9"}
{"name": "Nottingham Arabidopsis Stock Centre Seeds Database", "originalId": "1740", "websiteurl": "http://arabidopsis.info", "collectedfrom": "FAIRsharing", "alternativeNames": ["NASC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2sqcxs"}
{"name": "IsoArcH database", "originalId": "3319", "websiteurl": "https://isoarch.eu/", "collectedfrom": "FAIRsharing", "alternativeNames": ["IsoArcH"], "id": "https://fairsharing.org/fairsharing_records/3319"}
{"name": "Chile National Health Survey 2009-2010", "originalId": "2457", "websiteurl": "http://epi.minsal.cl/bases-de-datos/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Chile NHS 2009"], "id": "https://fairsharing.org/10.25504/FAIRsharing.6hb7c1"}
{"name": "Global Project Management System Tuberculosis Transportal", "originalId": "2881", "websiteurl": "https://tbindia.indiancst.com/GPMSTBTransportal/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GPMS TB Transportal"], "id": "https://fairsharing.org/10.25504/FAIRsharing.4APEVR"}
{"name": "Chinese National Arctic and Antarctic Data Center", "originalId": "2810", "websiteurl": "https://www.chinare.org.cn/en/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/fairsharing_records/2810"}
{"name": "Brainbase", "originalId": "2659", "websiteurl": "https://brainbase.io", "collectedfrom": "FAIRsharing", "alternativeNames": ["Brainbase"], "id": "https://fairsharing.org/10.25504/FAIRsharing.Zz0lIi"}
{"name": "Ocean Biodiversity Information System", "originalId": "2294", "websiteurl": "https://obis.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["OBIS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.3rv9m8"}
{"name": "Canadian Open Neuroscience Platform (CONP) Portal", "originalId": "3245", "websiteurl": "https://portal.conp.ca", "collectedfrom": "FAIRsharing", "alternativeNames": ["CONP Portal"], "id": "https://fairsharing.org/10.25504/FAIRsharing.7qwrhY"}
{"name": "AErosol RObotic NETwork", "originalId": "3170", "websiteurl": "https://aeronet.gsfc.nasa.gov/new_web/data.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["AERONET"], "id": "https://fairsharing.org/fairsharing_records/3170"}
{"name": "Arch", "originalId": "3672", "websiteurl": "https://arch.library.northwestern.edu/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/fairsharing_records/3672"}
{"name": "The Cardiovascular Research Grid", "originalId": "2012", "websiteurl": "https://www.cvrgrid.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CVRG"], "id": "https://fairsharing.org/10.25504/FAIRsharing.x80z26"}
{"name": "Code Ocean", "originalId": "2548", "websiteurl": "https://codeocean.com", "collectedfrom": "FAIRsharing", "alternativeNames": ["CO"], "id": "https://fairsharing.org/10.25504/FAIRsharing.thskvr"}
{"name": "NASA Goddard Earth Sciences Data and Information Services Center", "originalId": "2495", "websiteurl": "https://disc.gsfc.nasa.gov", "collectedfrom": "FAIRsharing", "alternativeNames": ["GES DISC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.7388wt"}
{"name": "Metabolonote", "originalId": "2615", "websiteurl": "http://metabolonote.kazusa.or.jp", "collectedfrom": "FAIRsharing", "alternativeNames": ["Metabolonote"], "id": "https://fairsharing.org/10.25504/FAIRsharing.d8fea5"}
{"name": "GenBank", "originalId": "1547", "websiteurl": "https://www.ncbi.nlm.nih.gov/genbank/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GenBank"], "id": "https://fairsharing.org/10.25504/FAIRsharing.9kahy4"}
{"name": "NIST Atomic Spectra Database", "originalId": "2621", "websiteurl": "https://www.nist.gov/pml/atomic-spectra-database", "collectedfrom": "FAIRsharing", "alternativeNames": ["ASD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.401958"}
{"name": "The Track Hub Registry", "originalId": "2736", "websiteurl": "https://www.trackhubregistry.org/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.a1de61"}
{"name": "DRSC Functional Genomics Resources", "originalId": "1583", "websiteurl": "http://www.flyrnai.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["DRSC-FGR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.sbnhkq"}
{"name": "Human Genetic Variation Database", "originalId": "2742", "websiteurl": "http://www.hgvd.genome.med.kyoto-u.ac.jp/", "collectedfrom": "FAIRsharing", "alternativeNames": ["HGVD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.c7edd8"}
{"name": "Functional ANnoTation Of the Mammalian genome Database", "originalId": "2788", "websiteurl": "https://fantom.gsc.riken.jp/", "collectedfrom": "FAIRsharing", "alternativeNames": ["FANTOM5"], "id": "https://fairsharing.org/10.25504/FAIRsharing.99c9b0"}
{"name": "Level-1 and Atmosphere Archive & Distribution System", "originalId": "3056", "websiteurl": "https://ladsweb.modaps.eosdis.nasa.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["LAADS DAAC"], "id": "https://fairsharing.org/fairsharing_records/3056"}
{"name": "Research Data Leeds Repository", "originalId": "3157", "websiteurl": "http://archive.researchdata.leeds.ac.uk/", "collectedfrom": "FAIRsharing", "alternativeNames": ["RDL"], "id": "https://fairsharing.org/10.25504/FAIRsharing.nhVgNw"}
{"name": "Primate Cell Type Database", "originalId": "2879", "websiteurl": "https://primatedatabase.com/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PCTD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.7IQk4a"}
{"name": "Discovery VIRUS COVID-19 Registry", "originalId": "3250", "websiteurl": "https://www.sccm.org/Research/Research/Discovery-Research-Network/VIRUS-COVID-19-Registry", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.ogTCME"}
{"name": "real-time quantitative PCR Primer Database", "originalId": "2499", "websiteurl": "http://biodb.swu.edu.cn/qprimerdb/", "collectedfrom": "FAIRsharing", "alternativeNames": ["qPrimerDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.qy4b7s"}
{"name": "Citrination", "originalId": "2538", "websiteurl": "https://citrination.com/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Citrination"], "id": "https://fairsharing.org/10.25504/FAIRsharing.x6y19r"}
