Deleted paths are not present in the indication_paths.yaml but still appear on the web page

[TanskaAnnna]

The deprecated_ids.txt file has this Graph ID added:DB00792_MESH_D065631_2 and this graph is not present in the indication_paths.yaml, but it is displayed on the web page: https://sulab.github.io/DrugMechDB/db00792-mesh-d065631-2.html. I don’t think this should happen.

[andrewsu]

It appears that the section responsible for deleting webpages for deprecated IDs is here https://github.com/SuLab/DrugMechDB/blob/main/parse.py#L112

However, it also appears that this block of code is within the loop for parsing the YAML file https://github.com/SuLab/DrugMechDB/blob/main/parse.py#L94, so it appears that files will only be deleted if the relevant path ID is in deprecated_ids.txt and there is an entry for the path in indication_paths.yaml. If this diagnosis is right, the fix should be to move the deletion block outside of the main data parsing loop. (@TanskaAnnna you could try the short-term fix to add a dummy entry back into indication_paths.yaml for DB00792_MESH_D065631_2, then merging, then deleting the dummy entry...)

[TanskaAnnna]

@andrewsu this is what I've tried: currently there is only one entry for DB00792_MESH_D065631 path in the indication_paths.yaml. I added another DB00792_MESH_D065631 path to the indication_paths.yaml to create DB00792_MESH_D065631_2. Instead of getting DB00792_MESH_D065631_2 in the indication_paths.yaml a path DB00792_MESH_D065631_3 was created. Then I managed to successfully delete that DB00792_MESH_D065631_3 path form the indication_paths.yaml and it does not appear in the webpage either. However I have no idea how to delete path DB00792_MESH_D065631_2. Maybe I should delete the DB00792_MESH_D065631_2 from the deprecated_ids.txt to be able to create one in the indication_paths.yaml?