Add run_checks method to checks module

[doulikecookiedough]

We would like to be able to run checks in python without spinning up the java engine (and going through the dispatcher).

In the checks module, add a new function run_checks that can take a check and the desired document and return an output. There may be checks where multiple output and statuses are returned, so we may want to consider returning a dictionary.

[doulikecookiedough]

Greetings @jeanetteclark, I was able to get the run_check pytest working successfully! I ended up refactoring some pytests as well, and running pytest will now execute all tests successfully in the feature-13-runcheck branch. What's left to do is code clean-up, and also returning a dictionary of the results.

Also, do you happen to have a python check handy that will run and return more than one result? I may not fully understand that process - but I will look for a check after I've wrapped up my to-do items.

In terms of making checks easier to test, I suggest that we create a metadig command line client - similar to how we have one for hashstore, which gets installed when we execute poetry install. It will take arguments which will run the run_check function - I imagine the process to test a check to look something like this:

# Check-out hashstore and install it
$ cd ~/Code/hashstore
~/Code/hashstore $ poetry install 

# Create a HashStore at your desired store path (ex. /docs/dou/hashstore)
~/Code/hashstore $ hashstore /path/to/store/ -chs -dp=3 -wp=2 -ap=SHA-256 -nsp=\"http://www.ns.test/v1\"

# Store data object and associated metadata documents for the check
~/Code/hashstore $ hashstore /path/to/store/ -storeobject -pid=persistent_identifier -path=/path/to/object\n~/Code/hashstore
~/Code/hashstore $ hashstore /path/to/store/ -storemetadata -pid=persistent_identifier -path=/path/to/metadata/object -formatid=https://ns.dataone.org/service/types/v2.0#SystemMetadata

# Run check
# `store_path` will be used to retrieve the hashstore location and get `StoreManager` properties
# `data_pids` will pass the data pids to run the checks against
# A `check_vars` dictionary will be created to be passed onto `run_check` in the metadig client
$ cd ~/Code/metadig-py
~/Code/metadig-py $ metadig -runcheck -store_path=/path/to/store -check_xml=path/to/check/xml/check.xml -eml_doc=path/to/eml/metadata/doc data_pids=[array,of,pids]

# Results will be printed to stdout

If this sounds good to you, I can add that as part of this feature branch (or I could also create a new sub-issue for it).