{"name": "Dryad", "originalId": "1998", "websiteurl": "http://datadryad.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Dryad"], "id": "https://fairsharing.org/10.25504/FAIRsharing.wkggtx"}
{"name": "Genomic Observatories Meta-Database", "originalId": "3019", "websiteurl": "https://geome-db.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GEOME"], "id": "https://fairsharing.org/10.25504/FAIRsharing.wOcTaM"}
{"name": "Food and Agriculture Microdata Catalogue", "originalId": "2892", "websiteurl": "https://microdata.fao.org/index.php/catalog", "collectedfrom": "FAIRsharing", "alternativeNames": ["FAM"], "id": "https://fairsharing.org/10.25504/FAIRsharing.8b493b"}
{"name": "Database of Somatic Mutations in Normal Cells", "originalId": "2893", "websiteurl": "http://dsmnc.big.ac.cn/", "collectedfrom": "FAIRsharing", "alternativeNames": ["DSMNC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.05e1a4"}
{"name": "Plant Natural Antisense Transcripts Database", "originalId": "1629", "websiteurl": "http://bis.zju.edu.cn/pnatdb/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PlantNATsDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.rn1pxg"}
{"name": "Global Terrestrial Network for Permafrost - Database", "originalId": "3114", "websiteurl": "http://gtnpdatabase.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GTN-P"], "id": "https://fairsharing.org/10.25504/FAIRsharing.44a554"}
{"name": "GERDA", "originalId": "3115", "websiteurl": "https://eng.geus.dk/products-services-facilities/data-and-maps/national-geophysical-database-gerda/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GERDA"], "id": "https://fairsharing.org/10.25504/FAIRsharing.893fc2"}
{"name": "Global Monitoring Laboratory Data Finder and Viewer", "originalId": "3131", "websiteurl": "https://esrl.noaa.gov/gmd/dv/data/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GML Data Finder and Viewer"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2877fa"}
{"name": "Climate Data Online", "originalId": "3138", "websiteurl": "https://www.ncdc.noaa.gov/cdo-web/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CDO"], "id": "https://fairsharing.org/10.25504/FAIRsharing.a00142"}
{"name": "Coral Reef Information System", "originalId": "3140", "websiteurl": "https://www.coris.noaa.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CoRIS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.ed5b45"}
{"name": "Allele frequency resource for research and teaching", "originalId": "1550", "websiteurl": "https://alfred.med.yale.edu/alfred/index.asp", "collectedfrom": "FAIRsharing", "alternativeNames": ["ALFRED"], "id": "https://fairsharing.org/10.25504/FAIRsharing.y2yct1"}
{"name": "Protein Circular Dichroism Data Bank", "originalId": "2142", "websiteurl": "http://pcddb.cryst.bbk.ac.uk", "collectedfrom": "FAIRsharing", "alternativeNames": ["PCDDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.65yfxp"}
{"name": "DDBJ Biosample", "originalId": "3011", "websiteurl": "https://www.ddbj.nig.ac.jp/biosample/index-e.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["DDBJ Biosample"], "id": "https://fairsharing.org/10.25504/FAIRsharing.20f490"}
{"name": "Bitbucket", "originalId": "3275", "websiteurl": "https://bitbucket.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Bitbucket"], "id": "https://fairsharing.org/10.25504/FAIRsharing.fc3431"}
{"name": "Atlas of Living Australia", "originalId": "3258", "websiteurl": "https://www.ala.org.au/", "collectedfrom": "FAIRsharing", "alternativeNames": ["ALA"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2f66da"}
{"name": "GitLab", "originalId": "3277", "websiteurl": "https://about.gitlab.com/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GitLab"], "id": "https://fairsharing.org/10.25504/FAIRsharing.530e61"}
{"name": "SourceForge", "originalId": "3278", "websiteurl": "https://sourceforge.net/", "collectedfrom": "FAIRsharing", "alternativeNames": ["SourceForge"], "id": "https://fairsharing.org/10.25504/FAIRsharing.b138b5"}
{"name": "Launchpad", "originalId": "3279", "websiteurl": "https://launchpad.net", "collectedfrom": "FAIRsharing", "alternativeNames": ["Launchpad"], "id": "https://fairsharing.org/10.25504/FAIRsharing.a2ba05"}
{"name": "Allen Brain Map Data Catalog", "originalId": "3687", "websiteurl": "https://knowledge.brain-map.org/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.618298"}
{"name": "Iowa State University's DataShare", "originalId": "2861", "websiteurl": "https://iastate.figshare.com/", "collectedfrom": "FAIRsharing", "alternativeNames": ["ISU DataShare"], "id": "https://fairsharing.org/10.25504/FAIRsharing.yOKiQs"}
{"name": "Savannah", "originalId": "3266", "websiteurl": "http://savannah.gnu.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Savannah"], "id": "https://fairsharing.org/10.25504/FAIRsharing.3f074b"}
{"name": "Neuroimaging Informatics Tools and Resources Collaboratory Image Repository", "originalId": "3290", "websiteurl": "https://www.nitrc.org/xnat/index.php", "collectedfrom": "FAIRsharing", "alternativeNames": ["NITRC-IR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.a9cfbf"}
{"name": "StellaBase", "originalId": "1785", "websiteurl": "http://stellabase.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["StellaBase"], "id": "https://fairsharing.org/10.25504/FAIRsharing.72qwj0"}
{"name": "LCI facility data repository", "originalId": "2321", "websiteurl": "http://ki.se/en/bionut/welcome-to-the-lci-facility", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.erhnxs"}
{"name": "FAIR4Health Metadata", "originalId": "3617", "websiteurl": "https://www.fair4health.eu/", "collectedfrom": "FAIRsharing", "alternativeNames": ["F4H-Metadata"], "id": "https://fairsharing.org/fairsharing_records/3617"}
{"name": "CESSDA Data Catalogue", "originalId": "3325", "websiteurl": "https://datacatalogue.cessda.eu/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CESSDA DC"], "id": "https://fairsharing.org/fairsharing_records/3325"}
