Merge pull request #260 from alliance-genome/SCRUM-4192_1

Replaced HighThroughPut to HTP for shorter name
alliance-genome · Jul 29, 2024 · 0a27a7b · 0a27a7b
2 parents 1ce3397 + e370e39
commit 0a27a7b
Show file tree

Hide file tree

Showing 3 changed files with 54 additions and 54 deletions.
diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
@@ -15837,22 +15837,7 @@
             "title": "HPTerm",
             "type": "object"
         },
-        "HighThroughputExpressionAssayValues": {
-            "description": "",
-            "enum": [
-                "MMO:0000659",
-                "MMO:0000648",
-                "MMO:0000650",
-                "MMO:0000649",
-                "MMO:0000664",
-                "MMO:0000666",
-                "MMO:0000000",
-                "MMO:0000862"
-            ],
-            "title": "HighThroughputExpressionAssayValues",
-            "type": "string"
-        },
-        "HighThroughputExpressionDatasetAnnotation": {
+        "HTPExpressionDatasetAnnotation": {
             "additionalProperties": false,
             "description": "An entry for a published high-throughput expression dataset annotation.",
             "properties": {
@@ -15937,10 +15922,10 @@
                 "date_created",
                 "internal"
             ],
-            "title": "HighThroughputExpressionDatasetAnnotation",
+            "title": "HTPExpressionDatasetAnnotation",
             "type": "object"
         },
-        "HighThroughputExpressionDatasetAnnotationDTO": {
+        "HTPExpressionDatasetAnnotationDTO": {
             "additionalProperties": false,
             "description": "A DTO entry for a published high-throughput expression dataset annotation.",
             "properties": {
@@ -16037,10 +16022,10 @@
                 "date_created",
                 "internal"
             ],
-            "title": "HighThroughputExpressionDatasetAnnotationDTO",
+            "title": "HTPExpressionDatasetAnnotationDTO",
             "type": "object"
         },
-        "HighThroughputExpressionDatasetSampleAnnotation": {
+        "HTPExpressionDatasetSampleAnnotation": {
             "additionalProperties": false,
             "description": "An entry with dataset sample object associations.",
             "properties": {
@@ -16185,10 +16170,10 @@
                 "data_provider",
                 "internal"
             ],
-            "title": "HighThroughputExpressionDatasetSampleAnnotation",
+            "title": "HTPExpressionDatasetSampleAnnotation",
             "type": "object"
         },
-        "HighThroughputExpressionDatasetSampleAnnotationDTO": {
+        "HTPExpressionDatasetSampleAnnotationDTO": {
             "additionalProperties": false,
             "description": "An entry with dataset sample object associations.",
             "properties": {
@@ -16325,9 +16310,24 @@
                 "data_provider_dto",
                 "internal"
             ],
-            "title": "HighThroughputExpressionDatasetSampleAnnotationDTO",
+            "title": "HTPExpressionDatasetSampleAnnotationDTO",
             "type": "object"
         },
+        "HighThroughputExpressionAssayValues": {
+            "description": "",
+            "enum": [
+                "MMO:0000659",
+                "MMO:0000648",
+                "MMO:0000650",
+                "MMO:0000649",
+                "MMO:0000664",
+                "MMO:0000666",
+                "MMO:0000000",
+                "MMO:0000862"
+            ],
+            "title": "HighThroughputExpressionAssayValues",
+            "type": "string"
+        },
         "Identifier": {
             "additionalProperties": false,
             "description": "",
@@ -16747,13 +16747,13 @@
                 },
                 "high_throughput_expression_dataset_annotation_ingest_set": {
                     "items": {
-                        "$ref": "#/$defs/HighThroughputExpressionDatasetAnnotationDTO"
+                        "$ref": "#/$defs/HTPExpressionDatasetAnnotationDTO"
                     },
                     "type": "array"
                 },
                 "high_throughput_expression_dataset_sample_annotation_ingest_set": {
                     "items": {
-                        "$ref": "#/$defs/HighThroughputExpressionDatasetSampleAnnotationDTO"
+                        "$ref": "#/$defs/HTPExpressionDatasetSampleAnnotationDTO"
                     },
                     "type": "array"
                 },
@@ -26449,13 +26449,13 @@
         },
         "high_throughput_expression_dataset_annotation_ingest_set": {
             "items": {
-                "$ref": "#/$defs/HighThroughputExpressionDatasetAnnotationDTO"
+                "$ref": "#/$defs/HTPExpressionDatasetAnnotationDTO"
             },
             "type": "array"
         },
         "high_throughput_expression_dataset_sample_annotation_ingest_set": {
             "items": {
-                "$ref": "#/$defs/HighThroughputExpressionDatasetSampleAnnotationDTO"
+                "$ref": "#/$defs/HTPExpressionDatasetSampleAnnotationDTO"
             },
             "type": "array"
         },

