Added enzymatic tissue dissociation fields

docs/jsonBrowser/type.md

@@ -190,7 +190,11 @@ schema_type | The type of the metadata schema entity. | string | yes |  |  | pro
 provenance | Provenance information provided by the system. | object | no | [See   provenance](.md#provenance) |  |  | 
 protocol_core | Core protocol-level information. | object | yes | [See core  protocol_core](core.md#protocol-core) | Protocol core |  | 
 method | How cells or organelles were dissociated. | object | yes | [See module  process_type_ontology](module.md#process-type-ontology) | Dissociation method |  | 
-reagents | A list of purchased reagents used in this protocol. | array | no | [See module  purchased_reagents](module.md#purchased-reagents) | Protocol reagents |  | 
+reagents | A list of purchased reagents used in this protocol. | array | no | [See module  purchased_reagents](module.md#purchased-reagents) | Purchased reagents |  | 
+digestion_time | Time of digestion of the specimen. | integer | no |  | Digestion time |  | 2; 5; 10
+digestion_time_unit | The unit in which the digestion time is expressed. | object | no | [See module  time_unit_ontology](module.md#time-unit-ontology) | Digestion time unit |  | 
+digestion_temperature | Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature). | number or string | no |  | Digestion temperature | frozen, cold, room temperature, warm | 4; 37; cold
+digestion_solution | Enzyme(s) or reagent(s) of the solution that was used for the digestion of the specimen. | array | no |  | Digestion solution | Citric-acid based, Detergent-based, Lysis buffer, Accutase, Collagenase, Collagenase A, Collagenase D, Collagenase I, Collagenase II, Collagenase IV, Dispase, Dispase II, DNAse I, Elastase, Hyaluronidase, Liberase, Papain, Protease, TrypLE, Trypsin | 
 
 ## iPSC induction protocol
 _Information about how a biomaterial is treated to become an induced pluripotent stem cell._

json_schema/type/protocol/biomaterial_collection/dissociation_protocol.json

@@ -54,7 +54,63 @@
                 "type": "object",
                 "$ref": "module/process/purchased_reagents.json"
             },
-            "user_friendly": "Protocol reagents"
+            "user_friendly": "Purchased reagents"
+        },
+        "digestion_time": {
+            "description": "Time of digestion of the specimen.",
+            "type": "integer",
+            "example": "2; 5; 10",
+            "user_friendly": "Digestion time"
+        },
+        "digestion_time_unit": {
+            "description": "The unit in which the digestion time is expressed.",
+            "type": "object",
+            "$ref": "module/ontology/time_unit_ontology.json",
+            "user_friendly": "Digestion time unit"
+        },
+        "digestion_temperature": {
+            "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature).",
+            "oneOf": [
+                {
+                    "type": "number"
+                },
+                {
+                    "type": "string",
+                    "enum": ["frozen", "cold", "room temperature", "warm"]        
+                }
+            ],
+            "example": "4; 37; cold",
+            "user_friendly": "Digestion temperature"
+        },
+        "digestion_solution": {
+            "description": "Enzyme(s) or reagent(s) of the solution that was used for the digestion of the specimen.",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "enum": [
+                    "Citric-acid based",
+                    "Detergent-based",
+                    "Lysis buffer",
+                    "Accutase",
+                    "Collagenase",
+                    "Collagenase A",
+                    "Collagenase D",
+                    "Collagenase I",
+                    "Collagenase II",
+                    "Collagenase IV",
+                    "Dispase",
+                    "Dispase II",
+                    "DNAse I",
+                    "Elastase",
+                    "Hyaluronidase",
+                    "Liberase",
+                    "Papain",
+                    "Protease",
+                    "TrypLE",
+                    "Trypsin"
+                ]
+            },
+            "user_friendly": "Digestion solution"
         }
     }
 }

json_schema/update_log.csv

@@ -1 +1,6 @@
 Schema,Change type,Change message,Version,Date
+type/protocol/biomaterial_collection/dissociation_protocol,minor,Changed user_friendly name of reagent field,,
+type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time field,,
+type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time_unit field,,
+type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_temperature field,,
+type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_solution field,,

src/human_readable_json.py

@@ -116,6 +116,17 @@ def generateMarkdown(self, schemas, entity_type):
 
                     # if link is not "":
                     #     print(schema["title"] + "\t "+ property + "\t"+ link)
+
+                    # add type values if oneOf values are there
+                    oneOf_types = [t['type'] for t in schema['properties'][property]['oneOf'] if 'type' in t.keys()] if 'oneOf' in schema['properties'][property].keys() else []
+                    schema['properties'][property]['type'] = ' or '.join(oneOf_types) if 'type' not in schema['properties'][property].keys() else schema['properties'][property]['type']
+                    oneOf_enum = []
+                    if 'oneOf' in schema['properties'][property].keys():
+                        for t in schema['properties'][property]['oneOf']:
+                            if 'enum' in t.keys():
+                                oneOf_enum.extend(t['enum'])
+                    if oneOf_enum:
+                        schema['properties'][property]['enum'] = oneOf_enum if 'enum' not in schema['properties'][property].keys() else schema['properties'][property]['enum']
 
                     if "enum" in schema["properties"][property]:
                         enum_values = ", ".join(str(enum) for enum in schema["properties"][property]["enum"])

src/schema_linter.py

@@ -31,7 +31,7 @@
 
 # Property attributes
 
-property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'bionetworks']
+property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'oneOf', 'bionetworks']
 
 ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self']
 
@@ -138,20 +138,24 @@ def lintSchema(self, path, ols_api):
             if 'user_friendly' not in properties[property].keys() and property not in ['schema_version', 'schema_type', 'describedBy', 'provenance']:
                 if schema_filename not in ['links']:
                     errors.append(schema_filename + ".json: Keyword `user_friendly` missing from property `" + property + "`.")
-
+            
             # Property must contain type attribute
-            if 'type' not in properties[property].keys():
+            oneOf_types = [t['type'] for t in properties[property]['oneOf'] if 'type' in t.keys()] if \
+                    'oneOf' in properties[property].keys() else []
+            if 'type' not in properties[property].keys() and not oneOf_types:
                 errors.append(schema_filename + ".json: Keyword `type` missing from property `" + property + "`.")
 
             else:
+                # assign type value to the property key
+                properties[property]['type'] = oneOf_types if 'type' not in properties[property].keys() else properties[property]['type']
                 # change property to list to test all values of array
                 properties[property]['type'] = properties[property]['type'] if isinstance(properties[property]['type'], list) else [properties[property]['type']]
 
                 for property_type in properties[property]['type']:
                     # type attribute must be set to one of the valid JSON types
                     if property_type not in ["string", "number", "boolean", "array", "object", "integer", "null"]:
                         errors.append(schema_filename + ".json: Type `" + property_type + "` is not a valid JSON type.")
-
+                    
                     # Property of type array must contain the attribute items
                     if property_type == "array" and 'items' not in properties[property].keys():
                         errors.append(schema_filename + ".json: Property `" + property + "` is type array but doesn't contain items.")