{"name": "Paired Omics Data Platform", "originalId": "3306", "websiteurl": "https://pairedomicsdata.bioinformatics.nl/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PoDP"], "id": "https://fairsharing.org/10.25504/FAIRsharing.9289d4"}
{"name": "Nematode Expression Pattern DataBase", "originalId": "2000", "websiteurl": "http://nematode.lab.nig.ac.jp/", "collectedfrom": "FAIRsharing", "alternativeNames": ["NextDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.xz5m1a"}
{"name": "University of Hong Kong DataHub", "originalId": "3173", "websiteurl": "https://datahub.hku.hk", "collectedfrom": "FAIRsharing", "alternativeNames": ["HKU DataHub"], "id": "https://fairsharing.org/10.25504/FAIRsharing.rafti9"}
{"name": "Data and Service Center for the Humanities", "originalId": "3311", "websiteurl": "https://meta.dasch.swiss/", "collectedfrom": "FAIRsharing", "alternativeNames": ["DaSCH"], "id": "https://fairsharing.org/10.25504/FAIRsharing.095469"}
{"name": "Advanced Spaceborne Thermal Emission and Reflection Radiometer", "originalId": "2797", "websiteurl": "https://asterweb.jpl.nasa.gov", "collectedfrom": "FAIRsharing", "alternativeNames": ["ASTER Data"], "id": "https://fairsharing.org/10.25504/FAIRsharing.00dfd8"}
{"name": "BioImage Archive", "originalId": "2830", "websiteurl": "https://www.ebi.ac.uk/bioimage-archive/", "collectedfrom": "FAIRsharing", "alternativeNames": ["BioImage Archive"], "id": "https://fairsharing.org/10.25504/FAIRsharing.x38D2k"}
{"name": "OmicsDB", "originalId": "2292", "websiteurl": "https://github.com/KeironO/omicsdb", "collectedfrom": "FAIRsharing", "alternativeNames": ["ODB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.1v4zw7"}
{"name": "TARKI Data Archive", "originalId": "3341", "websiteurl": "https://adatbank.tarki.hu/en/", "collectedfrom": "FAIRsharing", "alternativeNames": ["TARKI"], "id": "https://fairsharing.org/10.25504/FAIRsharing.d14d9f"}
{"name": "Comprehensive R Archive Network", "originalId": "2855", "websiteurl": "https://cran.r-project.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CRAN"], "id": "https://fairsharing.org/10.25504/FAIRsharing.1a283d"}
{"name": "Balearic Islands Coastal Observing and Forecasting System Data Repository", "originalId": "3342", "websiteurl": "http://apps.socib.es/data-catalog/", "collectedfrom": "FAIRsharing", "alternativeNames": ["SOCIB Data Repository"], "id": "https://fairsharing.org/10.25504/FAIRsharing.be094e"}
{"name": "Alternaria Genomes Database", "originalId": "2643", "websiteurl": "http://alternaria.vbi.vt.edu/index.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["AGD"], "id": "https://fairsharing.org/fairsharing_records/2643"}
{"name": "Microbial Database for Activated Sludge", "originalId": "3657", "websiteurl": "https://midasfieldguide.org/guide", "collectedfrom": "FAIRsharing", "alternativeNames": ["MiDAS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.b1716a"}
{"name": "The Troms\u00f8 Repository of Language and Linguistics", "originalId": "2929", "websiteurl": "https://trolling.uit.no/", "collectedfrom": "FAIRsharing", "alternativeNames": ["TROLLing"], "id": "https://fairsharing.org/10.25504/FAIRsharing.JGEjCW"}
{"name": "COVID-19 Data Portal", "originalId": "2934", "websiteurl": "https://www.covid19dataportal.org", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.f3b7a9"}
{"name": "GISAID EpiCoV\u2122 Database", "originalId": "2938", "websiteurl": "https://db.cngb.org/gisaid/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.ba6a09"}
{"name": "Stanford HIV Drug Resistance Database", "originalId": "2945", "websiteurl": "https://hivdb.stanford.edu/", "collectedfrom": "FAIRsharing", "alternativeNames": ["HIVDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.41737c"}
{"name": "Civic Learning, Engagement, and Action Data Sharing\tC", "originalId": "3199", "websiteurl": "https://www.icpsr.umich.edu/web/pages/civicleads/index.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["CivicLEADS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.aFsZlL"}
{"name": "European Centre for Disease Prevention and Control", "originalId": "2950", "websiteurl": "https://www.ecdc.europa.eu/en", "collectedfrom": "FAIRsharing", "alternativeNames": ["ECDC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.7ceb60"}
{"name": "Translational Data Catalog", "originalId": "3655", "websiteurl": "https://datacatalog.elixir-luxembourg.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["IMI Data Catalog"], "id": "https://fairsharing.org/10.25504/FAIRsharing.de533c"}
{"name": "National Pollutant Release Inventory", "originalId": "2970", "websiteurl": "https://www.canada.ca/en/services/environment/pollution-waste-management/national-pollutant-release-inventory.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["NPRI"], "id": "https://fairsharing.org/10.25504/FAIRsharing.f14e0b"}
{"name": "United States Department of Agriculture Economics, Statistics and Market Information System", "originalId": "2995", "websiteurl": "https://usda.library.cornell.edu/", "collectedfrom": "FAIRsharing", "alternativeNames": ["USDA ESMIS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.88b8d1"}
{"name": "World Ocean Database", "originalId": "3008", "websiteurl": "https://www.nodc.noaa.gov/OC5/WOD/pr_wod.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["WOD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.73ea53"}
{"name": "PAZAR", "originalId": "2032", "websiteurl": "http://www.pazar.info/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PAZAR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.33yggg"}
{"name": "protocols.io", "originalId": "3758", "websiteurl": "https://protocols.io/welcome", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/fairsharing_records/3758"}
{"name": "Scholars' Bank", "originalId": "3033", "websiteurl": "https://scholarsbank.uoregon.edu/xmlui/", "collectedfrom": "FAIRsharing", "alternativeNames": ["Scholar's Bank"], "id": "https://fairsharing.org/10.25504/FAIRsharing.86123d"}
