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Merge pull request #1647 from HumanCellAtlas/iz-hotfix-linting
[hotfix] fix linting errors
2 parents 0025897 + b26ab71 commit f0e3626

8 files changed

Lines changed: 57 additions & 29 deletions

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‎.github/workflows/schema-tests.yml‎

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@@ -31,6 +31,8 @@ jobs:
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defaults:
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run:
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working-directory: tests
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env:
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SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- name: Use Node.js
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cache-dependency-path: tests/package-lock.json
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- run: npm ci
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- run: npm run build --if-present
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- run: npm test
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- run: npm test

‎changelog.md‎

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@@ -6,6 +6,28 @@ Starting after v5.0.0 release, updates will be declared for schemas independentl
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and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). Unreleased changes may be indicated under the `Unreleased` heading.
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## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
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## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
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### [module/biomaterial/residence.json - v1.0.4] - 2026-02-09
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### Fixed
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Fixed describedBy pattern and type keyword to country_territory
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### [module/biomaterial/medical_history.json - v9.1.4] - 2026-02-09
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### Added
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Added items keyword to diet_specific
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### [module/ontology/file_format_ontology.json - v2.0.0] - 2026-02-09
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### Fixed
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Fixed class from format:1915 to EDAM:1915
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### [module/biomaterial/human_specific.json - v1.6.4] - 2026-02-09
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### Fixed
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Fixed describedBy pattern and type keyword to country_territory
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### [type/biomaterial/donor_organism.json - v18.3.4] - 2026-02-09
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### Fixed
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Fixed describedBy pattern and type keyword to country_territory
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### [module/biomaterial/medical_history.json - v9.1.0] - 2026-02-03
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### Added
@@ -15,8 +37,6 @@ Added household_smoking_exposure, vaping_status and marijuana_inhaled_status
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### Added
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Added household_smoking_exposure, vaping_status and marijuana_inhaled_status
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## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
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### [module/biomaterial/medical_history.json - v9.0.0] - 2025-12-15
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### Deprecated
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Deprecated alcohol_history

‎docs/jsonBrowser/module.md‎

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@@ -244,7 +244,7 @@ Location: module/ontology/file_format_ontology.json
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Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
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--- | --- | --- | --- | --- | --- | --- | ---
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text | The name of the file format. | string | yes | | File format | | FASTQ; JSON
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ontology | An ontology term identifier in the form prefix:accession. | string | no | | File format ontology ID | | format:1930; format:3464
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ontology | An ontology term identifier in the form prefix:accession. | string | no | | File format ontology ID | | EDAM:1930; EDAM:3464
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ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | | File format ontology label | | FASTQ; JSON
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## Enrichment ontology<a name='Enrichment ontology'></a>
@@ -600,7 +600,7 @@ Location: module/biomaterial/residence.json
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Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
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--- | --- | --- | --- | --- | --- | --- | ---
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country_territory | Country or territory of donor's residence. | | no | | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria
603+
country_territory | Country or territory of donor's residence. | string | no | | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria
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region | Region of donor's residence. | string | no | | Region | | Massachusetts; Catalonia; Ondo; Ontario
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locality | Nearest city, town, or village to location of donor's residence. | string | no | | Locality | | Singapore; Cambridge; Boston; Kingston
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duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no | | Duration of residence | | 20; 37; 45-65

‎json_schema/module/biomaterial/medical_history.json‎

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"type": "array",
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"user_friendly": "Diet Specific",
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"example": "gluten_free; fodmap; baby_formula; breastfeeding; elimination; keto; paleo",
179-
"enum": [
180-
"vegan",
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"vegetarian",
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"omnivore",
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"gluten_free",
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"fodmap",
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"baby_formula",
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"breastfeeding",
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"elimination",
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"keto",
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"paleo"
190-
],
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"items": {
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"type": "string",
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"enum": [
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"vegan",
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"vegetarian",
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"omnivore",
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"gluten_free",
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"fodmap",
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"baby_formula",
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"breastfeeding",
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"elimination",
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"keto",
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"paleo"
192+
]
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},
191194
"bionetworks": ["gut"]
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}
193196
},

