[DATALAD RUNCMD] Get latest validation reports with a summary

=== Do not change lines below === { "chain": [], "cmd": "duct dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^
dandi · Nov 5, 2024 · 72f0b63 · 72f0b63
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diff --git a/.duct/logs/2024.11.05T06.55.00-3536_info.json b/.duct/logs/2024.11.05T06.55.00-3536_info.json
@@ -0,0 +1 @@
+{"command": "dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO", "system": {"cpu_total": 4, "memory_total": 16757338112, "hostname": "fv-az529-595", "uid": 1001, "user": "runner"}, "env": {}, "gpu": null, "duct_version": "0.8.0", "schema_version": "0.2.0", "execution_summary": {"exit_code": 0, "command": "dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO", "logs_prefix": ".duct/logs/2024.11.05T06.55.00-3536_", "wall_clock_time": 262.1662666797638, "peak_rss": 2872619008, "average_rss": 1578682809.1076922, "peak_vsz": 3316166656, "average_vsz": 1922218157.2923074, "peak_pmem": 17.1, "average_pmem": 9.372307692307691, "peak_pcpu": 81.8, "average_pcpu": 75.4203846153846, "num_samples": 260, "num_reports": 6, "start_time": 1730789700.8055909, "end_time": 1730789962.9718575}, "output_paths": {"stdout": ".duct/logs/2024.11.05T06.55.00-3536_stdout", "stderr": ".duct/logs/2024.11.05T06.55.00-3536_stderr", "usage": ".duct/logs/2024.11.05T06.55.00-3536_usage.json", "info": ".duct/logs/2024.11.05T06.55.00-3536_info.json", "prefix": ".duct/logs/2024.11.05T06.55.00-3536_"}}
diff --git a/.duct/logs/2024.11.05T06.55.00-3536_stderr b/.duct/logs/2024.11.05T06.55.00-3536_stderr
diff --git a/.duct/logs/2024.11.05T06.55.00-3536_stdout b/.duct/logs/2024.11.05T06.55.00-3536_stdout
diff --git a/.duct/logs/2024.11.05T06.55.00-3536_usage.json b/.duct/logs/2024.11.05T06.55.00-3536_usage.json
@@ -0,0 +1,6 @@
+{"timestamp": "2024-11-05T06:55:00.815690+00:00", "num_samples": 1, "processes": {"3539": {"pcpu": 0.0, "pmem": 0.0, "rss": 9306112, "vsz": 17244160, "timestamp": "2024-11-05T06:55:00.815690+00:00", "etime": "00:00", "stat": {"Rs": 1}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 0.0, "pcpu": 0.0, "rss": 9306112, "vsz": 17244160}, "averages": {"rss": 9306112, "vsz": 17244160, "pmem": 0.0, "pcpu": 0.0, "num_samples": 1}}
+{"timestamp": "2024-11-05T06:56:01.323426+00:00", "num_samples": 60, "processes": {"3539": {"pcpu": 75.0, "pmem": 4.6, "rss": 773009408, "vsz": 1203712000, "timestamp": "2024-11-05T06:56:01.323426+00:00", "etime": "01:01", "stat": {"Ds": 1, "Ss": 14, "Rs": 39, "Ssl": 1, "Rsl": 5}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 4.6, "pcpu": 75.0, "rss": 773009408, "vsz": 1203712000}, "averages": {"rss": 420458154.6666666, "vsz": 474169685.3333333, "pmem": 2.4583333333333326, "pcpu": 63.17833333333333, "num_samples": 60}}
+{"timestamp": "2024-11-05T06:57:00.826621+00:00", "num_samples": 59, "processes": {"3539": {"pcpu": 79.1, "pmem": 8.7, "rss": 1463910400, "vsz": 1898254336, "timestamp": "2024-11-05T06:57:00.826621+00:00", "etime": "02:00", "stat": {"Rsl": 53, "Ssl": 5, "Dsl": 1}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 8.7, "pcpu": 79.1, "rss": 1463910400, "vsz": 1898254336}, "averages": {"rss": 1125802053.4237285, "vsz": 1557672769.0847454, "pmem": 6.667796610169488, "pcpu": 77.03220338983051, "num_samples": 59}}
+{"timestamp": "2024-11-05T06:58:01.335509+00:00", "num_samples": 60, "processes": {"3539": {"pcpu": 80.9, "pmem": 13.0, "rss": 2180268032, "vsz": 2619256832, "timestamp": "2024-11-05T06:58:01.335509+00:00", "etime": "03:01", "stat": {"Ssl": 12, "Rsl": 48}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 13.0, "pcpu": 80.9, "rss": 2180268032, "vsz": 2619256832}, "averages": {"rss": 1824007236.2666664, "vsz": 2260772249.6000004, "pmem": 10.838333333333336, "pcpu": 80.14666666666666, "num_samples": 60}}
