Finalize full reindex procedure

[yuanzhou]

• Update the step-by-step guide in both README.md and the script help instructions
• Remove misleading print outputs at the end of each command run
• Add a new command to delete those flushYYYYMMDD_fresh_index_* indices AFTER catch-up

Edited on 11/09/2024, catch-up threw this error on PROD

[2024-11-09 12:55:42] INFO in hubmap_translator:1362: Start executing _call_indexer() on uuid: 12dcb9de1b1aa098fabaf7991fd3cf78, entity_type: Upload
[2024-11-09 12:55:42] INFO in hubmap_translator:632: Start executing direct 'entities' updates for entity['uuid']=12dcb9de1b1aa098fabaf7991fd3cf78, entity['entity_type']=Upload
[2024-11-09 12:55:42] INFO in hubmap_translator:1567: Start executing _generate_doc() for Upload of uuid: 12dcb9de1b1aa098fabaf7991fd3cf78 for the entities index group.
[2024-11-09 12:55:42] ERROR in hubmap_translator:1754: Exceptions during executing hubmap_translator._generate_doc()
Traceback (most recent call last):
  File "/usr/src/app/src/hubmap_translator.py", line 1691, in _generate_doc
    entity['ancestors'] = self._relatives_for_index_group(  relative_ids=ancestor_ids
UnboundLocalError: local variable 'ancestor_ids' referenced before assignment
[2024-11-09 12:55:42] ERROR in hubmap_translator:654: Exception document generation for uuid: 12dcb9de1b1aa098fabaf7991fd3cf78, entity_type: Upload for 'entities' reindex caused 'local variable 'ancestor_ids' referenced before assignment'
Traceback (most recent call last):
  File "/usr/src/app/src/hubmap_translator.py", line 1691, in _generate_doc
    entity['ancestors'] = self._relatives_for_index_group(  relative_ids=ancestor_ids
UnboundLocalError: local variable 'ancestor_ids' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/src/hubmap_translator.py", line 641, in _transform_and_write_entity_to_index_group
    private_doc = self._generate_doc(   entity=doc_entity
  File "/usr/src/app/src/hubmap_translator.py", line 1757, in _generate_doc
    raise Exception(e)
Exception: local variable 'ancestor_ids' referenced before assignment
[2024-11-09 12:55:42] ERROR in hubmap_translator:657: For Upload 12dcb9de1b1aa098fabaf7991fd3cf78, failed to generate document for consortium indices.
[2024-11-09 12:55:42] INFO in hubmap_translator:667: Unable to find 'entities' transformer, indexing documents untransformed.
[2024-11-09 12:55:42] ERROR in hubmap_translator:1375: Encountered exception e=local variable 'private_doc' referenced before assignment executing _call_indexer() with uuid: 12dcb9de1b1aa098fabaf7991fd3cf78, entity_type: Upload
Traceback (most recent call last):
  File "/usr/src/app/src/hubmap_translator.py", line 1367, in _call_indexer
    self._transform_and_write_entity_to_index_group(entity=entity
  File "/usr/src/app/src/hubmap_translator.py", line 668, in _transform_and_write_entity_to_index_group
    docs_to_write_dict[self.index_group_es_indices[index_group]['private']] = private_doc
UnboundLocalError: local variable 'private_doc' referenced before assignment
[2024-11-09 12:55:42] INFO in hubmap_translator:1195: Finished executing reindex_entity() on uuid: 12dcb9de1b1aa098fabaf7991fd3cf78