Merge pull request #114 from psychoinformatics-de/fixexampels

Move and fix examples
psychoinformatics-de · Mar 18, 2024 · 4eb1de6 · 4eb1de6
2 parents 44f5fac + 05ffcd1
commit 4eb1de6
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diff --git a/src/examples/dataset-version/DatasetVersionObject-customproperties.yaml b/src/examples/dataset-version/DatasetVersionObject-customproperties.yaml
@@ -4,7 +4,8 @@ properties:
   - type: obo:NCIT_C90437
     label: Planned Number of Female Subjects
     range: xsd:nonNegativeInteger
-    value: 54
+    value: 
+      - "54"
     comment: >-
       A non-negative integer representing the number of planned female
       subjects/participants.
@@ -13,7 +14,9 @@ properties:
 relation:
   - meta_type: dlco:EntityObject
     meta_code: rmd
-    identifier: obo:OBI_0500002
+    identifier: 
+      obo:OBI_0500002:
 qualified_relation:
   - entity: rmd
-    had_role: obo:OBI_0500000
+    had_role: 
+      - obo:OBI_0500000
diff --git a/src/examples/dataset-version/DatasetVersionObject-datacite-nationalgallery.yaml b/src/examples/dataset-version/DatasetVersionObject-datacite-nationalgallery.yaml
@@ -30,16 +30,17 @@ description: >-
   temperature, relative humidity and air moisture content 24 hours a day,
   7 days a week over the last two decades.
 landing_page: https://research.ng-london.org.uk/scientific/env
-version: 1.0
-modified: 2024-01-02
+version: "1.0"
+modified: "2024-01-02"
 keyword:
   - "FOS: Earth and related environmental sciences"
   - temperature
   - relative humidity
   - illuminance
   - moisture content
   - Environmental monitoring
-identifier: https://doi.org/10.82433/9184-dy35
+identifier: 
+  https://doi.org/10.82433/9184-dy35:
 was_attributed_to:
   - meta_type: dlco:OrganizationObject
     meta_code: NG
@@ -69,7 +70,7 @@ relation:
     name: "Integrating Platforms for the European Research Infrastructure ON Heritage Science"
     identifier:
       https://cordis.europa.eu/project/id/871034:
-        notation: 871034
+        notation: "871034"
         schema_agency: European Commission
     sponsor:
       name: H2020 Excellent Science

diff --git a/src/examples/dataset-version/DatasetVersionObject-dats.yaml b/src/examples/dataset-version/DatasetVersionObject-dats.yaml
@@ -95,44 +95,58 @@ qualified_relation:
   # "name":"Homo sapiens"
   - entity: obo:NCBITaxon_9606
     # "identifierSource": "NCBI Taxonomy Database"
-    had_role: dlco:is_about
+    had_role:
+      - dlco:is_about
   # "name": "adult"
   - entity: obo:BTO_0001043
-    had_role: dlco:is_about
+    had_role:
+      - dlco:is_about
 license: licenses:CC-BY-ND-4.0
 keyword:
   - phantom
   - MRI
 properties:
   - label: Total number of sessions
-    value: 521
+    value:
+      - "521"
   - label: logo
-    value: logo.png
+    value:
+      - logo.png
   - label: CONP_status
-    value: CONP
+    value:
+      - CONP
   - label: files
-    value: 3771
+    value:
+      - "3771"
   - label: subjects
     type: obo:NCIT_C98703
-    value: 1
+    value:
+      - "1"
   - label: origin_consortium
-    value: IBIS
+    value:
+      - IBIS
   - label: origin_institution
-    value: McGill Centre for Integrative Neuroscience
+    value:
+      - McGill Centre for Integrative Neuroscience
   - label: origin_city
-    value: Montreal
+    value:
+      - Montreal
   - label: origin_province
-    value: Quebec
+    value:
+      - Quebec
   - label: origin_country
     type: obo:HSO_0000360
-    value: Canada
+    value:
+      - Canada
   - label: privacy
     comment: >-
       A qualifier to describe the data protection applied to the dataset.
       This is relevant for clinical data.
-    value: open
+    value:
+      - open
   - label: aggregation
     comment: >-
       "A qualifier indicating if the entity represents an
       'instance of dataset' or a 'collection of datasets'."
-    value: instance of dataset
+    value: 
+      - instance of dataset
diff --git a/src/examples/dataset-version/DatasetVersionObject-funding.yaml b/src/examples/dataset-version/DatasetVersionObject-funding.yaml
@@ -4,7 +4,8 @@ relation:
   - meta_type: dlco:GrantObject
     meta_code: sfb1451
     name: SFB1451
-    identifier: https://gepris.dfg.de/gepris/projekt/431549029
+    identifier: 
+      https://gepris.dfg.de/gepris/projekt/431549029:
     sponsor:
       name: Deutsche Forschungsgemeinschaft
 qualified_relation:

