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wasadewasade
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RESTful sample status (#3139)
* TST: tests for the sample status end points * API: add sample status endpoints * Defensive assertion on detail maker * Address @antgonza's comments * Limit memory use when caching prep info
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‎qiita_pet/handlers/rest/__init__.py

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@@ -8,7 +8,9 @@
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from .study import StudyHandler, StudyCreatorHandler, StudyStatusHandler
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from .study_samples import (StudySamplesHandler, StudySamplesInfoHandler,
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StudySamplesCategoriesHandler)
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StudySamplesCategoriesHandler,
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StudySamplesDetailHandler,
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StudySampleDetailHandler)
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from .study_person import StudyPersonHandler
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from .study_preparation import (StudyPrepCreatorHandler,
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StudyPrepArtifactCreatorHandler)
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(r"/api/v1/study/([0-9]+)/samples/categories=([a-zA-Z\-0-9\.:,_]*)",
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StudySamplesCategoriesHandler),
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(r"/api/v1/study/([0-9]+)/samples", StudySamplesHandler),
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(r"/api/v1/study/([0-9]+)/samples/status", StudySamplesDetailHandler),
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(r"/api/v1/study/([0-9]+)/sample/([a-zA-Z\-0-9\.]+)/status",
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StudySampleDetailHandler),
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(r"/api/v1/study/([0-9]+)/samples/info", StudySamplesInfoHandler),
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(r"/api/v1/person(.*)", StudyPersonHandler),
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(r"/api/v1/study/([0-9]+)/preparation/([0-9]+)/artifact",

‎qiita_pet/handlers/rest/study_samples.py

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@@ -5,13 +5,123 @@
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#
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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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from collections import defaultdict
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from tornado.escape import json_encode, json_decode
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import pandas as pd
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from qiita_db.handlers.oauth2 import authenticate_oauth
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from .rest_handler import RESTHandler
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def _sample_details(study, samples):
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def detail_maker(**kwargs):
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base = {'sample_id': None,
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'sample_found': False,
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'ebi_sample_accession': None,
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'preparation_id': None,
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'ebi_experiment_accession': None,
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'preparation_visibility': None,
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'preparation_type': None}
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assert set(kwargs).issubset(set(base)), "Unexpected key to set"
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base.update(kwargs)
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return base
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# cache sample detail for lookup
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study_samples = set(study.sample_template)
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sample_accessions = study.sample_template.ebi_sample_accessions
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# cache preparation information that we'll need
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# map of {sample_id: [indices, of, light, prep, info, ...]}
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sample_prep_mapping = defaultdict(list)
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pt_light = []
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offset = 0
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incoming_samples = set(samples)
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for pt in study.prep_templates():
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prep_samples = set(pt)
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overlap = incoming_samples & prep_samples
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if overlap:
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# cache if any of or query samples are present on the prep
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# reduce accessions to only samples of interest
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accessions = pt.ebi_experiment_accessions
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overlap_accessions = {i: accessions[i] for i in overlap}
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# store the detail we need
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pt_light.append((pt.id, overlap_accessions,
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pt.status, pt.data_type()))
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# only care about mapping the incoming samples
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for ptsample in overlap:
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sample_prep_mapping[ptsample].append(offset)
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offset += 1
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details = []
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for sample in samples:
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if sample in study_samples:
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# if the sample exists
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sample_acc = sample_accessions.get(sample)
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if sample in sample_prep_mapping:
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# if the sample is present in any prep, pull out the detail
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# specific to those preparations
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for pt_idx in sample_prep_mapping[sample]:
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ptid, ptacc, ptstatus, ptdtype = pt_light[pt_idx]
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details.append(detail_maker(
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sample_id=sample,
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sample_found=True,
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ebi_sample_accession=sample_acc,
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preparation_id=ptid,
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ebi_experiment_accession=ptacc.get(sample),
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preparation_visibility=ptstatus,
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preparation_type=ptdtype))
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else:
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# the sample is not present on any preparations
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details.append(detail_maker(
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sample_id=sample,
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sample_found=True,
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# it would be weird to have an EBI sample accession
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# but not be present on a preparation...?
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ebi_sample_accession=sample_acc))
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else:
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# the is not present, let's note and move ona
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details.append(detail_maker(sample_id=sample))
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return details
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class StudySampleDetailHandler(RESTHandler):
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@authenticate_oauth
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def get(self, study_id, sample_id):
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study = self.safe_get_study(study_id)
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sample_detail = _sample_details(study, [sample_id, ])
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self.write(json_encode(sample_detail))
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self.finish()
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class StudySamplesDetailHandler(RESTHandler):
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@authenticate_oauth
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def post(self, study_id):
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samples = json_decode(self.request.body)
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if 'sample_ids' not in samples:
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self.fail('Missing sample_id key', 400)
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return
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study = self.safe_get_study(study_id)
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samples_detail = _sample_details(study, samples['sample_ids'])
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self.write(json_encode(samples_detail))
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self.finish()
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class StudySamplesHandler(RESTHandler):
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@authenticate_oauth

