Validating a dataset
The description below assumes that a user has provided a SAFE formatted dataset and an additional ZIP file containing additional files:
Example.xlsxSupplementary_files.zip
The validation process is then typically to use the
safedata_validate command line tool to
run the validation, as shown in the tab below. You can also use the safedata_validator
package from within Python to do this, but you would only typically do this if you were
building this functionality into another application.
#!/bin/sh
# The code below assumes that the safedata_validator tools find a configuration
# file in one of the standard locations. If not, the path can be specified
# explicitly using, the -r flag:
# -r /path/to/safedata_validator_local_test.cfg
# Validate the dataset. If successful this step will export a dataset metadata
# file called SAFE_dataset.json
safedata_validate SAFE_dataset.xlsx
"""Example script to validate a dataset using safedata_validator from within Python."""
import simplejson
from safedata_validator.field import Dataset
from safedata_validator.resources import Resources
# Local paths to the configuration file and the dataset to be validated
config_path = "config.cfg"
dataset = "SAFE_dataset.xlsx"
# Create a Resources object from the config file and then create a dataset instance
# using those validation resources
resources = Resources(config_path)
ds = Dataset(resources)
# Load the dataset from the Excel workbook, which validates the content
ds.load_from_workbook(dataset)
# Export the validated metadata to a file
with open("SAFE_dataset.json") as json_file:
simplejson.dump(ds.to_json(), json_file)
Running validation checks the contents of the data file against the required data format and generates a report on the validation process. This report details the checks being carried out, highlights any issues with the dataset and generates a final pass or fail verdict. The notes in the report for any warning and errors raised should help resolve the problems and datasets must not be published until they pass validation!
The report details from a successful validation can be seen below:
- Checking Summary worksheet
- Loading core metadata
- Metadata for Core fields found: 1 records
- Loading project id metadata
- Metadata for Project IDs found: 1 records
- Valid project ids provided: 1
- Loading access metadata
- Metadata for Access details found: 1 records
- Dataset access: embargoed until 2026-05-14 00:00:00
- Loading author metadata
- Metadata for Authors found: 1 records
- Loading keywords metadata
- Metadata for Keywords found: 2 records
- Loading DOI metadata
- Metadata for DOI found: 1 records
- Loading temporal extent metadata
- Metadata for Date Extents found: 1 records
- Loading geographic extent metadata
- Metadata for Geographic Extents found: 1 records
- Loading funding metadata
- Metadata for Funding Bodies found: 1 records
- Loading permit metadata
- Metadata for Permits found: 1 records
- Loading external file metadata
- Metadata for External Files found: 3 records
- Loading sequenced taxa metadata
- Metadata for Sequenced Taxa Sheets found: 2 records
- Data worksheet Sequenced found.
- Data worksheet MoreSeqData found.
- Loading data worksheet metadata
- Metadata for Worksheets found: 7 records
- Data worksheet abundances_1 found.
- Data worksheet abundances_2 found.
- Data worksheet interactions_1 found.
- Data worksheet interactions_2 found.
- Data worksheet interactions_3 found.
- Data worksheet external_1 found.
- Data worksheet external_2 found.
- Summary formatted correctly
- Loading Locations worksheet
- Checking known locations
- Checking new locations
- Validating lat / long data
- Validating WKT data
- 6 locations loaded correctly
- Loading GBIFTaxa worksheet
- Reading taxa data
- Additional fields provided: 'comments'
- Validating row 1: crbo
- Taxon found in GBIF backbone (accepted)
- Validating row 2: dolic_sp
- Taxon found in GBIF backbone (accepted)
- Validating row 3: gannets
- Taxon found in GBIF backbone (accepted)
- Validating row 4: lost_orang
- Parent taxon (Pongo) accepted
- Taxon in GBIF backbone (accepted) with compatible parent information
- Validating row 5: morpho1
- Parent taxon (Formicidae) accepted
- Taxon of type morphospecies has valid parent information
- Validating row 6: bombines
- Parent taxon (Apidae) accepted
- Taxon of type tribe has valid parent information
- Validating row 7: new_gannet
- Parent taxon (Morus) accepted
- Canon GBIF usage ignored
- Taxon with ignored canon usage has valid parent information.
