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Dagster and referential integrity notebook generate alldocs collection in different ways #696

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Tracked by #318
eecavanna opened this issue Sep 20, 2024 · 2 comments · May be fixed by #786
Open
Tracked by #318

Dagster and referential integrity notebook generate alldocs collection in different ways #696

eecavanna opened this issue Sep 20, 2024 · 2 comments · May be fixed by #786
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@eecavanna
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eecavanna commented Sep 20, 2024 •
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There is some code in the ref integrity notebook that looks similar to your first commit, but batches the write operations to mongo. It is fairly performant (~30 sec with functional annotation) and uses LinkML's native schemaview to get all class ancestors for each doc.

for coll_name in collection_names:
    pbar.set_description(f"processing {coll_name}...")
    requests = []
    for doc in mdb[coll_name].find():
        doc_type = doc_cls(doc, coll_name=coll_name)
        slots_to_include = ["id"] + document_reference_ranged_slots[doc_type]
        new_doc = pick(slots_to_include, doc)
        new_doc["type"] = schema_view.class_ancestors(doc_type)
        requests.append(InsertOne(new_doc))
        if len(requests) == 1000: # ensure bulk-write batches aren't too huge
            result = mdb.alldocs.bulk_write(requests, ordered=False)
            pbar.update(result.inserted_count)
            requests.clear()
    if len(requests) > 0:
        result = mdb.alldocs.bulk_write(requests, ordered=False)
        pbar.update(result.inserted_count)
pbar.close()

Could you use this logic instead? It is fairly similar to your first commit

Originally posted by @PeopleMakeCulture in #694 (comment)
@eecavanna eecavanna mentioned this issue Sep 26, 2024
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@eecavanna
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As discussed on Slack, I'm thinking of there being a helper function (a.k.a. a "util" function) that generates the alldocs collection (I called this function "compile_alldocs_collection" in the diagram below). The Dagster op and the bulk referential integrity validation notebook would then each "import" that helper function insteading of having their own local implementation (which could fall "out of sync" with the other's over time).

image

@PeopleMakeCulture PeopleMakeCulture mentioned this issue Nov 13, 2024
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@PeopleMakeCulture PeopleMakeCulture self-assigned this Nov 19, 2024
@PeopleMakeCulture PeopleMakeCulture moved this to On stage in Polyneme mixset Nov 19, 2024
@mkshah605 mkshah605 linked a pull request Nov 21, 2024 that will close this issue
Work In Progress - 696 compile alldocs collection util #786
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@dwinston dwinston mentioned this issue Nov 26, 2024
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@eecavanna @PeopleMakeCulture appears to still be in progress. I'll move to the next sprint. FYI @dwinston

@dwinston dwinston mentioned this issue Nov 27, 2024
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2024 - Sprint 51 - December 2 - 13, 2024
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Work In Progress - 696 compile alldocs collection util microbiomedata/nmdc-runtime
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