43 update re iding process records to handle data objects wo data file description or url or with ID not found in the Database

[mbthornton-lbl]

This PR provides several updates to the commands in re_id_tool.py:

• Check for WorkflowRecords with orphand DataObject IDs in has_output and write to a failed_record_dump outfile
• Add option update-links to process records in order to test locally without filesystem changes
• Handle OmicsProcessing records with no has_output values
• Improved logging

Additionally this PR includes the results and logs for extract-records and process-records on:

• nmdc:sty-11-33fbta56 (Spruce)
• nmdc:sty-11-547rwq94 (EMP)
• nmdc:sty-11-076c9980 (Luquillo)
• nmdc:sty-11-dcqce727 (Crested Butte)

Workflows with an "orphan" data object ID (cannot be found in our DB or in any of the data_objects.json are written to a failed record dump, along with the rest of that Workflow's has_output data objects. If the failing Workflow is ReadQC, all workflows are failed.

[Michal-Babins]

Added methods to deal with unliked DO's and computing compliant file path. Extended Analysis activity set. Generated new data json dumps.

[Michal-Babins]

Implemented method to get has_input for legacy id, add method to fail omics processing record if DO is orphaned, added check for readbased analysis activity type.