diff --git a/src/examples/dataset-version/DatasetVersionObject-identifiers.json b/src/examples/dataset-version/DatasetVersionObject-identifiers.json
@@ -13,6 +13,9 @@
       "meta_type": "dlco:AgentObject",
       "meta_code": "carberry_ex2",
       "identifier": {
+        "https://en.wikipedia.org/wiki/Josiah_S._Carberry": {
+          "meta_id": "https://en.wikipedia.org/wiki/Josiah_S._Carberry"
+        },
         "http://orcid.org/0000-0002-1825-0097": {
           "meta_id": "http://orcid.org/0000-0002-1825-0097"
         }

diff --git a/src/examples/dataset-version/DatasetVersionObject-identifiers.yaml b/src/examples/dataset-version/DatasetVersionObject-identifiers.yaml
@@ -5,11 +5,13 @@ was_attributed_to:
   # by URI for a single identifier
   - meta_type: dlco:AgentObject
     meta_code: carberry_ex1
-    identifier: https://en.wikipedia.org/wiki/Josiah_S._Carberry
+    identifier: 
+      https://en.wikipedia.org/wiki/Josiah_S._Carberry:
   # by URI-as-a-key for any number of identifiers
   - meta_type: dlco:AgentObject
     meta_code: carberry_ex2
     identifier:
+      https://en.wikipedia.org/wiki/Josiah_S._Carberry:
       http://orcid.org/0000-0002-1825-0097:
   # by inline-declaration with a URI key
   - meta_type: dlco:AgentObject

diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.json b/src/examples/dataset-version/DatasetVersionObject-penguins.json
@@ -188,7 +188,7 @@
       "sponsor": {
         "name": "NSF Office of Polar Programs"
       },
-      "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false"
+      "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282"
     },
     {
       "meta_type": "dlco:GrantObject",
@@ -212,7 +212,7 @@
       "identifier": {
         "dlns:nsfaward/0741351": {
           "meta_id": "dlns:nsfaward/0741351",
-          "notation": "246505",
+          "notation": "0741351",
           "schema_agency": "US National Science Foundation"
         }
       },

diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.yaml b/src/examples/dataset-version/DatasetVersionObject-penguins.yaml
@@ -7,8 +7,8 @@ description: >-
   Station, Antarctica LTER, a member of the Long Term Ecological
   Research Network.
 landing_page: https://github.com/allisonhorst/palmerpenguins
-version: 0.1.0
-modified: 2020-07-16
+version: "0.1.0"
+modified: "2020-07-16"
 keyword:
   - penguins
   - sea ice
@@ -18,7 +18,8 @@ keyword:
   - antarctica
   - animal sexual behavior
   - isotopes
-identifier: https://doi.org/10.5281/zenodo.3960218
+identifier: 
+  https://doi.org/10.5281/zenodo.3960218:
 was_attributed_to:
   - meta_type: dlco:ResearchContributorObject
     meta_code: ahorst
@@ -75,17 +76,17 @@ relation:
     name: "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment"
     identifier:
       dlns:nsfaward/0217282:
-        notation: 0217282
+        notation: "0217282"
         schema_agency: US National Science Foundation
     sponsor:
       name: NSF Office of Polar Programs
-    cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false
+    cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282
   - meta_type: dlco:GrantObject
     meta_code: nsf0823101
     name: Palmer, Antarctica Long Term Ecological Research Project
     identifier:
       dlns:nsfaward/0823101:
-        notation: 0823101
+        notation: "0823101"
         schema_agency: US National Science Foundation
     sponsor:
       name: NSF Office of Polar Programs
@@ -95,7 +96,7 @@ relation:
     name: "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf"
     identifier:
       dlns:nsfaward/0741351:
-        notation: 0741351
+        notation: "0741351"
         schema_agency: US National Science Foundation
     sponsor:
       name: NSF Office of Polar Programs

