Merge dev to main in preparation of a release

artifacts/csv/ghga.csv

@@ -1,5 +1,5 @@
 # metamodel_version: 1.7.0
-# version: 0.6.0
+# version: 0.7.0
 id,mappings,description
 accession_mixin,,Mixin for entities that can be assigned a GHGA accession.
 agent,,"An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. Agents include a Person, Organization, or Software that performs an activity."

artifacts/derived_schema/creation/ghga_creation.py

@@ -1,5 +1,5 @@
 # Auto generated from ghga_creation.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-04-26T10:28:08
+# Generation date: 2022-04-29T13:43:08
 # Schema: GHGA-Metadata-Schema
 #
 # id: https://w3id.org/GHGA-Metadata-Schema
@@ -25,7 +25,7 @@
 from linkml_runtime.linkml_model.types import Integer, String
 
 metamodel_version = "1.7.0"
-version = "0.6.0"
+version = "0.7.0"
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs
@@ -787,7 +787,7 @@ class CreateSequencingProtocol(CreateProtocol):
     alias: str = None
     description: str = None
     sequencing_center: Optional[str] = None
-    paired_or_single_end: Optional[str] = None
+    paired_or_single_end: Optional[Union[str, "PairedOrSingleEndEnum"]] = None
     sequencing_read_length: Optional[str] = None
     index_sequence: Optional[str] = None
     target_coverage: Optional[str] = None
@@ -823,8 +823,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.sequencing_center is not None and not isinstance(self.sequencing_center, str):
             self.sequencing_center = str(self.sequencing_center)
 
-        if self.paired_or_single_end is not None and not isinstance(self.paired_or_single_end, str):
-            self.paired_or_single_end = str(self.paired_or_single_end)
+        if self.paired_or_single_end is not None and not isinstance(self.paired_or_single_end, PairedOrSingleEndEnum):
+            self.paired_or_single_end = PairedOrSingleEndEnum(self.paired_or_single_end)
 
         if self.sequencing_read_length is not None and not isinstance(self.sequencing_read_length, str):
             self.sequencing_read_length = str(self.sequencing_read_length)
@@ -1107,6 +1107,7 @@ class CreateSample(MaterialEntity):
     description: str = None
     alias: str = None
     type: Optional[str] = None
+    case_control_status: Optional[Union[str, "CaseControlStatusEnum"]] = None
     vital_status_at_sampling: Optional[Union[str, "VitalStatusEnum"]] = None
     isolation: Optional[str] = None
     storage: Optional[str] = None
@@ -1137,6 +1138,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.type is not None and not isinstance(self.type, str):
             self.type = str(self.type)
 
+        if self.case_control_status is not None and not isinstance(self.case_control_status, CaseControlStatusEnum):
+            self.case_control_status = CaseControlStatusEnum(self.case_control_status)
+
         if self.vital_status_at_sampling is not None and not isinstance(self.vital_status_at_sampling, VitalStatusEnum):
             self.vital_status_at_sampling = VitalStatusEnum(self.vital_status_at_sampling)
 
@@ -1610,9 +1614,9 @@ class CreateDataset(InformationContentEntity):
     alias: str = None
     type: Optional[str] = None
     has_study: Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]] = empty_list()
-    has_experiment: Optional[Union[Union[dict, CreateAnalysis], List[Union[dict, CreateAnalysis]]]] = empty_list()
-    has_sample: Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]] = empty_list()
-    has_analysis: Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]] = empty_list()
+    has_experiment: Optional[Union[Union[dict, CreateExperiment], List[Union[dict, CreateExperiment]]]] = empty_list()
+    has_sample: Optional[Union[Union[dict, CreateSample], List[Union[dict, CreateSample]]]] = empty_list()
+    has_analysis: Optional[Union[Union[dict, CreateAnalysis], List[Union[dict, CreateAnalysis]]]] = empty_list()
     has_publication: Optional[Union[Union[dict, "CreatePublication"], List[Union[dict, "CreatePublication"]]]] = empty_list()
     release_status: Optional[Union[str, "ReleaseStatusEnum"]] = None
     accession: Optional[str] = None
@@ -1656,15 +1660,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
         if not isinstance(self.has_experiment, list):
             self.has_experiment = [self.has_experiment] if self.has_experiment is not None else []
-        self.has_experiment = [v if isinstance(v, CreateAnalysis) else CreateAnalysis(**as_dict(v)) for v in self.has_experiment]
+        self.has_experiment = [v if isinstance(v, CreateExperiment) else CreateExperiment(**as_dict(v)) for v in self.has_experiment]
 
