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microbiomedata · Jun 15, 2022 · 8657135 · 8657135
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diff --git a/docs/schema-slides.html b/docs/schema-slides.html
diff --git a/json/nmdc.linkml.json b/json/nmdc.linkml.json
@@ -3664,7 +3664,8 @@
       "slot_uri": "prov:qualifiedAssociation",
       "multivalued": true,
       "range": "credit association",
-      "inlined": true
+      "inlined": true,
+      "inlined_as_list": true
     },
     "study image": {
       "name": "study image",
@@ -22265,7 +22266,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "zinc"
       ],
@@ -22297,7 +22297,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "manganese"
       ],
@@ -22329,7 +22328,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "ammonium nitrogen",
         "NH4-N"
@@ -22365,7 +22363,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "nitrate nitrogen",
         "NO3-N"
@@ -22398,7 +22395,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "nitrite nitrogen",
         "NO2-N"
@@ -22434,7 +22430,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "see_also": [
         "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF"
       ],
@@ -22474,7 +22469,6 @@
         }
       ],
       "from_schema": "https://microbiomedata/schema",
-      "source": "https://www.ornl.gov/content/bio-scales-0",
       "aliases": [
         "lbceq",
         "lime buffer capacity (at 5-day equilibrium)"
@@ -29413,7 +29407,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "zinc"
           ],
@@ -29447,7 +29440,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "manganese"
           ],
@@ -29481,7 +29473,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "ammonium nitrogen",
             "NH4-N"
@@ -29519,7 +29510,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "nitrate nitrogen",
             "NO3-N"
@@ -29554,7 +29544,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "nitrite nitrogen",
             "NO2-N"
@@ -29592,7 +29581,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "see_also": [
             "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF"
           ],
@@ -29634,7 +29622,6 @@
             }
           ],
           "from_schema": "https://microbiomedata/schema",
-          "source": "https://www.ornl.gov/content/bio-scales-0",
           "aliases": [
             "lbceq",
             "lime buffer capacity (at 5-day equilibrium)"
@@ -30164,7 +30151,7 @@
           "alias": "has_credit_associations",
           "owner": "study",
           "range": "credit association",
-          "inlined": true
+          "inlined_as_list": true
         },
         "study image": {
           "name": "study image",

diff --git a/jsonld-context/nmdc.context.jsonld b/jsonld-context/nmdc.context.jsonld
@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-06-03T12:47:32\n    Schema: NMDC\n    metamodel version: 1.7.0\n    model version: 4.0.0\n    \n    id: https://microbiomedata/schema\n    description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-06-15T10:42:44\n    Schema: NMDC\n    metamodel version: 1.7.0\n    model version: 4.0.0\n    \n    id: https://microbiomedata/schema\n    description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "CAS": "http://identifiers.org/cas/",
       "CATH": "http://identifiers.org/cath/",

diff --git a/python/annotation.py b/python/annotation.py
@@ -1,5 +1,5 @@
 # Auto generated from annotation.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:49
+# Generation date: 2022-06-15T10:43:01
 # Schema: NMDC-Annotation
 #
 # id: https://microbiomedata/schema/annotation

diff --git a/python/basic_slots.py b/python/basic_slots.py
@@ -1,5 +1,5 @@
 # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:38
+# Generation date: 2022-06-15T10:42:50
 # Schema: NMDC-Basic-Slots
 #
 # id: https://microbiomedata/schema/basic_slots

diff --git a/python/bioscales.py b/python/bioscales.py
@@ -1,5 +1,5 @@
 # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:48:07
+# Generation date: 2022-06-15T10:43:19
 # Schema: NMDC-Bioscales
 #
 # id: https://microbiomedata/schema/bioscales

diff --git a/python/core.py b/python/core.py
@@ -1,5 +1,5 @@
 # Auto generated from core.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:48:16
+# Generation date: 2022-06-15T10:43:31
 # Schema: NMDC-Core
 #
 # id: https://microbiomedata/schema/core

diff --git a/python/external_identifiers.py b/python/external_identifiers.py
@@ -1,5 +1,5 @@
 # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:53
+# Generation date: 2022-06-15T10:43:06
 # Schema: NMDC-External-Identifiers
 #
 # id: https://microbiomedata/schema/external_identifiers

diff --git a/python/mixs.py b/python/mixs.py
@@ -1,5 +1,5 @@
 # Auto generated from mixs.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:57
+# Generation date: 2022-06-15T10:43:10
 # Schema: mixs-schema
 #
 # id: https://microbiomedata/schema/mixs

diff --git a/python/nmdc.py b/python/nmdc.py
@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:48:09
+# Generation date: 2022-06-15T10:43:24
 # Schema: NMDC
 #
 # id: https://microbiomedata/schema
@@ -1681,7 +1681,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.MGnify_project_identifiers = [self.MGnify_project_identifiers] if self.MGnify_project_identifiers is not None else []
         self.MGnify_project_identifiers = [v if isinstance(v, ExternalIdentifier) else ExternalIdentifier(v) for v in self.MGnify_project_identifiers]
 
