EVA-1063 - Populate a default locus range (for use in Variant Browser) for a given species #155
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| { | ||
| "$group": { | ||
| "_id": None, | ||
| "topChrStartPick": {"$first": "$$ROOT"} |
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Are the 2 last stages making something different than ..., {"$sort": {"num_entries": -1}}, {"$limit:1}]?
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I was not sure if $limit guarantees ordering or it retrieves just one entry at random so I opted for $first. But looks like limit() does honor the order. so I will change this....
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yep, also a great optimization will be done:
When a $sort precedes a $limit and there are no intervening stages that modify the number of documents, the optimizer can coalesce the $limit into the $sort. This allows the $sort operation to only maintain the top n results as it progresses, where n is the specified limit, and ensures that MongoDB only needs to store n items in memory. This optimization still applies when allowDiskUse is true and the n items exceed the aggregation memory limit.
| from pymongo import MongoClient | ||
| from __init__ import * | ||
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| DEFAULT_LOCUS_RANGE_COLLECTION_NAME = "defaultLocusRange" |
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good idea. I assume you plan to make this available through some new webservice to un-hardcode it from the website?
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Yes. I intend to add a separate end point /default-locus-range similar to /annotation for a given species.
| import configparser | ||
| import urllib.parse | ||
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| from pymongo import MongoClient |
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can you add a requirements.txt and readme for installing the dependencies?
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