Pattern merge - replace workflow¶
This document is on how to merge new DOSDP design patterns into an ODK ontology and then how to replace the old classes with the new ones.
1. You need the tables in tsv format with the DOSDP filler data. Download the tsv tables to¶
$ODK-ONTOLOGY/src/patterns/data/default/
Make sure that the tsv filenames match that of the relevant yaml DOSDP pattern files.
2. Add the new matching pattern yaml filename to¶
$ODK-ONTOLOGY/src/patterns/dosdp-patterns/external.txt
3. Import the new pattern templates that you have just added to the external.txt list from external sources into the current working repository¶
cd ODK-ONTOLOGY/src/ontology
sh run.sh make update_patterns
4. make definitions.owl¶
cd ODK-ONTOLOGY/src/ontology
sh run.sh make ../patterns/definitions.owl IMP=false
5. Remove old classes and replace them with the equivalent and patternised new classes¶
cd ODK-ONTOLOGY/src/ontology
sh run.sh make remove_patternised_classes
6. Announce the pattern migration in an appropriate channel, for example on the phenotype-ontologies Slack channel.¶
For example:
I have migrated the ... table and changed the tab colour to blue. You can delete the tab if you wish.