-        self._normalize_inlined_as_dict(slot_name="has_credit_associations", slot_type=CreditAssociation, key_name="applies to person", keyed=False)
+        if not isinstance(self.has_credit_associations, list):
+            self.has_credit_associations = [self.has_credit_associations] if self.has_credit_associations is not None else []
+        self.has_credit_associations = [v if isinstance(v, CreditAssociation) else CreditAssociation(**as_dict(v)) for v in self.has_credit_associations]
 
         if not isinstance(self.study_image, list):
             self.study_image = [self.study_image] if self.study_image is not None else []

diff --git a/python/portal/emsl.py b/python/portal/emsl.py
@@ -1,5 +1,5 @@
 # Auto generated from emsl.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:47
+# Generation date: 2022-06-15T10:43:00
 # Schema: emsl
 #
 # id: https://microbiomedata/schema/emsl

diff --git a/python/portal/jgi_metagenomics.py b/python/portal/jgi_metagenomics.py
@@ -1,5 +1,5 @@
 # Auto generated from jgi_metagenomics.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:40
+# Generation date: 2022-06-15T10:42:52
 # Schema: jgi_metagenomics
 #
 # id: https://microbiomedata/schema/jgi_metagenomics

diff --git a/python/portal/jgi_metatranscriptomics.py b/python/portal/jgi_metatranscriptomics.py
@@ -1,5 +1,5 @@
 # Auto generated from jgi_metatranscriptomics.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:43
+# Generation date: 2022-06-15T10:42:56
 # Schema: jgi_metatranscriptomics
 #
 # id: https://microbiomedata/schema/jgi_metatranscriptomics

diff --git a/python/portal/mixs_inspired.py b/python/portal/mixs_inspired.py
@@ -1,5 +1,5 @@
 # Auto generated from mixs_inspired.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:42
+# Generation date: 2022-06-15T10:42:54
 # Schema: mixs_inspired
 #
 # id: https://microbiomedata/schema/mixs_inspired

diff --git a/python/portal/sample_id.py b/python/portal/sample_id.py
@@ -1,5 +1,5 @@
 # Auto generated from sample_id.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:47:45
+# Generation date: 2022-06-15T10:42:58
 # Schema: sample_id
 #
 # id: https://microbiomedata/schema/sample_id

diff --git a/python/prov.py b/python/prov.py
@@ -1,5 +1,5 @@
 # Auto generated from prov.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:48:04
+# Generation date: 2022-06-15T10:43:17
 # Schema: NMDC-PROV
 #
 # id: https://microbiomedata/schema/prov

diff --git a/python/workflow_execution_activity.py b/python/workflow_execution_activity.py
@@ -1,5 +1,5 @@
 # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-06-03T12:48:01
+# Generation date: 2022-06-15T10:43:14
 # Schema: NMDC-Workflow-Exectution
 #
 # id: https://microbiomedata/schema/workflow_execution_activity

diff --git a/test/test_credit_associations.py b/test/test_credit_associations.py
@@ -33,12 +33,18 @@ def test_sum(self):
         validator.validate_object(ca1, target_class=CreditAssociation)
         validator.validate_object(ca2, target_class=CreditAssociation)
 
-        try:
-            s.has_credit_associations.append(ca1)
-            s.has_credit_associations.append(ca2)
-            validator.validate_object(s, target_class=Study)
-        except Exception as e:
-            logging.error(traceback.format_exc())
+        # try:
+        #     s.has_credit_associations.append(ca1)
+        #     s.has_credit_associations.append(ca2)
+        #     validator.validate_object(s, target_class=Study)
+        # except Exception as e:
+        #     logging.error(traceback.format_exc())
+
+        s.has_credit_associations.append(ca1)
+        s.has_credit_associations.append(ca2)
+        validator.validate_object(s, target_class=Study)
+
+        print(s)
 
         self.assertEqual(type(s), Study)