- Validating row 8: Tiger leech
- Taxon found in GBIF backbone (accepted)
- Validating row 9: Brown leech
- Taxon found in GBIF backbone (accepted)
- Validating row 10: Clouded leopard
- Taxon found in GBIF backbone (accepted)
- Validating row 11: Flat headed cat
- Taxon found in GBIF backbone (accepted)
- Validating row 12: Brown rat
- Taxon found in GBIF backbone (accepted)
- Validating row 13: Moon rat
- Taxon found in GBIF backbone (accepted)
- Indexing taxonomic hierarchy
- Added kingdom Animalia
- Added phylum Annelida
- Added phylum Arthropoda
- Added phylum Chordata
- Added class Insecta
- Added class Mammalia
- Added class Clitellata
- Added class Aves
- Added order Arhynchobdellida
- Added order Carnivora
- Added order Rodentia
- Added order Erinaceomorpha
- Added order Primates
- Added order Hymenoptera
- Added order Suliformes
- Added family Muridae
- Added family Sulidae
- Added family Erinaceidae
- Added family Felidae
- Added family Hominidae
- Added family Haemadipsidae
- Added genus Prionailurus
- Added genus Rattus
- Added genus Echinosorex
- Added genus Neofelis
- Added genus Crematogaster
- Added genus Haemadipsa
- 13 taxa loaded correctly
- Loading sequenced taxonomy worksheet
- Reading bioinformatics taxon data from Sequenced
- Additional fields provided: 'comments'
- Loading row 1: ASV_100
- Loaded species: Saitozyma podzolica
- Loading row 2: ASV_101
- Loaded species: Trichoderma spirale
- Loading row 3: ASV_102
- Loaded species: Apiotrichum sporotrichoides
- Loading row 4: ASV_103
- Loaded genus: Trichoderma
- Loading row 5: ASV_104
- Loaded species: Mortierella elongata
- Loading row 6: ASV_105
- Loaded genus: Talaromyces
- Loading row 7: ASV_106
- Loaded species: Purpureocillium lilacinum
- Loading row 8: ASV_107
- Loaded species: Trichoderma harzianum
- Loading row 9: ASV_108
- Loaded species: Geoglossum difforme
- Loading row 10: ASV_109
- Loaded species: Trichoderma harzianum
- Loading row 11: ASV_110
- Loaded species: Pyrenochaetopsis leptospora
- Loading row 12: ASV_111
- Loaded species: Trichoderma koningiopsis
- Loading row 13: ASV_113
- Loaded species: Metarhizium carneum
- Loading row 14: ASV_114
- Loaded genus: Chloridium
- 14 taxa loaded correctly from Sequenced
- Loading sequenced taxonomy worksheet
- Reading bioinformatics taxon data from MoreSeqData
- Additional fields provided: 'comments'
- Loading row 1: TH_100
- Loaded species: Saitozyma podzolica
- Loading row 2: TH_101
- Loaded species: Trichoderma spirale
- Loading row 3: TH_102
- Loaded species: Apiotrichum sporotrichoides
- Loading row 4: TH_103
- Loaded genus: Trichoderma
- Loading row 5: TH_104
- Loaded species: Mortierella elongata
- Loading row 6: TH_105
- Loaded genus: Talaromyces
- Loading row 7: TH_106
- Loaded species: Purpureocillium lilacinum
- Loading row 8: TH_107
- Loaded species: Trichoderma harzianum
- Loading row 9: TH_108
- Loaded species: Geoglossum difforme
- Loading row 10: TH_109
- Loaded species: Trichoderma harzianum
