Test create-blob-node functionality

[billingross]

I want to write tests that I can run on the function while it is running on Google Cloud Platform.

Instead of maintaining different buckets for everything, I'd rather just use (1) bucket.

Test functionality:

• [x] Create a "fastq" object
• [x] Generate node query
• [x] Send it to a pubsub topic

[billingross]

Error:

mate_pair_name_0
    mate_pair = _search_string(
                ^^^^^^^^^^^^^^^
  File "/workspace/phase3/from-personalis/create-node-config.py", line 65, in _search_string
    pdb.set_trace()
    ^^^
NameError: name 'pdb' is not defined. Did you forget to import 'pdb'

I am using a dummy Fastq named trellis-v2-from-personalis/va_mvp_phase2/plate0/sample0/FASTQ/fastq0.fastq.gz and I think it is missing the required mate pair field which is throwing an error.

[billingross]

Error:

  File "/workspace/phase3/from-personalis/create-node-config.py", line 167, in read_group_name_1
    return {'readGroup': int(index)}
                       ^^^^^^^^^^
ValueError: invalid literal for int() with base 10: 'R1'

Realizing that I need to add read group and mate pair as separate elements in the Fastq name. For example: fastq_0_R1.fastq.gz where 0 indicates the read group and R1 indicates the mate pair.

[billingross]

Error:

  File "/workspace/main.py", line 381, in create_node_query
    logging.info(f"> Topic: {TRELLIS['TOPIC_DB_QUERY']}, message: {message}.")
                             ~~~~~~~^^^^^^^^^^^^^^^^^^
KeyError: 'TOPIC_DB_QUERY'

Need to add TOPIC_DB_QUERY to trellis-configuration.yaml.