+{"timestamp": "2024-11-05T06:59:00.865087+00:00", "num_samples": 59, "processes": {"3539": {"pcpu": 81.5, "pmem": 17.0, "rss": 2861477888, "vsz": 3304890368, "timestamp": "2024-11-05T06:59:00.865087+00:00", "etime": "04:00", "stat": {"Rsl": 47, "Ssl": 11, "Dsl": 1}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 17.0, "pcpu": 81.5, "rss": 2861477888, "vsz": 3304890368}, "averages": {"rss": 2526893073.355932, "vsz": 2968526223.186441, "pmem": 15.027118644067796, "pcpu": 80.72033898305087, "num_samples": 59}}
+{"timestamp": "2024-11-05T06:59:22.044296+00:00", "num_samples": 21, "processes": {"3539": {"pcpu": 81.8, "pmem": 17.1, "rss": 2872619008, "vsz": 3316166656, "timestamp": "2024-11-05T06:59:22.044296+00:00", "etime": "04:21", "stat": {"Rsl": 1, "Rs": 20}, "cmd": "/opt/hostedtoolcache/Python/3.12.7/x64/bin/python /opt/hostedtoolcache/Python/3.12.7/x64/bin/dandisets-linkml-status --include-unpublished --dandi-instance dandi -l INFO"}}, "totals": {"pmem": 17.1, "pcpu": 81.8, "rss": 2872619008, "vsz": 3316166656}, "averages": {"rss": 2870061348.5714283, "vsz": 3267486671.2380958, "pmem": 17.095238095238095, "pcpu": 81.06666666666666, "num_samples": 21}}
diff --git a/dandi-reports/001248/draft/metadata.json b/dandi-reports/001248/draft/metadata.json
@@ -31,9 +31,46 @@
   "dateCreated": "2024-11-03T19:10:38.048315+00:00",
   "description": "This Dandiset provides examples to drive standardization efforts throughout neurophysiology.",
   "assetsSummary": {
+    "species": [
+      {
+        "name": "Mus musculus - House mouse",
+        "schemaKey": "SpeciesType",
+        "identifier": "http://purl.obolibrary.org/obo/NCBITaxon_10090"
+      }
+    ],
+    "approach": [
+      {
+        "name": "microscopy approach; cell population imaging",
+        "schemaKey": "ApproachType"
+      }
+    ],
     "schemaKey": "AssetsSummary",
-    "numberOfBytes": 0,
-    "numberOfFiles": 0
+    "dataStandard": [
+      {
+        "name": "Neurodata Without Borders (NWB)",
+        "schemaKey": "StandardsType",
+        "identifier": "RRID:SCR_015242"
+      }
+    ],
+    "numberOfBytes": 4655345,
+    "numberOfFiles": 1,
+    "numberOfSubjects": 2,
+    "variableMeasured": [
+      "ProcessingModule",
+      "PlaneSegmentation",
+      "OpticalChannel",
+      "ImagingPlane"
+    ],
+    "measurementTechnique": [
+      {
+        "name": "surgical technique",
+        "schemaKey": "MeasurementTechniqueType"
+      },
+      {
+        "name": "analytical technique",
+        "schemaKey": "MeasurementTechniqueType"
+      }
+    ]
   },
   "schemaVersion": "0.6.8",
   "manifestLocation": [

diff --git a/dandi-reports/001248/draft/metadata.yaml b/dandi-reports/001248/draft/metadata.yaml
@@ -2,9 +2,31 @@ access:
 - schemaKey: AccessRequirements
   status: dandi:OpenAccess
 assetsSummary:
-  numberOfBytes: 0
-  numberOfFiles: 0
+  approach:
+  - name: microscopy approach; cell population imaging
+    schemaKey: ApproachType
+  dataStandard:
+  - identifier: RRID:SCR_015242
+    name: Neurodata Without Borders (NWB)
+    schemaKey: StandardsType
+  measurementTechnique:
+  - name: surgical technique
+    schemaKey: MeasurementTechniqueType
+  - name: analytical technique
+    schemaKey: MeasurementTechniqueType
+  numberOfBytes: 4655345
+  numberOfFiles: 1
+  numberOfSubjects: 2
   schemaKey: AssetsSummary
+  species:
+  - identifier: http://purl.obolibrary.org/obo/NCBITaxon_10090
+    name: Mus musculus - House mouse
+    schemaKey: SpeciesType
+  variableMeasured:
+  - ProcessingModule
+  - PlaneSegmentation
+  - OpticalChannel
+  - ImagingPlane
 citation: Reimer, Marike (2024) Standardized Neuromorphology Prototypes (Version draft)
   [Data set]. DANDI archive. https://dandiarchive.org/dandiset/001248/draft
 contributor:

diff --git a/dandi-reports/dandi-linkml-schema.yml b/dandi-reports/dandi-linkml-schema.yml
@@ -408,9 +408,9 @@ slots:
     name: access
     notes:
     - 'pydantic2linkml: Unable to express the default factory, <function CommonModel.<lambda>
-      at 0x7fab19ebf6a0>, in LinkML.'