diff --git a/model/schema/highThroughputExpression.yaml b/model/schema/highThroughputExpression.yaml
@@ -40,7 +40,7 @@ emit_prefixes:
 
 classes:
 
-  HighThroughputExpressionDatasetAnnotation:
+  HTPExpressionDatasetAnnotation:
     is_a: AuditedObject
     description: >-
       An entry for a published high-throughput expression dataset annotation.
@@ -68,7 +68,7 @@ classes:
         description: >-
           The list of publications associated with this dataset
 
-  HighThroughputExpressionDatasetAnnotationDTO:
+  HTPExpressionDatasetAnnotationDTO:
     is_a: SubmittedObjectDTO
     description: >-
       A DTO entry for a published high-throughput expression dataset annotation.
@@ -98,7 +98,7 @@ classes:
         description: >-
           The list of publications associated with this dataset
 
-  HighThroughputExpressionDatasetSampleAnnotation:
+  HTPExpressionDatasetSampleAnnotation:
     is_a: SubmittedObject
     description: >-
      An entry with dataset sample object associations.
@@ -149,7 +149,7 @@ classes:
             At least htp_expression_sample_id, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated OR
             at least htp_expression_sample_title, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated
 
-  HighThroughputExpressionDatasetSampleAnnotationDTO:
+  HTPExpressionDatasetSampleAnnotationDTO:
     is_a: SubmittedObjectDTO
     description: >-
      An entry with dataset sample object associations.
@@ -336,13 +336,13 @@ slots:
   abundance: # abundance in agr_schemas json
     description: >-
       The free text describing the amount of sample used
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: string
 
   assembly_versions: # assemblyVersions in agr_schemas json
     description: >-
       single or paired end sequencing; might be better in experiment info
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: string
     multivalued: true
 
@@ -377,15 +377,15 @@ slots:
   category_tags:
     description: >-
       A list of controlled vocabulary terms to describe the experiment
-    domain: HighThroughputExpressionDatasetAnnotation
+    domain: HTPExpressionDatasetAnnotation
     range: VocabularyTerm
     multivalued: true
     required: true
 
   category_tag_names:
     description: >-
       A list of controlled vocabulary terms to describe the experiment
-    domain: HighThroughputExpressionDatasetAnnotationDTO
+    domain: HTPExpressionDatasetAnnotationDTO
     range: string
     multivalued: true
     required: true
@@ -407,21 +407,21 @@ slots:
   dataset_ids: # datasetIds in agr_schemas datasetSampleAnnotation.json
     description: >-
       list of primary dataset ids that a sample is associated with
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: uriorcurie
     multivalued: true
 
   genomic_information: # genomicInformation in agr_schemas datasetSampleAnnotation.json
     description: >-
       A collection of information that represents the strain or genomic background of the sample, either an id or free text
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: BioSampleGenomicInformation
 
   genomic_information_dto: # genomicInformation in agr_schemas datasetSampleAnnotation.json
     description: >-
       A collection of information that represents the strain or genomic background of the sample, either an id or free text
     inlined: true
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: BioSampleGenomicInformationDTO
 
   htp_expression_dataset: # datasetId in agr_schemas datasetAnnotation.json
@@ -440,20 +440,20 @@ slots:
   htp_expression_sample_age: # sampleAge in agr_schemas json
     description: >-
       a collection of terms that when used together represent the age and stage of the sample
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: BioSampleAge
 