- Loading row 11: TH_110
- Loaded species: Pyrenochaetopsis leptospora
- Loading row 12: TH_111
- Loaded species: Trichoderma koningiopsis
- Loading row 13: TH_113
- Loaded species: Metarhizium carneum
- Loading row 14: TH_114
- Loaded genus: Chloridium
- 14 taxa loaded correctly from MoreSeqData
- Checking worksheet 'abundances_1'
- Validating field metadata
- Validating field data
- Checking field tiger_count
- Checking field brown_count
- Worksheet 'abundances_1' contains 6 descriptors, 2 data rows and 2 fields
- Dataframe formatted correctly
- Checking worksheet 'abundances_2'
- Validating field metadata
- Validating field data
- Checking field common_name
- Checking field leech_count
- Worksheet 'abundances_2' contains 6 descriptors, 4 data rows and 2 fields
- Dataframe formatted correctly
- Checking worksheet 'interactions_1'
- Validating field metadata
- Validating field data
- Checking field predator
- Checking field prey
- Checking field outcome
? Label descriptions for interacting taxa incomplete or missing
- Worksheet 'interactions_1' contains 6 descriptors, 2 data rows and 3 fields
- Dataframe formatted correctly
- Checking worksheet 'interactions_2'
- Validating field metadata
- Validating field data
- Checking field outcome
- Worksheet 'interactions_2' contains 6 descriptors, 2 data rows and 1 fields
- Dataframe formatted correctly
- Checking worksheet 'interactions_3'
- Validating field metadata
- Validating field data
- Checking field prey
- Checking field outcome
- Worksheet 'interactions_3' contains 7 descriptors, 2 data rows and 2 fields
- Dataframe formatted correctly
- Checking worksheet 'external_1'
- Validating field metadata
- Validating field data
- Checking field Altitude
- Checking field DEM
- Worksheet 'external_1' contains 6 descriptors, 8 data rows and 2 fields
- Dataframe formatted correctly
- Checking worksheet 'external_2'
- Validating field metadata
- Validating field data
- Checking field Altitude
- Checking field Bait_trap_image
- Worksheet 'external_2' contains 7 descriptors, 8 data rows and 2 fields
- Dataframe formatted correctly
- Running final checking
- Checking provided locations and taxa all used in data worksheets
? Location list cannot be validated when external data files are used
? Taxon list cannot be validated when external data files are used
- Checking temporal and geographic extents
? The Latitudinal extent is set in Summary but also is populated from the data - this may be deliberate!
? The Longitudinal extent is set in Summary but also is populated from the data - this may be deliberate!
- PASS: file formatted correctly but with 5 warnings
Successful validation will also generate a JSON file containing the detailed metadata for the dataset. This file is used to provide information for the publication process and also the detailed metadata to be uploaded to the metadata server. This file is very long and is not really intended to be read, but the contents can be shown below.