{"name": "SeaWiFS Bio-optical Archive and Storage System", "originalId": "3034", "websiteurl": "https://seabass.gsfc.nasa.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["SeaBASS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.f384c3"}
{"name": "Atmospheric Science Data Center", "originalId": "3049", "websiteurl": "https://asdc.larc.nasa.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["ASDC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.d9d234"}
{"name": "Autism Brain Imaging Data Exchange", "originalId": "2244", "websiteurl": "http://fcon_1000.projects.nitrc.org/indi/abide/", "collectedfrom": "FAIRsharing", "alternativeNames": ["ABIDE"], "id": "https://fairsharing.org/10.25504/FAIRsharing.16v73e"}
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@ -0,0 +1,893 @@
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{"name": "IUPHAR/BPS Guide to PHARMACOLOGY", "originalId": "1933", "websiteurl": "https://www.guidetopharmacology.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["Guide to Pharmacology"], "id": "https://fairsharing.org/10.25504/FAIRsharing.f1dv0"}
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{"name": "Database of small human non-coding RNAs", "originalId": "2248", "websiteurl": "http://lisanwanglab.org/DASHR", "collectedfrom": "FAIRsharing", "alternativeNames": ["DASHR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.ztvs34"}
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{"name": "National Biodiversity Network Atlas", "originalId": "2818", "websiteurl": "https://nbnatlas.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["NBN Atlas"], "id": "https://fairsharing.org/10.25504/FAIRsharing.p7YFEc"}
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{"name": "Side Effect Resource", "originalId": "1876", "websiteurl": "http://sideeffects.embl.de", "collectedfrom": "FAIRsharing", "alternativeNames": ["SIDER"], "id": "https://fairsharing.org/10.25504/FAIRsharing.zzaykv"}
{"name": "NCBI Cancer Chromosome Database", "originalId": "1965", "websiteurl": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes", "collectedfrom": "FAIRsharing", "alternativeNames": ["Cancer Chromosomes"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2cyh1h"}
{"name": "Human Gene Database", "originalId": "2123", "websiteurl": "https://www.genecards.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GeneCards"], "id": "https://fairsharing.org/10.25504/FAIRsharing.g7jbvn"}
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{"name": "IRESite", "originalId": "1820", "websiteurl": "http://www.iresite.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["IRESite"], "id": "https://fairsharing.org/10.25504/FAIRsharing.kd39j4"}
{"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking", "originalId": "1943", "websiteurl": "http://www.yeastract.com", "collectedfrom": "FAIRsharing", "alternativeNames": ["YEASTRACT"], "id": "https://fairsharing.org/10.25504/FAIRsharing.mphj4z"}
{"name": "4DNucleome Data Portal", "originalId": "2771", "websiteurl": "https://data.4dnucleome.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["4DN"], "id": "https://fairsharing.org/10.25504/FAIRsharing.CugtbQ"}
{"name": "iProX", "originalId": "2834", "websiteurl": "https://www.iprox.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["iProX"], "id": "https://fairsharing.org/10.25504/FAIRsharing.4Sj3vE"}
{"name": "Integrated Marine Information System", "originalId": "3097", "websiteurl": "http://www.vliz.be/en/integrated-marine-information-system", "collectedfrom": "FAIRsharing", "alternativeNames": ["IMIS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.48ZQkn"}
{"name": "Interferome", "originalId": "2229", "websiteurl": "http://www.interferome.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["Interferome"], "id": "https://fairsharing.org/10.25504/FAIRsharing.pp67qc"}
{"name": "VDJdb: a curated database of T-cell receptors with known antigen specificity", "originalId": "2514", "websiteurl": "https://vdjdb.cdr3.net", "collectedfrom": "FAIRsharing", "alternativeNames": ["VDJdb"], "id": "https://fairsharing.org/10.25504/FAIRsharing.nwz68"}
{"name": "Pathogen Host Interactions", "originalId": "1760", "websiteurl": "http://www.phi-base.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PHI-base"], "id": "https://fairsharing.org/10.25504/FAIRsharing.73cqdk"}
{"name": "CaltechDATA", "originalId": "2672", "websiteurl": "https://data.caltech.edu", "collectedfrom": "FAIRsharing", "alternativeNames": ["CaltechDATA"], "id": "https://fairsharing.org/10.25504/FAIRsharing.S09se7"}
{"name": "Legume Information System", "originalId": "2579", "websiteurl": "https://legumeinfo.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["LIS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.BZKHEH"}
{"name": "Small Molecule Pathway Database", "originalId": "1887", "websiteurl": "http://www.smpdb.ca/", "collectedfrom": "FAIRsharing", "alternativeNames": ["SMPDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.y1zyaq"}
{"name": "TreeGenes", "originalId": "2594", "websiteurl": "https://treegenesdb.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["TreeGenes"], "id": "https://fairsharing.org/10.25504/FAIRsharing.lCVfCv"}
{"name": "ProteomicsDB", "originalId": "2518", "websiteurl": "https://www.proteomicsdb.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PrDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.6y9h91"}
{"name": "Metabolomics Workbench", "originalId": "2206", "websiteurl": "https://www.metabolomicsworkbench.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["MW"], "id": "https://fairsharing.org/10.25504/FAIRsharing.xfrgsf"}
{"name": "Archive of Data on Disability to Enable Policy and research", "originalId": "3057", "websiteurl": "https://www.icpsr.umich.edu/web/pages/ADDEP/index.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["ADDEP"], "id": "https://fairsharing.org/10.25504/FAIRsharing.wmB5Os"}