+      at 0x7fbf2c5c36a0>, in LinkML.'
     - 'pydantic2linkml: Unable to translate the logic contained in the after validation
-      function, <function AccessRequirements.open_or_embargoed at 0x7fab19e49b20>.'
+      function, <function AccessRequirements.open_or_embargoed at 0x7fbf2c541b20>.'
     range: AccessRequirements
     required: false
     multivalued: true
@@ -717,7 +717,7 @@ slots:
     name: relatedResource
     notes:
     - 'pydantic2linkml: Unable to translate the logic contained in the after validation
-      function, <function Resource.identifier_or_url at 0x7fab19e4bf60>.'
+      function, <function Resource.identifier_or_url at 0x7fbf2c543f60>.'
     range: Resource
     required: false
     multivalued: true
@@ -819,7 +819,7 @@ slots:
     name: vendor
     notes:
     - 'pydantic2linkml: Unable to translate the logic contained in the after validation
-      function, <function Contributor.ensure_contact_person_has_email at 0x7fab19e491c0>.'
+      function, <function Contributor.ensure_contact_person_has_email at 0x7fbf2c5411c0>.'
     range: Organization
     required: false
   version:
@@ -1024,13 +1024,13 @@ classes:
     - 'pydantic2linkml: Impossible to generate slot usage entry for the access slot.
       The slot representation of the access field in the BareAsset Pydantic model
       has changes in value in meta slots: [''notes''] .'
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the wasGeneratedBy
-      slot. The slot representation of the wasGeneratedBy field in the BareAsset Pydantic
-      model lacks meta slots: [''range''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the schemaKey
       slot. The slot representation of the schemaKey field in the BareAsset Pydantic
       model has changes in value in meta slots: [''ifabsent'', ''notes'', ''range'']
       .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the wasGeneratedBy
+      slot. The slot representation of the wasGeneratedBy field in the BareAsset Pydantic
+      model lacks meta slots: [''range''] .'
     is_a: CommonModel
     slots:
     - approach
@@ -1187,24 +1187,24 @@ classes:
   Dandiset:
     name: Dandiset
     notes:
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the contributor
-      slot. The slot representation of the contributor field in the Dandiset Pydantic
-      model has changes in value in meta slots: [''notes'', ''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the description
       slot. The slot representation of the description field in the Dandiset Pydantic
       model has changes in value in meta slots: [''required''] .'
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the license slot.
-      The slot representation of the license field in the Dandiset Pydantic model
-      has changes in value in meta slots: [''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the name slot.
       The slot representation of the name field in the Dandiset Pydantic model has
       changes in value in meta slots: [''required''] .'
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the id slot. The
-      slot representation of the id field in the Dandiset Pydantic model has changes
-      in value in meta slots: [''required''] .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the contributor
+      slot. The slot representation of the contributor field in the Dandiset Pydantic
+      model has changes in value in meta slots: [''notes'', ''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the wasGeneratedBy
       slot. The slot representation of the wasGeneratedBy field in the Dandiset Pydantic
       model has changes in value in meta slots: [''range''] .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the license slot.
+      The slot representation of the license field in the Dandiset Pydantic model
+      has changes in value in meta slots: [''required''] .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the id slot. The
+      slot representation of the id field in the Dandiset Pydantic model has changes
+      in value in meta slots: [''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the schemaKey
       slot. The slot representation of the schemaKey field in the Dandiset Pydantic
       model has changes in value in meta slots: [''ifabsent'', ''notes'', ''range'']
@@ -1327,13 +1327,13 @@ classes:
   Organization:
     name: Organization
     notes:
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the includeInCitation
-      slot. The slot representation of the includeInCitation field in the Organization
-      Pydantic model has changes in value in meta slots: [''ifabsent''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the schemaKey
       slot. The slot representation of the schemaKey field in the Organization Pydantic
       model has changes in value in meta slots: [''any_of'', ''ifabsent'', ''notes'']
       .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the includeInCitation
+      slot. The slot representation of the includeInCitation field in the Organization
+      Pydantic model has changes in value in meta slots: [''ifabsent''] .'
     is_a: Contributor
     slots:
     - contactPoint
@@ -1376,13 +1376,13 @@ classes:
   Person:
     name: Person
     notes:
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the name slot.