JSON metadata contents
{
"project_ids": [
1
],
"title": "Example data for the safedata system",
"description": "This is an example dataset",
"authors": [
{
"name": "Orme, David",
"affiliation": "Imperial College London",
"email": "d.orme@imperial.ac.uk",
"orcid": "0000-0002-7005-1394"
}
],
"filename": "Example.xlsx",
"external_files": [
{
"file": "bait_trap_images.zip",
"description": "Zip file containing 5000 JPEG images of bait trap cards"
},
{
"file": "My_raster_1.tiff",
"description": "A second raster file containing altitudes"
},
{
"file": "My_raster_2.tiff",
"description": "A raster file containing altitudes"
}
],
"access": "Embargo",
"embargo_date": "2026-05-14",
"access_conditions": null,
"funders": [
{
"body": "NERC",
"type": "Standard grant",
"ref": "NE/K006339/1",
"url": "https://gtr.ukri.org/projects?ref=NE%2FK006339%2F1"
}
],
"permits": [
{
"type": "Research",
"authority": "Sabah Biodiversity Centre",
"number": "ABC-123-456"
}
],
"keywords": [
"Keyword 1",
"Keyword 2"
],
"dataworksheets": [
{
"taxa_fields": [],
"max_row": 8,
"max_col": 2,
"name": "abundances_1",
"title": "Abundances example 1",
"description": "Example worksheet showing the first method for recording species abundances",
"descriptors": [
"field_type",
"taxon_name",
"method",
"description",
"units",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "tiger_count",
"description": "quadrat count",
"field_type": "abundance",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "brown_count",
"description": "quadrat count",
"field_type": "abundance",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
}
],
"field_name_row": 6,
"n_data_row": 2
},
{
"taxa_fields": [
"common_name"
],
"max_row": 10,
"max_col": 2,
"name": "abundances_2",
"title": "Abundances example 2",
"description": "Example worksheet showing the second method for recording species abundances",
"descriptors": [
"field_type",
"taxon_field",
"method",
"description",
"units",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "common_name",
"description": "Species found",
"field_type": "taxa",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "leech_count",
"description": "Number found",
"field_type": "abundance",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
}
],
"field_name_row": 6,
"n_data_row": 4
},
{
"taxa_fields": [
"predator",
"prey"
],
"max_row": 8,
"max_col": 3,
"name": "interactions_1",
"title": "Interactions example 1",
"description": "Example worksheet showing the first method for recording species interactions",
"descriptors": [
"field_type",
"interaction_field",
"levels",
"method",
"description",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "predator",
"description": "Predator observed",
"field_type": "taxa",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "prey",
"description": "Prey observed",
"field_type": "taxa",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
},
{
"field_name": "outcome",
"description": "Outcome of predation event",
"field_type": "categorical interaction",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 3
}
],
"field_name_row": 6,
"n_data_row": 2
},
{
"taxa_fields": [],
"max_row": 8,
"max_col": 1,
"name": "interactions_2",
"title": "Interactions example 2",
"description": "Example worksheet showing the second method for recording species interactions",
"descriptors": [
"field_type",
"interaction_name",
"levels",
"method",
"description",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "outcome",
"description": "Outcome of predation event",
"field_type": "categorical interaction",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
}
],
"field_name_row": 6,
"n_data_row": 2
},
{
"taxa_fields": [
"prey"
],
"max_row": 9,
"max_col": 2,
"name": "interactions_3",
"title": "Interactions example 3",
"description": "Example worksheet showing the third method for recording species interactions",
"descriptors": [
"field_type",
"interaction_name",
"interaction_field",
"levels",
"method",
"description",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "prey",
"description": "Prey observed",
"field_type": "taxa",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "outcome",
"description": "Outcome of predation event",
"field_type": "categorical interaction",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
}
],
"field_name_row": 7,
"n_data_row": 2
},
{
"taxa_fields": [],
"max_row": 14,
"max_col": 2,
"name": "external_1",
"title": "External file example 1",
"description": "Example worksheet showing the second method for including information from external files",
"descriptors": [
"field_type",
"description",
"method",
"taxon_name",