   htp_expression_sample_age_dto: # sampleAge in agr_schemas json
     description: >-
       a collection of terms that when used together represent the age and stage of the sample
     inlined: true
-    domain: HighThroughputExpressionDatasetSampleAnnotationDTO
+    domain: HTPExpressionDatasetSampleAnnotationDTO
     range: BioSampleAgeDTO
 
   htp_expression_sample:
     description: >-
       The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: ExternalDataBaseEntity
     multivalued: false
     required: false
@@ -462,15 +462,15 @@ slots:
     description: >-
       The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId
     inlined: true
-    domain: HighThroughputExpressionDatasetSampleAnnotationDTO
+    domain: HTPExpressionDatasetSampleAnnotationDTO
     range: ExternalDataBaseEntityDTO
     multivalued: false
     required: false
 
   htp_expression_sample_locations: # sampleLocations in agr_schemas json
     description: >-
       A collection of terms that when used together represents the location within an organism from which the sample was taken
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: AnatomicalSite
     multivalued: true
 
@@ -479,47 +479,47 @@ slots:
       A collection of terms that when used together represents the location within an organism from which the sample was taken
     inlined: true
     inlined_as_list: true
-    domain: HighThroughputExpressionDatasetSampleAnnotationDTO
+    domain: HTPExpressionDatasetSampleAnnotationDTO
     range: AnatomicalSiteDTO
     multivalued: true
 
   htp_expression_sample_title: # sampleTitle in agr_schemas json
     description: >-
       The free text title of the sample
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: string
 
   htp_expression_sample_type: # sampleType in agr_schemas json
     description: >-
       Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below.
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: OBITerm
     required: true
 
   htp_expression_sample_type_curie: # sampleType in agr_schemas json
     description: >-
       Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below.
-    domain: HighThroughputExpressionDatasetSampleAnnotationDTO
+    domain: HTPExpressionDatasetSampleAnnotationDTO
     range: string
     required: true
 
   microarray_sample_details: # microarraySampleDetails in agr_schemas datasetSampleAnnotation.json
     description: >-
       collection of information that is specific for microarray samples
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: MicroarraySampleDetails
 
   microarray_sample_details_dto: # microarraySampleDetails in agr_schemas datasetSampleAnnotation.json
     description: >-
       collection of information that is specific for microarray samples
     inlined: true
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: MicroarraySampleDetails
 
   number_of_channels:
     description: >-
       For microarrays, the number of channels used; This can be one of two values: 1 or 2
-    domain: HighThroughputExpressionDatasetAnnotation
+    domain: HTPExpressionDatasetAnnotation
     range: integer
     multivalued: false
     required: false
@@ -545,7 +545,7 @@ slots:
   sequencing_format: # sequencingFormat in agr_schemas json
     description: >-
       single or paired end sequencing; might be better in experiment info
-    domain: HighThroughputExpressionDatasetSampleAnnotation
+    domain: HTPExpressionDatasetSampleAnnotation
     range: VocabularyTerm # accepted values: 'single' OR 'paired'
 
   stage:
@@ -564,7 +564,7 @@ slots:
   sub_series:
     description: >-
       If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset
-    domain: HighThroughputExpressionDatasetAnnotation
+    domain: HTPExpressionDatasetAnnotation
     range: uriorcurie
     multivalued: true
     required: false

diff --git a/model/schema/ingest.yaml b/model/schema/ingest.yaml
@@ -332,14 +332,14 @@ slots:
 
   high_throughput_expression_dataset_annotation_ingest_set:
     domain: Ingest
-    range: HighThroughputExpressionDatasetAnnotationDTO
+    range: HTPExpressionDatasetAnnotationDTO
     multivalued: true
     mixins:
       - object_set
 
   high_throughput_expression_dataset_sample_annotation_ingest_set:
     domain: Ingest
-    range: HighThroughputExpressionDatasetSampleAnnotationDTO
+    range: HTPExpressionDatasetSampleAnnotationDTO
     multivalued: true
     mixins:
       - object_set