Create sample database queries

[billingross]

Create queries corresponding to the following triggers:

• [x] RelateFastqToReadGroup
• [x] RelateReadGroupToSample
• [x] RelateFastqMatePair

[billingross]

When defining queries, strings must all be on a single line. For instance, the Cypher string cannot be split over multiple lines or else the yaml module will not read it the query document.

[billingross]

Error:

KeyError: "> db-query: Database query 'relateFastqToReadGroup' is not available. Check that is has been added to config/database-queries.yaml."

Love to see my own error messages. For some reason db-query is not reading my database queries. From the previous line:

> db-query: Defined queries: dict_keys([]).

Testing the logic locally...

[billingross]

I made a test script. This is the whole script:

#!/usr/bin/env python3

import yaml
import trellisdata

with open("database-queries.yaml", 'r') as file_handle:
    queries_document = file_handle.read()
queries = yaml.load_all(queries_document, Loader=yaml.FullLoader)

QUERY_DICT = {}
for query in queries:
    QUERY_DICT[query.name] = query
print(QUERY_DICT)

And everything works fine. This is the logic I copy-pasted from db-query. So now my thought is that either

• there is other logic that is interfering with this
• there is some weird state issue where the database-queries.yaml file is not being updated

I've turned on the DEVELOPMENT flag for this function so that it gets a new copy of the database-queries.yaml file every time.

[billingross]

Alright, now I've got a new error so I think it was just an issue of the state not being updated. Turn on DEVELOPMENT when doing development, noted.