add some linkml dev notes

Author: elichad

rocrate_validator/profiles/workflow-ro-crate-linkml/notes.md

@@ -0,0 +1,37 @@
+# Development notes for LinkML Workflow RO-Crate profile
+
+## Setup
+1. Create a folder for the profile under `rocrate_validator/profiles`
+1. Copy across `profile.ttl` from another profile & update that metadata for the new profile.
+    In particular, change the token for the profile to a new and unique name, e.g.
+    `prof:hasToken "workflow-ro-crate-linkml"`. This is the name which can be used to 
+    select the profile using `--profile-identifier` argument
+1. Create a `profile-name.yaml` file - this is where you will write the LinkML.
+1. Create a test folder for the profile under `tests/integration/profiles`
+1. Copy the style of other profiles' tests to build up a test suite for the profile.
+   Add any required RO-Crate test data under `tests/crates/` and create corresponding 
+   classes in `tests/ro_crates.py` which can be used to fetch the data during the tests
+
+## Converting LinkML to SHACL
+
+```
+linkml generate shacl --include-annotations --non-closed workflow-ro-crate.yaml > workflow-ro-crate.ttl
+```
+
+## Error message "The requirement check cannot be None"
+
+Occurred intermittently when running the validator on test cases - the first run would be fine, but later runs would then have this error. It's something to do with how the SHACL checks are instantiated in Python. Maybe a caching issue? 
+
+Resolved by ensuring generated SHACL uses non-closed shapes (which should be the case in most profiles?) Not sure why this works.
+
+``` 
+[2024-10-10 15:22:13,315] WARNING in models: Unexpected error during check <rocrate_validator.requirements.shacl.checks.SHACLCheck object at 0x7f4e2195aea0> - PropertyShape -        
+ mainEntity of Main Workflow entity existence: Check if the Main Workflow is specified through a `mainEntity` property in the root data entity (2807297706545425892) - PropertyShape - mainEntity of     
+ Main Workflow entity existence: Check if the Main Workflow is specified through a `mainEntity` property in the root data entity (2807297706545425892).  Exception: The requirement check cannot be      
+ None                                                                                                                                                                                                 
+ [2024-10-10 15:22:13,316] WARNING in models: Consider reporting this as a bug.                                                                                                     
+ [2024-10-10 15:22:13,629] WARNING in models: Unexpected error during check <rocrate_validator.requirements.shacl.checks.SHACLCheck object at 0x7f4e2195acf0> - PropertyShape -        
+ mainEntity of RootDataEntity: Check if the Main Workflow is specified through a `mainEntity` property in the root data entity (2807297706545425892) - PropertyShape - mainEntity of RootDataEntity:     
+ Check if the Main Workflow is specified through a `mainEntity` property in the root data entity (2807297706545425892).  Exception: The requirement check cannot be None                              
+ [2024-10-10 15:22:13,629] WARNING in models: Consider reporting this as a bug.    
+ ```