New LinkML validation error categorization

.duct/logs/2024.10.21T18.49.51-44317_info.json

@@ -0,0 +1 @@
+{"command": "dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO", "system": {"cpu_total": 8, "memory_total": 17179869184, "hostname": "needle.lan", "uid": 502, "user": "isaac"}, "env": {}, "gpu": null, "duct_version": "0.6.0", "schema_version": "0.1.1", "execution_summary": {"exit_code": 0, "command": "dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO", "logs_prefix": ".duct/logs/2024.10.21T18.49.51-44317_", "wall_clock_time": 300.8351628780365, "peak_rss": null, "average_rss": null, "peak_vsz": null, "average_vsz": null, "peak_pmem": null, "average_pmem": null, "peak_pcpu": null, "average_pcpu": null, "num_samples": 0, "num_reports": 1}, "output_paths": {"stdout": ".duct/logs/2024.10.21T18.49.51-44317_stdout", "stderr": ".duct/logs/2024.10.21T18.49.51-44317_stderr", "usage": ".duct/logs/2024.10.21T18.49.51-44317_usage.json", "info": ".duct/logs/2024.10.21T18.49.51-44317_info.json", "prefix": ".duct/logs/2024.10.21T18.49.51-44317_"}}

dandi-reports/000003/0.230629.1955/linkml_validation_errs.json

@@ -5,70 +5,199 @@
     "message": "Additional properties are not allowed ('@context', 'datePublished', 'doi', 'publishedBy' were unexpected) in /",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "Additional properties are not allowed ('@context', 'datePublished', 'doi', 'publishedBy' were unexpected)",
+      "absolute_path": [],
+      "absolute_schema_path": [
+        "additionalProperties"
+      ],
+      "validator": "additionalProperties",
+      "validator_value": false
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'name': 'hippocampus', 'schemaKey': 'Anatomy', 'identifier': 'UBERON:0002421'} is not of type 'string' in /about/0",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'name': 'hippocampus', 'schemaKey': 'Anatomy', 'identifier': 'UBERON:0002421'} is not of type 'string'",
+      "absolute_path": [
+        "about",
+        0
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "about",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'name': 'Senzai, Yuta', 'roleName': ['dcite:Author', 'dcite:ContactPerson', 'dcite:DataCollector', 'dcite:FormalAnalysis'], 'schemaKey': 'Person', 'affiliation': [], 'includeInCitation': True} is not of type 'string' in /contributor/0",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'name': 'Senzai, Yuta', 'roleName': ['dcite:Author', 'dcite:ContactPerson', 'dcite:DataCollector', 'dcite:FormalAnalysis'], 'schemaKey': 'Person', 'affiliation': [], 'includeInCitation': True} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        0
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'name': 'Fernandez-Ruiz, Antonio', 'roleName': ['dcite:Author', 'dcite:FormalAnalysis'], 'schemaKey': 'Person', 'identifier': '0000-0001-8481-0796', 'affiliation': [], 'includeInCitation': True} is not of type 'string' in /contributor/1",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'name': 'Fernandez-Ruiz, Antonio', 'roleName': ['dcite:Author', 'dcite:FormalAnalysis'], 'schemaKey': 'Person', 'identifier': '0000-0001-8481-0796', 'affiliation': [], 'includeInCitation': True} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        1
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'name': 'Buzs\u00e1ki, Gy\u00f6rgy', 'roleName': ['dcite:Author'], 'schemaKey': 'Person', 'identifier': '0000-0002-3100-4800', 'affiliation': [{'name': 'New York University Langone Medical Center', 'schemaKey': 'Affiliation', 'identifier': 'https://ror.org/005dvqh91'}], 'includeInCitation': True} is not of type 'string' in /contributor/2",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'name': 'Buzs\u00e1ki, Gy\u00f6rgy', 'roleName': ['dcite:Author'], 'schemaKey': 'Person', 'identifier': '0000-0002-3100-4800', 'affiliation': [{'name': 'New York University Langone Medical Center', 'schemaKey': 'Affiliation', 'identifier': 'https://ror.org/005dvqh91'}], 'includeInCitation': True} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        2
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'url': 'https://www.nih.gov/', 'name': 'National Institutes of Health', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/01cwqze88', 'awardNumber': 'NIHMH54671, MH107396, NS090583', 'contactPoint': [], 'includeInCitation': False} is not of type 'string' in /contributor/3",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'url': 'https://www.nih.gov/', 'name': 'National Institutes of Health', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/01cwqze88', 'awardNumber': 'NIHMH54671, MH107396, NS090583', 'contactPoint': [], 'includeInCitation': False} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        3
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'url': 'http://hnf.jp/', 'name': 'Nakajima Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/000k40t10', 'contactPoint': [], 'includeInCitation': False} is not of type 'string' in /contributor/4",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'url': 'http://hnf.jp/', 'name': 'Nakajima Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/000k40t10', 'contactPoint': [], 'includeInCitation': False} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        4
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'url': 'http://www.nsf.gov/', 'name': 'National Science Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/021nxhr62', 'awardNumber': 'PIRE', 'contactPoint': [], 'includeInCitation': False} is not of type 'string' in /contributor/5",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'url': 'http://www.nsf.gov/', 'name': 'National Science Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/021nxhr62', 'awardNumber': 'PIRE', 'contactPoint': [], 'includeInCitation': False} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        5
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   },
   {
     "type": "jsonschema validation",
     "severity": "ERROR",
     "message": "{'url': 'https://www.simonsfoundation.org', 'name': 'Simons Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/01cmst727', 'contactPoint': [], 'includeInCitation': False} is not of type 'string' in /contributor/6",
     "instance_index": 0,
     "instantiates": "Dandiset",
-    "context": []
+    "context": [],
+    "source": {
+      "message": "{'url': 'https://www.simonsfoundation.org', 'name': 'Simons Foundation', 'roleName': ['dcite:Funder'], 'schemaKey': 'Organization', 'identifier': 'https://ror.org/01cmst727', 'contactPoint': [], 'includeInCitation': False} is not of type 'string'",
+      "absolute_path": [
+        "contributor",
+        6
+      ],
+      "absolute_schema_path": [
+        "properties",
+        "contributor",
+        "items",
+        "type"
+      ],
+      "validator": "type",
+      "validator_value": "string"
+    }
   }
 ]