         if not isinstance(self.has_sample, list):
             self.has_sample = [self.has_sample] if self.has_sample is not None else []
-        self.has_sample = [v if isinstance(v, CreateStudy) else CreateStudy(**as_dict(v)) for v in self.has_sample]
+        self.has_sample = [v if isinstance(v, CreateSample) else CreateSample(**as_dict(v)) for v in self.has_sample]
 
         if not isinstance(self.has_analysis, list):
             self.has_analysis = [self.has_analysis] if self.has_analysis is not None else []
-        self.has_analysis = [v if isinstance(v, CreateStudy) else CreateStudy(**as_dict(v)) for v in self.has_analysis]
+        self.has_analysis = [v if isinstance(v, CreateAnalysis) else CreateAnalysis(**as_dict(v)) for v in self.has_analysis]
 
         if not isinstance(self.has_publication, list):
             self.has_publication = [self.has_publication] if self.has_publication is not None else []
@@ -2523,6 +2527,34 @@ class FileFormatEnum(EnumDefinitionImpl):
         description="Enum to capture file types.",
     )
 
+class CaseControlStatusEnum(EnumDefinitionImpl):
+    """
+    Enum to capture whether a Sample in a Study is to be considered as Case or Control.
+    """
+    control = PermissibleValue(text="control",
+                                     description="The Sample is to be treated as Control")
+    case = PermissibleValue(text="case",
+                               description="The Sample is to be treated as Case")
+
+    _defn = EnumDefinition(
+        name="CaseControlStatusEnum",
+        description="Enum to capture whether a Sample in a Study is to be considered as Case or Control.",
+    )
+
+class PairedOrSingleEndEnum(EnumDefinitionImpl):
+    """
+    Enum to capture whether a sequencing experiment generates reads that are Paired-end or Single-end.
+    """
+    paired = PermissibleValue(text="paired",
+                                   description="The reads are Paired-end")
+    single = PermissibleValue(text="single",
+                                   description="The reads are Single-end")
+
+    _defn = EnumDefinition(
+        name="PairedOrSingleEndEnum",
+        description="Enum to capture whether a sequencing experiment generates reads that are Paired-end or Single-end.",
+    )
+
 class SubmissionStatusEnum(EnumDefinitionImpl):
     """
     Enum to capture the status of a Submission.
@@ -2921,7 +2953,7 @@ class slots:
                    model_uri=GHGA.index_sequence, domain=None, range=Optional[str])
 
 slots.paired_or_single_end = Slot(uri=GHGA.paired_or_single_end, name="paired or single end", curie=GHGA.curie('paired_or_single_end'),
-                   model_uri=GHGA.paired_or_single_end, domain=None, range=Optional[str])
+                   model_uri=GHGA.paired_or_single_end, domain=None, range=Optional[Union[str, "PairedOrSingleEndEnum"]])
 
 slots.reference_chromosome = Slot(uri=GHGA.reference_chromosome, name="reference chromosome", curie=GHGA.curie('reference_chromosome'),
                    model_uri=GHGA.reference_chromosome, domain=None, range=Optional[str])
@@ -2962,6 +2994,9 @@ class slots:
 slots.sample_barcode_read = Slot(uri=GHGA.sample_barcode_read, name="sample barcode read", curie=GHGA.curie('sample_barcode_read'),
                    model_uri=GHGA.sample_barcode_read, domain=None, range=Optional[str])
 
+slots.case_control_status = Slot(uri=GHGA.case_control_status, name="case control status", curie=GHGA.curie('case_control_status'),
+                   model_uri=GHGA.case_control_status, domain=None, range=Optional[Union[str, "CaseControlStatusEnum"]])
+
 slots.vital_status_at_sampling = Slot(uri=GHGA.vital_status_at_sampling, name="vital status at sampling", curie=GHGA.curie('vital_status_at_sampling'),
                    model_uri=GHGA.vital_status_at_sampling, domain=None, range=Optional[Union[str, "VitalStatusEnum"]])
 