{"name": "The Chemical Probes Portal", "originalId": "2334", "websiteurl": "http://www.chemicalprobes.org", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.yrkkbt"}
{"name": "Hardwood Genomics Project", "originalId": "2439", "websiteurl": "http://www.hardwoodgenomics.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["HWG"], "id": "https://fairsharing.org/10.25504/FAIRsharing.srgkaf"}
{"name": "Hymenoptera Genome Database", "originalId": "2733", "websiteurl": "http://hymenopteragenome.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["HGD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.250fc8"}
{"name": "Environmental Data Portal", "originalId": "2683", "websiteurl": "https://www.envidat.ch/", "collectedfrom": "FAIRsharing", "alternativeNames": ["EnviDat"], "id": "https://fairsharing.org/10.25504/FAIRsharing.0VV4KB"}
{"name": "EBRAINS", "originalId": "2975", "websiteurl": "https://ebrains.eu", "collectedfrom": "FAIRsharing", "alternativeNames": ["EBRAINS"], "id": "https://fairsharing.org/10.25504/FAIRsharing.XO6ppp"}
{"name": "PseudoBase", "originalId": "2098", "websiteurl": "http://www.ekevanbatenburg.nl/pb", "collectedfrom": "FAIRsharing", "alternativeNames": ["PseudoBase"], "id": "https://fairsharing.org/10.25504/FAIRsharing.5ey5w6"}
{"name": "euL1db, the European database of L1-HS retrotransposon insertions in humans", "originalId": "2172", "websiteurl": "http://eul1db.unice.fr", "collectedfrom": "FAIRsharing", "alternativeNames": ["euL1db"], "id": "https://fairsharing.org/10.25504/FAIRsharing.ekrvbq"}
{"name": "The human DEPhOsphorylation Database", "originalId": "2178", "websiteurl": "http://www.depod.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["DEPOD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.q9j2e3"}
{"name": "Finnish Social Science Data Archive", "originalId": "2997", "websiteurl": "https://www.fsd.tuni.fi", "collectedfrom": "FAIRsharing", "alternativeNames": ["FSD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2okP6D"}
{"name": "RCSB Protein Data Bank", "originalId": "2044", "websiteurl": "https://www.rcsb.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["RCSB PDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2t35ja"}
{"name": "CollecTF", "originalId": "2144", "websiteurl": "http://collectf.umbc.edu", "collectedfrom": "FAIRsharing", "alternativeNames": ["CollecTF"], "id": "https://fairsharing.org/10.25504/FAIRsharing.g2cf4x"}
{"name": "MGI Mouse Gene Expression Database", "originalId": "2185", "websiteurl": "http://www.informatics.jax.org/expression.shtml", "collectedfrom": "FAIRsharing", "alternativeNames": ["GXD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.q9neh8"}
{"name": "Virus Pathogen Database and Analysis Resource", "originalId": "1697", "websiteurl": "http://www.viprbrc.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["ViPR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2qx8n8"}
{"name": "International Mouse Phenotyping Consortium", "originalId": "2977", "websiteurl": "https://www.mousephenotype.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["IMPC"], "id": "https://fairsharing.org/10.25504/FAIRsharing.LdoU1I"}
{"name": "Quantitative Trait Loci Archive", "originalId": "2023", "websiteurl": "http://phenome.jax.org/db/q?rtn=qtl/home", "collectedfrom": "FAIRsharing", "alternativeNames": ["QTL Archive"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2g4cfa"}
{"name": "Restriction enzymes and methylases database", "originalId": "2009", "websiteurl": "http://rebase.neb.com", "collectedfrom": "FAIRsharing", "alternativeNames": ["REBASE"], "id": "https://fairsharing.org/10.25504/FAIRsharing.9sb9qh"}
{"name": "HealthData.gov", "originalId": "2246", "websiteurl": "https://www.healthdata.gov/", "collectedfrom": "FAIRsharing", "alternativeNames": ["HealthData.gov"], "id": "https://fairsharing.org/10.25504/FAIRsharing.kcpnmb"}
{"name": "Ascidian Network for In Situ Expression and Embryological Data", "originalId": "2278", "websiteurl": "https://www.aniseed.cnrs.fr/", "collectedfrom": "FAIRsharing", "alternativeNames": ["ANISEED"], "id": "https://fairsharing.org/10.25504/FAIRsharing.xp1x9c"}
{"name": "Mouse Phenome Database", "originalId": "1616", "websiteurl": "http://phenome.jax.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["MPD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.h6enr1"}
{"name": "coastMap", "originalId": "2812", "websiteurl": "https://www.hzg.de/institutes_platforms/coastmap/index.php.en", "collectedfrom": "FAIRsharing", "alternativeNames": ["coastMap"], "id": "https://fairsharing.org/10.25504/FAIRsharing.278768"}
{"name": "Database of Genomic Variants Archive", "originalId": "2156", "websiteurl": "http://www.ebi.ac.uk/dgva/", "collectedfrom": "FAIRsharing", "alternativeNames": ["DGVa"], "id": "https://fairsharing.org/10.25504/FAIRsharing.txkh36"}
{"name": "Refractive Index Database", "originalId": "2655", "websiteurl": "https://refractiveindex.info", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.60127f"}
{"name": "NanoCommons Knowledge Base", "originalId": "2979", "websiteurl": "https://www.nanocommons.eu/nanocommons-knowledge-base/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/fairsharing_records/2979"}
{"name": "Norwegian Centre for Research Data", "originalId": "2597", "websiteurl": "https://nsd.no/en/", "collectedfrom": "FAIRsharing", "alternativeNames": ["NSD"], "id": "https://fairsharing.org/10.25504/FAIRsharing.mKDii0"}
{"name": "VertNet", "originalId": "2190", "websiteurl": "http://www.vertnet.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["VertNet"], "id": "https://fairsharing.org/10.25504/FAIRsharing.ctdss6"}
{"name": "Phytozome", "originalId": "2734", "websiteurl": "https://phytozome.jgi.doe.gov/pz/portal.html", "collectedfrom": "FAIRsharing", "alternativeNames": ["Phytozome"], "id": "https://fairsharing.org/fairsharing_records/2734"}
{"name": "PeanutBase", "originalId": "2581", "websiteurl": "https://peanutbase.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["PeanutBase"], "id": "https://fairsharing.org/10.25504/FAIRsharing.fYFurb"}
