NSLS2 / NSLS2/isstools

Exercise on new db

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Dominant language
Python
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7
Forks
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PR merge metrics
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Description

today's exercise:

  • Generate a 'start' document with some metadata about a spectrum, an 'event' document with the spectrum, and the other required documents.
  • Insert them into a development, disposable MongoDB database (mongodb://xf08id-ca1:27017/dev_analyzed_data).
  • Access the saved metadata and data (as xarray.Dataset).
  • Search for the saved spectra based on recency, element metadata, and E0 metadata.

The following needs to be wrapped into an easy-to-use function:

from event_model import compose_run
compose_run()
compose_run?
bundle = compose_run(metadata={'Sample_name': 'Pt', 'compound': 'Pt', 'Element' : 'Pt', 'Edge' : 'L3', 'E0': 11564})
bundle
bundle.start_doc
from suitcase.mongo_normalized import Serializer
ser = Serializer('mongodb://xf08id-ca1:27017/dev_analyzed_data', 'mongodb://xf08id-ca1:27017/dev_analyzed_data')
ser
ser('start', bundle.start_doc)
bundle.compose_descriptor(data_keys={'Energy' : {'dtype' : 'array', 'source' : '', 'shape' : [-1]},''})
bundle.compose_descriptor(data_keys={'Energy' : {'dtype' : 'array', 'source' : '', 'shape' : [-1]}, 'mu_norm' : {'dtype' : 'array', 'source' : '', 'shape' : [-1]}})
bundle2 = bundle.compose_descriptor(data_keys={'Energy' : {'dtype' : 'array', 'source' : '', 'shape' : [-1]}, 'mu_norm' : {'dtype' : 'array', 'source' : '', 'shape' : [-1]}}, name='primary')
bundle2
ser('descriptor', bundle2.descriptor_doc)
bundle2.compose_event(data={'Energy' : [1,2,3], 'mu_norm' : [0.1, 0.2, 0.3]}, timestamps={'Energy':0, 'mu_norm' : 0})
ser('event', _22)
bundle.compose_stop()
ser('stop', _24)
from databroker._drivers.mongo_normalized import BlueskyMongoCatalog
uri = "mongodb://xf08id-ca1:27017/dev_analyzed_data"
catalog = BlueskyMongoCatalog(uri, uri)
catalog
catalog[-1]
catalog[-1].primary
catalog[-1].primary.read()
len(catalog.search({'Element':'Pt'}))
len(catalog.search({'Element':'Co'}))
catalog[-1].metadata
len(catalog.search({'E0':{'$lt' : 10000}}))
len(catalog.search({'E0':{'$gt' : 10000}}))

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

The issue names compose_run, suitcase.mongo_normalized.Serializer, and databroker._drivers.mongo_normalized.BlueskyMongoCatalog as entry points, but identifies no repository file or test. Start by locating those APIs and define done as an easy-to-use function covering the document generation, MongoDB storage and access, and metadata searches described in the exercise.

Written by the indexing model from the issue text.

Assessment

Tech stack
mongodb, python
Domain
database
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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