@@ -3344,13 +3379,13 @@ class slots:
                    model_uri=GHGA.create_dataset_has_study, domain=CreateDataset, range=Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]])
 
 slots.create_dataset_has_experiment = Slot(uri=GHGA.has_experiment, name="create dataset_has experiment", curie=GHGA.curie('has_experiment'),
-                   model_uri=GHGA.create_dataset_has_experiment, domain=CreateDataset, range=Optional[Union[Union[dict, CreateAnalysis], List[Union[dict, CreateAnalysis]]]])
+                   model_uri=GHGA.create_dataset_has_experiment, domain=CreateDataset, range=Optional[Union[Union[dict, CreateExperiment], List[Union[dict, CreateExperiment]]]])
 
 slots.create_dataset_has_sample = Slot(uri=GHGA.has_sample, name="create dataset_has sample", curie=GHGA.curie('has_sample'),
-                   model_uri=GHGA.create_dataset_has_sample, domain=CreateDataset, range=Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]])
+                   model_uri=GHGA.create_dataset_has_sample, domain=CreateDataset, range=Optional[Union[Union[dict, CreateSample], List[Union[dict, CreateSample]]]])
 
 slots.create_dataset_has_analysis = Slot(uri=GHGA.has_analysis, name="create dataset_has analysis", curie=GHGA.curie('has_analysis'),
-                   model_uri=GHGA.create_dataset_has_analysis, domain=CreateDataset, range=Optional[Union[Union[dict, CreateStudy], List[Union[dict, CreateStudy]]]])
+                   model_uri=GHGA.create_dataset_has_analysis, domain=CreateDataset, range=Optional[Union[Union[dict, CreateAnalysis], List[Union[dict, CreateAnalysis]]]])
 
 slots.create_dataset_has_file = Slot(uri=GHGA.has_file, name="create dataset_has file", curie=GHGA.curie('has_file'),
                    model_uri=GHGA.create_dataset_has_file, domain=CreateDataset, range=Union[Union[dict, CreateFile], List[Union[dict, CreateFile]]])

artifacts/derived_schema/creation/ghga_creation.schema.json

@@ -63,6 +63,15 @@
          "title": "BiologicalSexEnum",
          "type": "string"
       },
+      "CaseControlStatusEnum": {
+         "description": "Enum to capture whether a Sample in a Study is to be considered as Case or Control.",
+         "enum": [
+            "control",
+            "case"
+         ],
+         "title": "CaseControlStatusEnum",
+         "type": "string"
+      },
       "CreateAgent": {
          "additionalProperties": false,
          "description": "An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. Agents include a Person, Organization, or Software that performs an activity.",
@@ -980,7 +989,7 @@
                "items": {
                   "oneOf": [
                      {
-                        "$ref": "#/$defs/CreateStudy"
+                        "$ref": "#/$defs/CreateAnalysis"
                      },
                      {
                         "type": "string"
@@ -1012,11 +1021,11 @@
                ]
             },
             "has_experiment": {
-               "description": "One or more Analysis entities that are referenced by this Dataset.",
+               "description": "One or more Experiment entities that are referenced by this Dataset.",
                "items": {
                   "oneOf": [
                      {
-                        "$ref": "#/$defs/CreateAnalysis"
+                        "$ref": "#/$defs/CreateExperiment"
                      },
                      {
                         "type": "string"
@@ -1058,7 +1067,7 @@
                "items": {
                   "oneOf": [
                      {
-                        "$ref": "#/$defs/CreateStudy"
+                        "$ref": "#/$defs/CreateSample"
                      },
                      {
                         "type": "string"
@@ -2372,6 +2381,10 @@
                "description": "The alias for an entity.",
                "type": "string"
             },
+            "case_control_status": {
+               "$ref": "#/$defs/CaseControlStatusEnum",
+               "description": "Whether the sample is to be treated as Case or Control in a Study."
+            },
             "description": {
                "description": "Short textual description of the sample (How the sample was collected, sample source, protocol followed for processing the sample etc).",
                "type": "string"
@@ -2545,8 +2558,8 @@
                "type": "string"
             },
             "paired_or_single_end": {
-               "description": "Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing. The number that identifies each read direction in a paired-end nucleotide sequencing replications.",
-               "type": "string"
+               "$ref": "#/$defs/PairedOrSingleEndEnum",
+               "description": "Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing. The number that identifies each read direction in a paired-end nucleotide sequencing replications."
             },
             "sample_barcode_read": {
                "description": "The type of read that contains the sample barcode (eg: index1/index2/read1/read2).",
@@ -3102,6 +3115,15 @@
          "title": "FileFormatEnum",
          "type": "string"
       },
+      "PairedOrSingleEndEnum": {
+         "description": "Enum to capture whether a sequencing experiment generates reads that are Paired-end or Single-end.",
+         "enum": [
+            "paired",
+            "single"
+         ],
+         "title": "PairedOrSingleEndEnum",
+         "type": "string"
+      },
       "ReleaseStatusEnum": {
          "description": "Enum to capture the release status of an entity.",
          "enum": [
@@ -3187,6 +3209,6 @@
    "required": [],
    "title": "GHGA-Metadata-Schema",
    "type": "object",
-   "version": "0.6.0"
+   "version": "0.7.0"
 }
 