{"name": "Drug Target Commons", "originalId": "3316", "websiteurl": "http://www.drugtargetcommons.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["DTC"], "id": "https://fairsharing.org/fairsharing_records/3316"}
{"name": "Protein Data Bank in Europe - Knowledge Base", "originalId": "2775", "websiteurl": "http://pdbe-kb.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["PDBe-KB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.sFzdV7"}
{"name": "Kyoto Encyclopedia of Genes and Genomes", "originalId": "2189", "websiteurl": "http://www.genome.jp/kegg/", "collectedfrom": "FAIRsharing", "alternativeNames": ["KEGG"], "id": "https://fairsharing.org/10.25504/FAIRsharing.327nbg"}
{"name": "PomBase", "originalId": "1683", "websiteurl": "http://www.pombase.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["PomBase"], "id": "https://fairsharing.org/10.25504/FAIRsharing.8jsya3"}
{"name": "Information system for G protein-coupled receptors", "originalId": "1832", "websiteurl": "http://gpcrdb.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GPCRdb"], "id": "https://fairsharing.org/10.25504/FAIRsharing.e4n3an"}
{"name": "Protein Data Bank Japan", "originalId": "2031", "websiteurl": "http://www.pdbj.org/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.rs2815"}
{"name": "LNCipedia", "originalId": "2647", "websiteurl": "https://lncipedia.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["LNCipedia"], "id": "https://fairsharing.org/10.25504/FAIRsharing.84c1a7"}
{"name": "Maize Genetics and Genomics Database", "originalId": "1948", "websiteurl": "https://www.maizegdb.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["MaizeGDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.aq280w"}
{"name": "Omics Discovery Index", "originalId": "2519", "websiteurl": "http://www.omicsdi.org/home", "collectedfrom": "FAIRsharing", "alternativeNames": ["OmicsDI"], "id": "https://fairsharing.org/10.25504/FAIRsharing.re1278"}
{"name": "Cell Centered Database", "originalId": "2020", "websiteurl": "http://ccdb.ucsd.edu/home", "collectedfrom": "FAIRsharing", "alternativeNames": ["CCDB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.t5ha5j"}
{"name": "World-2DPAGE Repository", "originalId": "2063", "websiteurl": "https://world-2dpage.expasy.org/repository/", "collectedfrom": "FAIRsharing", "alternativeNames": ["World-2DPAGE"], "id": "https://fairsharing.org/10.25504/FAIRsharing.we178a"}
{"name": "Microbial Genome Annotation & Analysis Platform", "originalId": "2390", "websiteurl": "http://www.genoscope.cns.fr/agc/microscope/home/", "collectedfrom": "FAIRsharing", "alternativeNames": ["MicroScope"], "id": "https://fairsharing.org/10.25504/FAIRsharing.3t5qc3"}
{"name": "China National GeneBank DataBase", "originalId": "2748", "websiteurl": "https://db.cngb.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CNGBdb"], "id": "https://fairsharing.org/10.25504/FAIRsharing.9btRvC"}
{"name": "The Triticeae Toolbox", "originalId": "2442", "websiteurl": "https://triticeaetoolbox.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["T3"], "id": "https://fairsharing.org/10.25504/FAIRsharing.55ev2y"}
{"name": "System for Earth Sample Registration Catalog", "originalId": "2447", "websiteurl": "http://www.geosamples.org", "collectedfrom": "FAIRsharing", "alternativeNames": ["SESAR Catalog"], "id": "https://fairsharing.org/10.25504/FAIRsharing.ys5ta3"}
{"name": "EMODnet Human Activities", "originalId": "2981", "websiteurl": "https://www.emodnet-humanactivities.eu/", "collectedfrom": "FAIRsharing", "alternativeNames": [null], "id": "https://fairsharing.org/10.25504/FAIRsharing.VErHgW"}
{"name": "Biodiversity Heritage Library", "originalId": "2886", "websiteurl": "https://biodiversitylibrary.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["BHL"], "id": "https://fairsharing.org/10.25504/FAIRsharing.yNNTvk"}
{"name": "Database of Interacting Proteins", "originalId": "2089", "websiteurl": "https://dip.doe-mbi.ucla.edu/dip/Main.cgi", "collectedfrom": "FAIRsharing", "alternativeNames": ["DIP"], "id": "https://fairsharing.org/10.25504/FAIRsharing.qje0v8"}
{"name": "UniProt Knowledgebase", "originalId": "2077", "websiteurl": "https://www.uniprot.org/uniprot/", "collectedfrom": "FAIRsharing", "alternativeNames": ["UniProtKB"], "id": "https://fairsharing.org/10.25504/FAIRsharing.s1ne3g"}
{"name": "Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource", "originalId": "1955", "websiteurl": "http://www.informatics.jax.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["MGI"], "id": "https://fairsharing.org/10.25504/FAIRsharing.fcwyhz"}
{"name": "GrainGenes, a Database for Triticeae and Avena", "originalId": "2351", "websiteurl": "https://wheat.pw.usda.gov/GG3/", "collectedfrom": "FAIRsharing", "alternativeNames": ["GrainGenes"], "id": "https://fairsharing.org/10.25504/FAIRsharing.pcs58g"}
{"name": "Termini-Oriented Protein Function INferred Database", "originalId": "1693", "websiteurl": "https://topfind.clip.msl.ubc.ca/", "collectedfrom": "FAIRsharing", "alternativeNames": ["TopFIND"], "id": "https://fairsharing.org/10.25504/FAIRsharing.rkpmhn"}
{"name": "Geothermal Data Repository", "originalId": "3580", "websiteurl": "https://gdr.openei.org/home", "collectedfrom": "FAIRsharing", "alternativeNames": ["GDR"], "id": "https://fairsharing.org/10.25504/FAIRsharing.c28bae"}
{"name": "CottonGen", "originalId": "2573", "websiteurl": "https://www.cottongen.org/", "collectedfrom": "FAIRsharing", "alternativeNames": ["CottonGen"], "id": "https://fairsharing.org/10.25504/FAIRsharing.2f668a"}

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@ -0,0 +1,34 @@
import requests
import json
url = "https://api.fairsharing.org/users/sign_in"
payload="{\"user\": {\"login\":\"andrea.mannocci@isti.cnr.it\",\"password\":\"sovietsoyouz\"} }"
headers = {
'Accept': 'application/json',
'Content-Type': 'application/json'
}
response = requests.request("POST", url, headers=headers, data=payload)
# print(response.text)
token = response.json()['jwt']