‎json_schema/module/biomaterial/residence.json‎

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"describedBy": {
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"description": "The URL reference to the schema.",
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"type": "string",
18-
"pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/human_specific"
18+
"pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/residence"
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},
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"schema_version": {
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"description": "The version number of the schema in major.minor.patch format.",
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2525
},
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"country_territory": {
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"description": "Country or territory of donor's residence.",
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"type": "string",
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"enum": [
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"Afghanistan",
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"Albania",

‎json_schema/module/ontology/file_format_ontology.json‎

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"type": "string",
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"graph_restriction": {
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"ontologies" : ["obo:edam"],
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"classes": ["format:1915"],
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"classes": ["EDAM:1915"],
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"relations": ["rdfs:subClassOf"],
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"direct": false,
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"include_self": false
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},
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"example": "format:1930; format:3464",
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"example": "EDAM:1930; EDAM:3464",
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"user_friendly": "File format ontology ID"
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},
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"ontology_label": {

‎json_schema/versions.json‎

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{
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"last_update_date": "2026-02-03T18:05:22Z",
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"last_update_date": "2026-02-09T12:55:32Z",
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"version_numbers": {
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"core": {
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"biomaterial": {
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"disease_profile": "1.1.0",
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"familial_relationship": "6.0.3",
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"growth_conditions": "6.4.2",
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"human_specific": "1.6.0",
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"medical_history": "9.1.0",
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"human_specific": "1.6.4",
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"medical_history": "9.1.4",
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"medical_tests": "1.0.0",
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"mouse_specific": "1.0.8",
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"preservation_storage": "6.1.1",
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"reproductive_history": "1.0.0",
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"residence": "1.0.0",
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"residence": "1.0.4",
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"state_of_specimen": "6.0.0",
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"timecourse": "2.0.2"
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},
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"enrichment_ontology": "1.2.6",
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"ethnicity_ontology": "5.3.9",
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"file_content_ontology": "2.0.0",
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"file_format_ontology": "1.0.0",
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"file_format_ontology": "2.0.0",
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"gender_identity_ontology": "1.0.0",
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"instrument_ontology": "5.3.6",
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"length_unit_ontology": "5.3.5",
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"biomaterial": {
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"cell_line": "16.0.0",
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"cell_suspension": "14.1.0",
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"donor_organism": "18.3.0",
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"donor_organism": "18.3.4",
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"imaged_specimen": "3.5.0",
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"organoid": "11.5.0",
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"specimen_from_organism": "11.1.0"

‎src/schema_linter.py‎

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# Property attributes
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property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'oneOf', 'bionetworks', 'minLength']
34+
property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'oneOf', 'anyOf', 'bionetworks', 'minLength']
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ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self']
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# Property must contain type attribute
143143
oneOf_types = [t['type'] for t in properties[property]['oneOf'] if 'type' in t.keys()] if \
144144
'oneOf' in properties[property].keys() else []
145-
if 'type' not in properties[property].keys() and not oneOf_types:
145+
anyOf_types = [t['type'] for t in properties[property]['anyOf'] if 'type' in t.keys()] if \
146+
'anyOf' in properties[property].keys() else []
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if 'type' not in properties[property].keys() and not oneOf_types and not anyOf_types:
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errors.append(schema_filename + ".json: Keyword `type` missing from property `" + property + "`.")
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else:
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if __name__ == "__main__":
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# As of November 2024, we are now using the OLS4 for ontology checkup
322-
ols_api = 'https://www.ebi.ac.uk/ols/api'
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ols_api = 'http://www.ebi.ac.uk/ols/api'
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schema_path = '../json_schema' if cwd == 'src' else 'json_schema'
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jsons = [os.path.join(dirpath, f)

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