artifacts/derived_schema/creation/ghga_creation.yaml

@@ -2,7 +2,7 @@ id: https://w3id.org/GHGA-Metadata-Schema
 name: GHGA-Metadata-Schema
 description: >-
   The metadata schema for the German Human Genome-Phenome Archive (GHGA).
-version: 0.6.0
+version: 0.7.0
 imports:
 - linkml:types
 
@@ -153,6 +153,24 @@ enums:
         description: >-
           Other format.
 
+  case control status enum:
+    description: >-
+      Enum to capture whether a Sample in a Study is to be considered as Case or Control.
+    permissible_values:
+      control:
+        description: The Sample is to be treated as Control
+      case:
+        description: The Sample is to be treated as Case
+
+  paired or single end enum:
+    description: >-
+      Enum to capture whether a sequencing experiment generates reads that are Paired-end
+      or Single-end.
+    permissible_values:
+      paired:
+        description: The reads are Paired-end
+      single:
+        description: The reads are Single-end
 
   submission status enum:
     description: >-
@@ -233,7 +251,7 @@ enums:
         description: Age above 80.
       unknown:
         description: Age range unknown.
-comments: This schema was autogenerated from the GHGA Metadata Schema 0.6.0 and is
+comments: This schema was autogenerated from the GHGA Metadata Schema 0.7.0 and is
   intended solely for consumption by GHGA microservices.
 slots:
   schema type:
@@ -881,6 +899,10 @@ slots:
       reads for paired-end sequencing.
       The number that identifies each read direction in a paired-end nucleotide sequencing
       replications.
+    range: paired or single end enum
+    in_subset:
+    - recommended
+    - public
 
   reference chromosome:
     description: >-
@@ -982,6 +1004,14 @@ slots:
     - recommended
     - public
 
+  case control status:
+    description: >-
+      Whether the sample is to be treated as Case or Control in a Study.
+    range: case control status enum
+    in_subset:
+    - recommended
+    - public
+
   vital status at sampling:
     description: >-
       Vital Status of an Individual at the point of sampling (eg:'Alive', 'Deceased').
@@ -1736,6 +1766,7 @@ classes:
     - name
     - type
     - description
+    - case control status
     - vital status at sampling
     - isolation
     - storage
@@ -2120,31 +2151,32 @@ classes:
         inlined_as_list: true
       has experiment:
         description: >-
-          One or more Analysis entities that are referenced by this Dataset.
-        range: create analysis
+          One or more Experiment entities that are referenced by this Dataset.
+        range: create experiment
         multivalued: true
         inlined: true
         inlined_as_list: true
         required: false
       has sample:
         description: >-
           One or more Sample entities that are referenced by this Dataset.
-        range: create study
+        range: create sample
         multivalued: true
         required: false
         inlined: true
         inlined_as_list: true
       has analysis:
         description: >-
           One or more Analysis entities that are referenced by this Dataset.
-        range: create study
+        range: create analysis
         multivalued: true
         inlined: true
         inlined_as_list: true
         required: false
       has file:
         description: >-
           One or more File entities that collectively are part of this Dataset.
+        range: create file
         required: true
         multivalued: true
         inlined: true