search

SD2E / opil

The Open Protocol Interface Language (OPIL) is intended as a standard language for protocol interfaces
5 stars 1 forks source link

Name not set for Strateos Parameters #182

Open tramyn opened 3 years ago

tramyn commented 3 years ago

This is a feature request to add names to opil.Parameters when converting from a strateos protocol to opil. Intent Parser need names (human readable names), instead of IDs when displaying tables to a Document for users to specify information about a protocol. When IP iterate through these opil.Parameters, IP is picking up parameters without the name field set. It will be valuable for IP to have this feature supported. Refer to CellFreeRiboswitches as an example.

bbartley commented 3 years ago

I think this was a result of the autogeneration code getting confused about sbol:name vs opil:name. The problem originated in the sbol_factory code and was fixed in SynBioDex/sbol_factory@aea0e2f5a05281f3ba090ebc70f17a44ab6f9bde. A test has been added in OPIL here: 48014d1a1a423b4e6201099a3ade7bbcf8d43627.

I'm going to go ahead and close this. The fix will be included in the next release 1.0b5

bbartley commented 3 years ago

There is an ontology issue which results in the opil:name property only being created on Parameter objects. All other opil objects default to sbol:name. It is difficult to solve this issue without introducing into the ontology an OPIL base class to affix the opil:name to.