-      The slot representation of the name field in the Person Pydantic model has changes
-      in value in meta slots: [''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the schemaKey
       slot. The slot representation of the schemaKey field in the Person Pydantic
       model has changes in value in meta slots: [''any_of'', ''ifabsent'', ''notes'']
       .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the name slot.
+      The slot representation of the name field in the Person Pydantic model has changes
+      in value in meta slots: [''required''] .'
     is_a: Contributor
     slots:
     - affiliation
@@ -1455,12 +1455,12 @@ classes:
     - 'pydantic2linkml: Impossible to generate slot usage entry for the id slot. The
       slot representation of the id field in the PublishedDandiset Pydantic model
       has changes in value in meta slots: [''pattern''] .'
-    - 'pydantic2linkml: Impossible to generate slot usage entry for the url slot.
-      The slot representation of the url field in the PublishedDandiset Pydantic model
-      has changes in value in meta slots: [''required''] .'
     - 'pydantic2linkml: Impossible to generate slot usage entry for the schemaKey
       slot. The slot representation of the schemaKey field in the PublishedDandiset
       Pydantic model has changes in value in meta slots: [''notes''] .'
+    - 'pydantic2linkml: Impossible to generate slot usage entry for the url slot.
+      The slot representation of the url field in the PublishedDandiset Pydantic model
+      has changes in value in meta slots: [''required''] .'
     is_a: Dandiset
     mixins:
     - Publishable

diff --git a/dandi-reports/summary.md b/dandi-reports/summary.md
@@ -707,11 +707,11 @@
 | [001207](./001207/) | [draft](./001207/draft/metadata.yaml) | 0 | [1 (1)](./001207/draft/linkml_validation_errs.yaml) | 2024-10-17T18:26:57.249951+00:00 | Invalid | 0.6.8 |
 | [001208](./001208/) | [draft](./001208/draft/metadata.yaml) | 0 | [1 (1)](./001208/draft/linkml_validation_errs.yaml) | 2024-10-18T15:54:58.216914+00:00 | Invalid | 0.6.8 |
 | [001209](./001209/) | [draft](./001209/draft/metadata.yaml) | 0 | [4 (4)](./001209/draft/linkml_validation_errs.yaml) | 2024-10-21T15:39:48.115291+00:00 | Valid | 0.6.8 |
-| [001210](./001210/) | [draft](./001210/draft/metadata.yaml) | 0 | [1 (1)](./001210/draft/linkml_validation_errs.yaml) | 2024-10-18T20:19:25.338948+00:00 | Invalid | 0.6.8 |
+| [001210](./001210/) | [draft](./001210/draft/metadata.yaml) | 0 | [1 (1)](./001210/draft/linkml_validation_errs.yaml) | 2024-11-04T16:52:07.504617+00:00 | Invalid | 0.6.8 |
 | [001211](./001211/) | [draft](./001211/draft/metadata.yaml) | 0 | [34 (34)](./001211/draft/linkml_validation_errs.yaml) | 2024-10-21T22:06:53.868955+00:00 | Valid | 0.6.8 |
 | [001212](./001212/) | [0.241023.0931](./001212/0.241023.0931/metadata.yaml) | 0 | [20 (20)](./001212/0.241023.0931/linkml_validation_errs.yaml) | 2024-10-23T09:31:40.811057+00:00 | Valid | 0.6.8 |
 | [001212](./001212/) | [draft](./001212/draft/metadata.yaml) | 0 | [20 (1 + 19)](./001212/draft/linkml_validation_errs.yaml) | 2024-10-23T09:31:39.560158+00:00 | Published | 0.6.8 |
 | [001245](./001245/) | [draft](./001245/draft/metadata.yaml) | 0 | [11 (11)](./001245/draft/linkml_validation_errs.yaml) | 2024-10-30T16:53:34.643665+00:00 | Valid | 0.6.8 |
 | [001246](./001246/) | [draft](./001246/draft/metadata.yaml) | 0 | [1 (1)](./001246/draft/linkml_validation_errs.yaml) | 2024-10-29T19:39:37.231865+00:00 | Invalid | 0.6.8 |
 | [001247](./001247/) | [draft](./001247/draft/metadata.yaml) | 0 | [1 (1)](./001247/draft/linkml_validation_errs.yaml) | 2024-11-03T18:55:57.695563+00:00 | Invalid | 0.6.8 |
-| [001248](./001248/) | [draft](./001248/draft/metadata.yaml) | 0 | [1 (1)](./001248/draft/linkml_validation_errs.yaml) | 2024-11-03T19:10:57.658454+00:00 | Invalid | 0.6.8 |
+| [001248](./001248/) | [draft](./001248/draft/metadata.yaml) | 0 | [1 (1)](./001248/draft/linkml_validation_errs.yaml) | 2024-11-04T18:25:49.814439+00:00 | Valid | 0.6.8 |