# print(jwt)
# Get the JWT from the response.text to use in the next part.
headers = {
'Accept': 'application/json',
'Content-Type': 'application/json',
'Authorization': 'Bearer ' + token,
}
print(headers)
with open('./fairsharing.json', 'w') as file_out:
for page in range(1, 5):
url = 'https://api.fairsharing.org/databases/?page[number]=%s&page[size]=500' % page
print(url)
response = requests.request("GET", url, headers=headers)
file_out.writelines('\n'.join([json.dumps(record) for record in response.json()['data']]))
file_out.write('\n')

@ -1,39 +0,0 @@
# -*- coding: utf-8 -*-
import csv
import os
import json
import click
import logging
from pathlib import Path
from dotenv import find_dotenv, load_dotenv
def get_value_or_none(obj, key):
if key in obj:
return obj[key]['value']
else:
return None
@click.command()
@click.argument('input_filepath', type=click.Path(exists=True))
@click.argument('output_filepath', type=click.Path())
def main(input_filepath, output_filepath):
""" Runs data processing scripts to turn raw data from (../raw) into
cleaned data ready to be analyzed (saved in ../processed).
"""
logger = logging.getLogger(__name__)
logger.info('making final data set from raw data')
if __name__ == '__main__':
log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
logging.basicConfig(level=logging.INFO, format=log_fmt)
# not used in this stub but often useful for finding various files
project_dir = Path(__file__).resolve().parents[2]
# find .env automagically by walking up directories until it's found, then
# load up the .env entries as environment variables
load_dotenv(find_dotenv())
main()

@ -0,0 +1,67 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "datasource",
"orderField" : "name",
"queueMaxSize" : "2000",
"groupMaxSize" : "50",
"slidingWindowSize" : "200",
"idPath":"$.id",
"rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ],
"includeChildren" : "true",
"maxIterations": "20"
},
"pace" : {
"clustering" : [
{ "name" : "sortedngrampairs", "fields" : [ "name" ], "params" : { "max" : 2, "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "name" ], "params" : { "max" : 1, "len" : "3" } },
{ "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } }
],
"decisionTree" : {
"start": {
"fields": [
{
"field": "websiteurl",
"comparator": "domainExactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1,
"aggregation": "AVG",
"positive": "layer2",
"negative": "NO_MATCH",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "name",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {
}
}
],
"threshold": 0.9,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{ "name" : "name", "type" : "String", "path" : "$.name" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl" }
],
"blacklists" : {
"legalname" : []
},
"synonyms": {}
}
}

@ -0,0 +1,76 @@
# coding=utf-8
from pyspark import SparkContext
from pyspark import SparkConf
from pyspark.sql import SparkSession
import json
#!/usr/bin/python
import os
import sys
import shutil
def deleteDir(x):
try:
shutil.rmtree(x)
except OSError as e:
print("Error: %s - %s." % (e.filename, e.strerror))
def stringToArray(x):
try:
return eval(x)
except:
return []
def testValidJSON(x):
try:
json.loads(x)
return True
except:
return False
conf = SparkConf().setAppName('fairshare').setMaster('local[*]')
sc = SparkContext(conf=conf)
spark = SparkSession.builder.config(conf=conf).getOrCreate()
deleteDir("datasources")
fairsharing_path = "../data/raw/fairsharing_dump_api_02_2022.json"
opendoar_path = "../data/raw/openDoar.tsv"
re3data_path = "../data/raw/re3data.tsv"
roar_path = "../data/raw/export_roar_CSV.csv"
# #FAIRSHARING V1.0
# #FILE STRUCTURE: Full name of record | Short name | FAIRsharing URL | Homepage URL of the resource | Country Field | Subjects
# fairsharing = sc.textFile("/Users/miconis/Desktop/Fairsharing dedup/registries_analysis/data/raw/FAIRsharingDBrec_summary20210304.csv")
# fairsharing = fairsharing.filter(lambda x: " FAIRsharing URL " not in x.split("|")).map(lambda x: dict(fullname=x.split("|")[0], shortname=x.split("|")[1], fairshare_url=x.split("|")[2], homepage_url=x.split("|")[3], country=x.split("|")[4], subjects=x.split("|")[5]))
# fairsharing = fairsharing.map(lambda x: dict(id=x['fairshare_url'], originalId=x['fairshare_url'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=[x['shortname']], collectedfrom="FAIRsharing"))
#
# print "FAIRSHARING:" + str(fairsharing.count())
#FAIRSHARING (file structure: )
fairsharing = sc.textFile(fairsharing_path).filter(testValidJSON).map(json.loads)
fairsharing = fairsharing.map(lambda x: dict(id=x['attributes']['url'], originalId=x['id'], websiteurl=x['attributes']['metadata']['homepage'], name=x['attributes']['metadata']['name'], alternativeNames=[x['attributes']['abbreviation']], collectedfrom="FAIRsharing"))
print("FAIRSHARING DS", fairsharing.count())
#OPENDOAR (file structure: OpenAIREID orgIdentifier repositoryName alternativeNames repositoryURL description type updateDate startDate subject contentType institution metadataPolicy dataPolicy submissionPolicy contentPolicy software api)
opendoar = sc.textFile(opendoar_path)
opendoar = opendoar.filter(lambda x: "system_metadata.id" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[1], alternativeNames=x.split("\t")[2], opendoar_id=x.split("\t")[0], homepage_url=x.split("\t")[3], subjects=x.split("\t")[9], openaire_id="opendoar::"+x.split("\t")[0]))