‎qiita_pet/test/rest/test_sample_detail.py

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# -----------------------------------------------------------------------------
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# Copyright (c) 2014--, The Qiita Development Team.
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#
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# Distributed under the terms of the BSD 3-clause License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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from unittest import main, TestCase
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from tornado.escape import json_decode
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import qiita_db
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from qiita_pet.test.rest.test_base import RESTHandlerTestCase
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from qiita_pet.handlers.rest.study_samples import _sample_details
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class SupportTests(TestCase):
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def test_samples_detail(self):
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exp = [{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 1,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 2,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': 'doesnotexist',
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'sample_found': False,
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'ebi_sample_accession': None,
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'preparation_id': None,
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'ebi_experiment_accession': None,
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'preparation_visibility': None,
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'preparation_type': None}]
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obs = _sample_details(qiita_db.study.Study(1),
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['1.SKD7.640191', 'doesnotexist'])
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self.assertEqual(len(obs), len(exp))
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self.assertEqual(obs, exp)
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class SampleDetailHandlerTests(RESTHandlerTestCase):
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def test_get_missing_sample(self):
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exp = [{'sample_id': 'doesnotexist',
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'sample_found': False,
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'ebi_sample_accession': None,
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'preparation_id': None,
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'ebi_experiment_accession': None,
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'preparation_visibility': None,
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'preparation_type': None}, ]
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response = self.get('/api/v1/study/1/sample/doesnotexist/status',
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headers=self.headers)
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self.assertEqual(response.code, 200)
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obs = json_decode(response.body)
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self.assertEqual(obs, exp)
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def test_get_valid_sample(self):
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exp = [{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 1,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 2,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'}]
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response = self.get('/api/v1/study/1/sample/1.SKD7.640191/status',
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headers=self.headers)
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self.assertEqual(response.code, 200)
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obs = json_decode(response.body)
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self.assertEqual(obs, exp)
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def test_post_samples_status_bad_request(self):
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body = {'malformed': 'with garbage'}
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response = self.post('/api/v1/study/1/samples/status',
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headers=self.headers,
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data=body, asjson=True)
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self.assertEqual(response.code, 400)
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def test_post_samples_status(self):
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exp = [{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 1,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': '1.SKD7.640191',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000021',
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'preparation_id': 2,
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'ebi_experiment_accession': 'ERX0000021',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': 'doesnotexist',
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'sample_found': False,
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'ebi_sample_accession': None,
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'preparation_id': None,
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'ebi_experiment_accession': None,
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'preparation_visibility': None,
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'preparation_type': None},
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{'sample_id': '1.SKM5.640177',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000005',
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'preparation_id': 1,
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'ebi_experiment_accession': 'ERX0000005',
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'preparation_visibility': 'private',
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'preparation_type': '18S'},
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{'sample_id': '1.SKM5.640177',
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'sample_found': True,
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'ebi_sample_accession': 'ERS000005',
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'preparation_id': 2,
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'ebi_experiment_accession': 'ERX0000005',
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'preparation_visibility': 'private',
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'preparation_type': '18S'}]
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body = {'sample_ids': ['1.SKD7.640191', 'doesnotexist',
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'1.SKM5.640177']}
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response = self.post('/api/v1/study/1/samples/status',
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headers=self.headers,
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data=body, asjson=True)
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self.assertEqual(response.code, 200)
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obs = json_decode(response.body)
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self.assertEqual(obs, exp)
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if __name__ == '__main__':
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main()

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