Feature/ebi search dump migration #332
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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
mberacochea
approved these changes
Jan 25, 2024
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| sample_metadata = {} | ||
| for sample_metadata_entry in analysis.sample.metadata.all(): | ||
| if (vn := sample_metadata_entry.var.var_name) in sample_annotations_to_index: |
| if page.number > mp: | ||
| logger.warning("Skipping remaining pages") | ||
| break | ||
| logger.info(f"Dumping {page.number = }/{paginated_analyses.num_pages}") |
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Typo?
Suggested change
| logger.info(f"Dumping {page.number = }/{paginated_analyses.num_pages}") | |
| logger.info(f"Dumping {page.number}/{paginated_analyses.num_pages}") |
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This one wasn't actually a typo, this is just the short-hand f string syntax typically useful in logs to print var names along with values, i.e. outputs
Dumping page.number=1/999
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This PR:
last_updatedfields be auto-nows. This is so that if the object changes, it'll be included in the next incremental EBI Search indexing.