"units",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "Altitude",
"description": "Altitude in metres",
"field_type": "numeric",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "DEM",
"description": "DEM file used for altitude",
"field_type": "file",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
}
],
"field_name_row": 6,
"n_data_row": 8
},
{
"taxa_fields": [],
"max_row": 15,
"max_col": 2,
"name": "external_2",
"title": "External file example 2",
"description": "Example worksheet showing the first method for including information from external files",
"descriptors": [
"field_type",
"description",
"method",
"taxon_name",
"units",
"file_container",
"field_name"
],
"external": null,
"fields": [
{
"field_name": "Altitude",
"description": "Altitude in metres",
"field_type": "numeric",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 1
},
{
"field_name": "Bait_trap_image",
"description": "Image of bait trap card",
"field_type": "file",
"units": null,
"method": null,
"levels": null,
"taxon_field": null,
"taxon_name": null,
"interaction_field": null,
"interaction_name": null,
"range": null,
"col_idx": 2
}
],
"field_name_row": 7,
"n_data_row": 8
}
],
"gbif_timestamp": "2023-08-28",
"gbif_taxa": [
{
"worksheet_name": "crbo",
"taxon_id": 1324716,
"parent_id": 1324306,
"taxon_name": "Crematogaster borneensis",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "dolic_sp",
"taxon_id": 1314182,
"parent_id": 4342,
"taxon_name": "Dolichoderus",
"taxon_rank": "genus",
"taxon_status": "accepted"
},
{
"worksheet_name": "gannets",
"taxon_id": 2480962,
"parent_id": 9351,
"taxon_name": "Morus",
"taxon_rank": "genus",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 5219531,
"parent_id": 5483,
"taxon_name": "Pongo",
"taxon_rank": "genus",
"taxon_status": "accepted"
},
{
"worksheet_name": "lost_orang",
"taxon_id": 9311132,
"parent_id": 5219531,
"taxon_name": "Pongo tapanuliensis",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 4342,
"parent_id": 1457,
"taxon_name": "Formicidae",
"taxon_rank": "family",
"taxon_status": "accepted"
},
{
"worksheet_name": "morpho1",
"taxon_id": -1,
"parent_id": 4342,
"taxon_name": "NA",
"taxon_rank": "morphospecies",
"taxon_status": "user"
},
{
"worksheet_name": null,
"taxon_id": 4334,
"parent_id": 1457,
"taxon_name": "Apidae",
"taxon_rank": "family",
"taxon_status": "accepted"
},
{
"worksheet_name": "bombines",
"taxon_id": -1,
"parent_id": 4334,
"taxon_name": "Bombini",
"taxon_rank": "tribe",
"taxon_status": "user"
},
{
"worksheet_name": null,
"taxon_id": 2480962,
"parent_id": 9351,
"taxon_name": "Morus",
"taxon_rank": "genus",
"taxon_status": "accepted"
},
{
"worksheet_name": "new_gannet",
"taxon_id": -1,
"parent_id": 2480962,
"taxon_name": "Morus rubra",
"taxon_rank": "species",
"taxon_status": "user"
},
{
"worksheet_name": "Tiger leech",
"taxon_id": 9065333,
"parent_id": 4810276,
"taxon_name": "Haemadipsa picta",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "Brown leech",
"taxon_id": 8997397,
"parent_id": 4810276,
"taxon_name": "Haemadipsa zeylanica",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "Clouded leopard",
"taxon_id": 2435079,
"parent_id": 2435078,
"taxon_name": "Neofelis nebulosa",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "Flat headed cat",
"taxon_id": 2434917,
"parent_id": 2434894,
"taxon_name": "Prionailurus planiceps",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "Brown rat",
"taxon_id": 2439261,
"parent_id": 2439223,
"taxon_name": "Rattus norvegicus",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": "Moon rat",
"taxon_id": 2437114,
"parent_id": 2437113,
"taxon_name": "Echinosorex gymnura",
"taxon_rank": "species",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 1,
"parent_id": null,
"taxon_name": "Animalia",
"taxon_rank": "kingdom",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 42,
"parent_id": 1,
"taxon_name": "Annelida",
"taxon_rank": "phylum",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 54,
"parent_id": 1,
"taxon_name": "Arthropoda",
"taxon_rank": "phylum",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 44,
"parent_id": 1,
"taxon_name": "Chordata",
"taxon_rank": "phylum",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 216,
"parent_id": 54,
"taxon_name": "Insecta",
"taxon_rank": "class",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 359,
"parent_id": 44,
"taxon_name": "Mammalia",
"taxon_rank": "class",
"taxon_status": "accepted"
},
{
"worksheet_name": null,
"taxon_id": 255,
"parent_id": 42,
"taxon_name": "Clitellata",
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],
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}