Describe the bug
The ingest graph validator does not properly recognise orphaned entities due to recent changes in ingest. Before, only certain entities were attached to projects - Now, biomaterials are linked to the project through the "PROJECTS" relationship, which has broken the test for No orphaned entities
Observe no matchs, but one of the donors is not actually linked to any other biomaterials so it should be returned
Expected behaviour
There should be at least 1 error, informing the user that they have an orphaned biomaterial.
Proposed solution
Since biomaterials are directly connected to the project, the easiest way is to change the query for this:
MATCH (n)
WHERE NOT EXISTS ((n)--(:process))
AND NOT (n:supplementary_file)
AND NOT (n:process)
RETURN n, "Entity does not have linkings with any other entity", labels(n)
This assumes that the only other entities to not be related to processes are processes themselves.
ESapenaVentura
commented
1 year ago
Describe the bug The ingest graph validator does not properly recognise orphaned entities due to recent changes in ingest. Before, only certain entities were attached to projects - Now, biomaterials are linked to the project through the "PROJECTS" relationship, which has broken the test for No orphaned entities
To Reproduce Steps to reproduce the behaviour:
ingest-graph-validator hydrate ingest 27302955-dd62-445c-8ba8-ad6346f8998b(May take a while)Expected behaviour There should be at least 1 error, informing the user that they have an orphaned biomaterial.
Proposed solution Since biomaterials are directly connected to the project, the easiest way is to change the query for this:
This assumes that the only other entities to not be related to processes are processes themselves.
Changing the query to search for any p
Environment
Browser