Adding reference spec to config

[manasaV3]

Motivation

In some cases, to establish the relationships between entities we will not be able to use the entity defined in the config, and will have to reference an entity created by a different deposition. We need to define an alternative option than the destination_glob_finder for referencing those, as globbing for them might not always be able to reliably produced the expected result. This can be see in cases, where we need to reference entities with ids.

Notes on ref_spec:

The ref_spec should not be required. It should only be added for cases where the entity defined by the config is not to be used.
Recommended structure for the reference spec:

  <name_of_entity>_ref_spec:
  - key: foo
     value: bar
  - key: hello
     value: world

Definition of Done

1. The metadata configs for alignment, tomograms, annotation can support an optional reference spec for their relevant entities.
2. Any configs that is a deposition of tomogram or annotation has the reference_spec defined to point to the relevant alignment.

Tasks

alignments

• Add optional tiltseries_ref_spec to alignments config metadata.
• For configs where there are no tiltseries, but require an alignment to be defined, we should create a tiltseries_ref_spec with key=deposition_id and value=deposition which has the relevant tiltseries
• Update the templates

To be defined: How should default config handle this

tomogram

• Add optional alignment_ref_spec to tomogram config metadata.
• For configs where an existing alignment should be referenced, an alignment_ref_spec with key=deposition_id and value=deposition which has the relevant alignment
• Update the templates

annotation

• Add optional alignment_ref_spec to annotation config metadata.
• For configs where an existing alignment should be referenced, an alignment_ref_spec with key=deposition_id and value=deposition which has the relevant alignment
• Update the templates

[manasaV3]

This is no longer needed, as it was confirmed with @uermel that if a deposition config will only contain an alignment entity or voxelspacing entity that is related to its tomograms and annotations.