dandi-reports/000003/0.230629.1955/linkml_validation_errs.yaml

@@ -4,13 +4,34 @@
   message: Additional properties are not allowed ('@context', 'datePublished', 'doi',
     'publishedBy' were unexpected) in /
   severity: ERROR
+  source:
+    absolute_path: []
+    absolute_schema_path:
+    - additionalProperties
+    message: Additional properties are not allowed ('@context', 'datePublished', 'doi',
+      'publishedBy' were unexpected)
+    validator: additionalProperties
+    validator_value: false
   type: jsonschema validation
 - context: []
   instance_index: 0
   instantiates: Dandiset
   message: '{''name'': ''hippocampus'', ''schemaKey'': ''Anatomy'', ''identifier'':
     ''UBERON:0002421''} is not of type ''string'' in /about/0'
   severity: ERROR
+  source:
+    absolute_path:
+    - about
+    - 0
+    absolute_schema_path:
+    - properties
+    - about
+    - items
+    - type
+    message: '{''name'': ''hippocampus'', ''schemaKey'': ''Anatomy'', ''identifier'':
+      ''UBERON:0002421''} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -20,6 +41,20 @@
     ''affiliation'': [], ''includeInCitation'': True} is not of type ''string'' in
     /contributor/0'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 0
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''name'': ''Senzai, Yuta'', ''roleName'': [''dcite:Author'', ''dcite:ContactPerson'',
+      ''dcite:DataCollector'', ''dcite:FormalAnalysis''], ''schemaKey'': ''Person'',
+      ''affiliation'': [], ''includeInCitation'': True} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -29,6 +64,20 @@
     ''affiliation'': [], ''includeInCitation'': True} is not of type ''string'' in
     /contributor/1'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 1
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''name'': ''Fernandez-Ruiz, Antonio'', ''roleName'': [''dcite:Author'',
+      ''dcite:FormalAnalysis''], ''schemaKey'': ''Person'', ''identifier'': ''0000-0001-8481-0796'',
+      ''affiliation'': [], ''includeInCitation'': True} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -39,6 +88,21 @@
     'https://ror.org/005dvqh91'}], 'includeInCitation': True} is not of type 'string'
     in /contributor/2"
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 2
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: "{'name': 'Buzs\xE1ki, Gy\xF6rgy', 'roleName': ['dcite:Author'], 'schemaKey':
+      'Person', 'identifier': '0000-0002-3100-4800', 'affiliation': [{'name': 'New
+      York University Langone Medical Center', 'schemaKey': 'Affiliation', 'identifier':
+      'https://ror.org/005dvqh91'}], 'includeInCitation': True} is not of type 'string'"
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -49,6 +113,22 @@
     ''contactPoint'': [], ''includeInCitation'': False} is not of type ''string''
     in /contributor/3'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 3
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''url'': ''https://www.nih.gov/'', ''name'': ''National Institutes
+      of Health'', ''roleName'': [''dcite:Funder''], ''schemaKey'': ''Organization'',
+      ''identifier'': ''https://ror.org/01cwqze88'', ''awardNumber'': ''NIHMH54671,
+      MH107396, NS090583'', ''contactPoint'': [], ''includeInCitation'': False} is
+      not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -58,6 +138,20 @@
     ''contactPoint'': [], ''includeInCitation'': False} is not of type ''string''
     in /contributor/4'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 4
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''url'': ''http://hnf.jp/'', ''name'': ''Nakajima Foundation'', ''roleName'':
+      [''dcite:Funder''], ''schemaKey'': ''Organization'', ''identifier'': ''https://ror.org/000k40t10'',
+      ''contactPoint'': [], ''includeInCitation'': False} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -67,6 +161,21 @@
     ''https://ror.org/021nxhr62'', ''awardNumber'': ''PIRE'', ''contactPoint'': [],
     ''includeInCitation'': False} is not of type ''string'' in /contributor/5'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 5
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''url'': ''http://www.nsf.gov/'', ''name'': ''National Science Foundation'',
+      ''roleName'': [''dcite:Funder''], ''schemaKey'': ''Organization'', ''identifier'':
+      ''https://ror.org/021nxhr62'', ''awardNumber'': ''PIRE'', ''contactPoint'':
+      [], ''includeInCitation'': False} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation
 - context: []
   instance_index: 0
@@ -76,4 +185,19 @@
     ''https://ror.org/01cmst727'', ''contactPoint'': [], ''includeInCitation'': False}
     is not of type ''string'' in /contributor/6'
   severity: ERROR
+  source:
+    absolute_path:
+    - contributor
+    - 6
+    absolute_schema_path:
+    - properties
+    - contributor
+    - items
+    - type
+    message: '{''url'': ''https://www.simonsfoundation.org'', ''name'': ''Simons Foundation'',
+      ''roleName'': [''dcite:Funder''], ''schemaKey'': ''Organization'', ''identifier'':
+      ''https://ror.org/01cmst727'', ''contactPoint'': [], ''includeInCitation'':
+      False} is not of type ''string'''
+    validator: type
+    validator_value: string
   type: jsonschema validation