This is a WIP, but the analysis should be nearly done.

I've moved the logic for "Runs" of EBI Search Dump:
- Code that reads the analysis data from the DB and flat files -> https://github.com/EBI-Metagenomics/MetagenomicsSearchDump/blob/master/src/input/metagenomicsDB.py#L191
  - I've replaced the file reading bits with calls to Mongo / MySQL.  Which
    makes the code independent from the filesystem.
- Code that generates the xml output file for **one** analysis: https://github.com/EBI-Metagenomics/MetagenomicsSearchDump/blob/master/src/output/run.py

We need to port the Samples and Studies; and the analysis aggregation.

The aggregation is required to merge the analysis into XML bundles that EBI Search
ingest.

AnalysesAggregation script -> https://github.com/EBI-Metagenomics/MetagenomicsSearchDump/blob/master/src/RunEntryAggregator.py

Another task: Is to add a indexed_at field on Analyses, Samples and Studies.
This is going to be useful to have incremental dump generation, instead of
having to re-generate all the files. Moving to this will also required
the modification of the AnalysesAggregation script OR for us to move
to EBI Search incremental dumps (https://www.ebi.ac.uk/seqdb/confluence/display/EXT/Preparation+for+incremental+indexing)

Last one. EBI Search also supports JSONs (https://www.ebi.ac.uk/seqdb/confluence/display/EXT/JSON+data+format)

# Conflicts:
#	emgcli/__init__.py
#	pyproject.toml

# Conflicts:
#	emgapi/models.py
#	emgcli/__init__.py
#	pyproject.toml

# Conflicts:
#	emgcli/__init__.py
#	pyproject.toml

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