diff --git a/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml b/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml
@@ -6,7 +6,8 @@ title: >-
   "Data files associated with the manuscript:Effects of facilitated family case conferencing for ..."
 description: >-
   Palliative care planning for nursing home residents with advanced dementia ...
-identifier: https://doi.org/10.4225/59/59672c09f4a4b
+identifier:
+  https://doi.org/10.4225/59/59672c09f4a4b:
 #  "datePublished": "2017",
 distribution:
   meta_type: dlco:FileContainerObject

diff --git a/src/examples/dataset-version/DatasetVersionObject-samplesrc.yaml b/src/examples/dataset-version/DatasetVersionObject-samplesrc.yaml
@@ -1,7 +1,9 @@
 qualified_relation:
   # sampled from organism homo sapiens
   - entity: http://snomed.info/id/337915000
-    had_role: obo:HSO_0000244
+    had_role:
+      - obo:HSO_0000244
   # sampled from anatomical entity liver
   - entity: obo:BTO_0000759
-    had_role: obo:HSO_0000243
+    had_role:
+      - obo:HSO_0000243
diff --git a/src/examples/dataset-version/DatasetVersionObject-topic.yaml b/src/examples/dataset-version/DatasetVersionObject-topic.yaml
@@ -1,7 +1,9 @@
 relation:
   - meta_type: dlco:EntityObject
     meta_code: disease_cancer
-    identifier: obo:DOID_162
+    identifier:
+      obo:DOID_162:
 qualified_relation:
   - entity: disease_cancer
-    had_role: dlco:is_about
+    had_role:
+      - dlco:is_about
diff --git a/...asetVersionObject-dataverse-rtmefmri.yaml → ...asetVersionObject-dataverse-rtmefmri.yaml b/...asetVersionObject-dataverse-rtmefmri.yaml → ...asetVersionObject-dataverse-rtmefmri.yaml
@@ -15,10 +15,12 @@ keyword:
   - Engineering
   - Medicine, Health and Life Sciences
   - Physics
-identifier: https://doi.org/10.34894/R1TNL8
+identifier: 
+  https://doi.org/10.34894/R1TNL8:
 custom_licenses:
   customlicenses:humanhealthdata:
-    identifier: "https://dataverse.nl/api/datasets/:persistentId/versions/1.4/customlicense?persistentId=doi:10.34894/R1TNL8"
+    identifier:
+      https://dataverse.nl/api/datasets/:persistentId/versions/1.4/customlicense?persistentId=doi:10.34894/R1TNL8:
     license_text: "<h2>Data user agreement for accessing limited human health data</h2>\n
       <br>\n<i><b>By clicking \"Accept\", I agree to the terms presented below.</b></i>\n
       <br><br>\n<p>I request access to the <i><b>rt-me-fMRI</b></i> dataset collected

diff --git a/tests/dataset-version-schema/validation/DatasetVersionObject.valid.cfg.yaml b/tests/dataset-version-schema/validation/DatasetVersionObject.valid.cfg.yaml
@@ -1,7 +1,20 @@
 schema: src/linkml/schemas/dataset-version.yaml
 target_class: DatasetVersionObject
 data_sources:
+  - tests/dataset-version-schema/validation/DatasetVersionObject-dataverse-rtmefmri.yaml
+  - src/examples/dataset-version/DatasetVersionObject-affiliation.yaml
+  - src/examples/dataset-version/DatasetVersionObject-customlicense.yaml
+  - src/examples/dataset-version/DatasetVersionObject-customproperties.yaml
+  - src/examples/dataset-version/DatasetVersionObject-datacite-nationalgallery.yaml
+  - src/examples/dataset-version/DatasetVersionObject-dats.yaml
+  - src/examples/dataset-version/DatasetVersionObject-funding.yaml
+  - src/examples/dataset-version/DatasetVersionObject-identifiers.yaml
+  - src/examples/dataset-version/DatasetVersionObject-penguins.yaml
+  - src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.yaml
+  - src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml
   - src/examples/dataset-version/DatasetVersionObject-roleattribution.yaml
+  - src/examples/dataset-version/DatasetVersionObject-samplesrc.yaml
+  - src/examples/dataset-version/DatasetVersionObject-topic.yaml
 plugins:
   JsonschemaValidationPlugin:
     closed: true