validator and ingestor to scicat for pizza ontology

Example/ingest_to_scicat.py

@@ -31,8 +31,8 @@ class SciCatClient:
 
 if __name__ == "__main__":
     SCICAT_API_URL = "http://scicat-rockit-p65-test1.desy.de/api/v3"
-    TOKEN = ""
-    
+    TOKEN = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJfaWQiOiI2NTAxN2M1ODY4Yjg4NWVlMzJkYWQ4YzgiLCJ1c2VybmFtZSI6ImluZ2VzdG9yIiwiZW1haWwiOiJzY2ljYXRpbmdlc3RvckB5b3VyLnNpdGUiLCJhdXRoU3RyYXRlZ3kiOiJsb2NhbCIsIl9fdiI6MCwiaWQiOiI2NTAxN2M1ODY4Yjg4NWVlMzJkYWQ4YzgiLCJpYXQiOjE3MTgyNzc1MzMsImV4cCI6MTcxODMyMDczM30.QV7unKhciguIFsbv-f8A3FQewh93Bue2xGUjFoBckJk"
+
     dataset_metadata = {
         "principalInvestigator": "Dr. John Doe",
         "owner": "Institution Name",

Example/validate_and_ingest.py

+from linkml.validator import validate
+from ingest_to_scicat import SciCatClient
+import yaml
+import requests
+# instance ={'pizzas' :  
+#       [{"id": "1",
+#       "title": "Margherita",
+#       "description": "Classic pizza with tomato sauce and mozzarella cheese.",
+#       "hasBase": ["ThinAndCrispyBase"],
+#       "hasTopping": ["MozzarellaTopping", "SlicedTomatoTopping"],
+#       "hasCountryOfOrigin": ["Italy"]}],
+#     }
+with open('pizza_dataset.yaml') as yaml_data:
+    instance = yaml.safe_load(yaml_data)
+
+
+report = validate(instance, "pizza.yaml", "PizzaCollection")
+SCICAT_API_URL = "http://scicat-rockit-p65-test1.desy.de/api/v3"
+TOKEN = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJfaWQiOiI2NTAxN2M1ODY4Yjg4NWVlMzJkYWQ4YzgiLCJ1c2VybmFtZSI6ImluZ2VzdG9yIiwiZW1haWwiOiJzY2ljYXRpbmdlc3RvckB5b3VyLnNpdGUiLCJhdXRoU3RyYXRlZ3kiOiJsb2NhbCIsIl9fdiI6MCwiaWQiOiI2NTAxN2M1ODY4Yjg4NWVlMzJkYWQ4YzgiLCJpYXQiOjE3MTg2MTU4NTYsImV4cCI6MTcxODY1OTA1Nn0.Zdcq8Qy93HnVBZBFb5DhnIn0Zq71FUwCmObXJSfCdZo"
+
+dataset_metadata = {
+        "principalInvestigator": "Dr. John Doe",
+        "owner": "Institution Name",
+        "contactEmail": "anjali@example.com",
+        "sourceFolder": "i am new",
+        "scientificMetadata":instance,
+        # "pid": "sdfsdfkjsdhfsd",
+        "size": 123456,
+        "creationLocation": "magrathea",
+        "creationTime": "2024-06-12T12:00:00Z",
+        "type": "raw",
+        "instrumentId": "Instrument001",
+        "proposalId": "Proposal001",
+        "dataFormat": "HDF5",
+        "isPublished": False,
+        "ownerGroup": "hasylab",
+        "accessGroups": ["Group001"],
+        "description": "Description of the dataset",
+        "keywords": ["example", "data", "keywords"],
+        "license": "CC BY 4.0"
+    }
+
+client = SciCatClient(SCICAT_API_URL, TOKEN)
+    
+if not report.results:
+    print('The instance is valid!')
+    try:
+        response = client.upload_dataset(dataset_metadata)
+        print("Dataset uploaded successfully:", response)
+    except requests.exceptions.HTTPError as err:
+        print("Error uploading dataset:", err)
+else:
+    for result in report.results:
+        print(result.message)
+

Example/validator.py

-from linkml.validator import validate
-
-instance ={'pizzas' :  
-      [{"id": "1",
-      "title": "Margherita",
-      "description": "Classic pizza with tomato sauce and mozzarella cheese.",
-      "hasBase": ["ThinAndCrispyBase"],
-      "hasTopping": ["MozzarellaTopping", "SlicedTomatoTopping"],
-      "hasCountryOfOrigin": ["Italy"]}],
-    }
-
-report = validate(instance, "pizza.yaml", "PizzaCollection")
-
-if not report.results:
-    print('The instance is valid!')
-else:
-    for result in report.results:
-        print(result.message)
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