DSERV-570 Clickhouse Data Ingestion #329
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pedrohr
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pedrohr
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Oct 9, 2024
| # every collection has particular edge cases | ||
| # this is needed until we have all collections loaded | ||
| import pdb | ||
| pdb.set_trace() |
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for now, I thought about leaving this until we ingest all collections into Clickhouse. Every dataset has its own small edge cases and we will have to adapt to each one of them.
I can also remove this for the PR, please let me know your thoughts.
mingjiecn
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Oct 9, 2024
| inverse_name: str | ||
| biological_process: str | ||
| accessible_via: | ||
| name: e-qtls |
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unrelated question, what is name in accessible_via for?
mingjiecn
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Oct 9, 2024
data/db/clickhouse.py
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| 'to': relationship['to'] | ||
| } | ||
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| for s in clickhouse_schema: |
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Can you explain what does the code to here for relationship?
pedrohr
commented
Oct 17, 2024
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| temp_file_path = temp_file.name | ||
| onto = get_ontology(temp_file_path).load() | ||
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we are no longer going to download each ontology file on the fly. Each owl file will have to be passed individually
mingjiecn
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Oct 17, 2024
data/schema-config.yaml
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| from: sequence variant | ||
| to: protein | ||
| from: variants | ||
| to: proteins |
mingjiecn
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Oct 17, 2024
data/schema-config.yaml
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| @@ -281,8 +281,8 @@ transcribed to: | |||
| label_as_edge: TRANSCRIBED_TO | |||
| db_collection_name: genes_transcripts | |||
| relationship: | |||
| from: gene | |||
| to: transcript | |||
| from: genes | |||
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can also from mm_genes to mm_transcripts
mingjiecn
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Oct 17, 2024
| if data.get('_from') is not None and data.get('_to') is not None: | ||
| # removing collection prefix from _from and _to. E.g. genes/ENSG00000148584 => ENSG00000148584 | ||
| processed_data.append(data['_from'].split('/')[-1]) | ||
| processed_data.append(data['_to'].split('/')[-1]) |
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how do you figure out which collection to go if there are more than one collection in from or to?
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good catch, will look into this!
mingjiecn
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Oct 17, 2024
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Some thoughts:
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ottojolanki
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DSERV-541 Adding CA Ids to Variants
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