opendoar = opendoar.map(lambda x: dict(id=x['openaire_id'], originalId=x['opendoar_id'], websiteurl=x['homepage_url'], name=json.loads(x['fullname'])['name'], alternativeNames=x['alternativeNames'], collectedfrom="OpenDOAR"))
print("OPENDOAR DS", opendoar.count())
#RE3DATA (file structure: openaire_id re3data_id repository_name additional_name repository_url repository_id description type size update_date start_date end_date subject mission_statement content_type provider_type keyword institution policy database_access database_license data_access data_license data_upload data_upload_license software versioning api pid_system citation_guideline_url aid_system enhanced_publication quality_management certificate metadata_standard syndication remarks entry_date last_update)
re3data = sc.textFile(re3data_path)
re3data = re3data.filter(lambda x: "repositoryName.language" not in x.split("\t")).map(lambda x: dict(fullname=x.split("\t")[1], shortname=x.split("\t")[3], re3data_id=x.split("\t")[0], homepage_url=x.split("\t")[4], subjects=x.split("\t")[14], openaire_id="re3data::"+x.split("\t")[0]))
re3data = re3data.map(lambda x: dict(id=x['openaire_id'], originalId=x['re3data_id'], websiteurl=x['homepage_url'], name=x['fullname'], alternativeNames=stringToArray(x['shortname']), collectedfrom="re3data"))
print("RE3DATA", re3data.count())
#ROAR (file structure: "eprintid","rev_number","eprint_status","userid","importid","source","dir","datestamp","lastmod","status_changed","type","succeeds","commentary","metadata_visibility","latitude","longitude","relation_type","relation_uri","item_issues_id","item_issues_type","item_issues_description","item_issues_timestamp","item_issues_status","item_issues_reported_by","item_issues_resolved_by","item_issues_comment","item_issues_count","sword_depositor","sword_slug","exemplar","home_page","title","oai_pmh","sword_endpoint","rss_feed","twitter_feed","description","fulltext","open_access","mandate","organisation_title","organisation_home_page","location_country","location_city","location_latitude","location_longitude","software","geoname","version","subjects","date","note","suggestions","activity_low","activity_medium","activity_high","recordcount","recordhistory","fulltexts_total","fulltexts_docs","fulltexts_rtotal","fulltexts_rdocs","registry_name","registry_id","submit_to","submitted_to_name","submitted_to_done","webometrics_rank","webometrics_size","webometrics_visibility","webometrics_rich_files","webometrics_scholar","monthly_deposits","total_deposits","association")
roar = sc.textFile(roar_path)
roar = roar.filter(lambda x: "\"eprintid\"" not in x.split(",")).filter(lambda x: len(x.split(","))>31).map(lambda x: dict(id=x.split(",")[0], homepage_url=x.split(",")[30], title=x.split(",")[31])).filter(lambda x: x['title'] != "" and x['homepage_url'] != "")
roar = roar.map(lambda x: dict(id="roar::"+x['id'].replace("\"",""), originalId=x['id'].replace("\"",""), websiteurl=x['homepage_url'].replace("\"",""), name=x['title'].replace("\"", ""), alternativeNames=[], collectedfrom="roar"))
roar = roar.filter(lambda x: x['id'] != "" and x['name'] != "")
roar = roar.map(lambda x: (x['id'], x)).reduceByKey(lambda x, y: x).map(lambda x: x[1])
print "ROAR:" + str(roar.count())
all_ds = fairsharing.union(opendoar).union(re3data).union(roar)
all_ds.map(json.dumps).saveAsTextFile("datasources")

@ -0,0 +1,52 @@
# coding=utf-8
from pyspark import SparkContext
from pyspark import SparkConf
from pyspark.sql import SparkSession
import json
from datetime import datetime
def isRe3data(x):
for id in x:
if 're3data' in id:
return True
return False
def relToRe3data(x):
rel = []
re3data = ''
for id in x:
if 're3data' in id:
re3data = id
for id in x:
rel.append((re3data, id))
return rel
conf = SparkConf().setAppName('FAIRsharing').setMaster('local[*]')
sc = SparkContext(conf=conf)
spark = SparkSession.builder.config(conf=conf).getOrCreate()
datasources = sc.textFile("datasources").map(json.loads)
print("TOTAL DS", datasources.count())
print("ROAR", datasources.filter(lambda x: "roar" in x['collectedfrom']).count())
print("FAIRsharing", datasources.filter(lambda x: "FAIRsharing" in x['collectedfrom']).count())
print("OpenDOAR", datasources.filter(lambda x: "OpenDOAR" in x['collectedfrom']).count())
print("re3data", datasources.filter(lambda x: "re3data" in x['collectedfrom']).count())
mergerels = spark.read.load("mergerels").rdd
print("Number of mergerels", mergerels.count())
#TO RE3DATA
# mergerels = mergerels.map(lambda x: (x['source'], x['target'])).groupByKey().filter(lambda x: isRe3data(x[1])).flatMap(lambda x: relToRe3data(x[1])).map(lambda x: dict(source=x[0], target=x[1]))
joinRes = mergerels.map(lambda x: (x['target'], x['source'])).join(datasources.map(lambda x: (x['id'], x)))
joinRes = joinRes.map(lambda x: dict(dedup_id=x[1][0], duplicate_id=x[0], original_id=x[1][1]['originalId'], name=x[1][1]['name'].replace("\"",""), collectedfrom=x[1][1]['collectedfrom'])).sortBy(lambda x: x['dedup_id'])
#CREATE CSV FILE (file structure: dedup_id; duplicate_id; original_id; name; collectedfrom
csv_name = "ds_dedup_" + str(datetime.now()).split(".")[0].replace(" ", "_").replace(":", ".") + ".csv"
f = open(csv_name, "w")
f.write("dedup_id;duplicate_id;original_id;name;collectedfrom\n")
for row in joinRes.collect():
line = row['dedup_id'] + ";" + row['duplicate_id'] + ";" + row['original_id'] + ";\"" + row['name'] + "\";" + row['collectedfrom'] + "\n"
f.write(line.encode("utf-8"))
f.close()
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