def test_genecounts_multiple_records_and_stages_no_gaps(self):
rec1 = self.makeIndexRecord(1)
self.makeIndexStage(rec1, 10, 'Prot-sxn', 100, '18.5')
self.makeIndexStage(rec1, 10, 'Prot-sxn', 200, 'E')
self.makeIndexStage(rec1, 20, 'RT-PCR', 100, '18.5')
self.makeIndexStage(rec1, 20, 'RT-PCR', 200, 'E')
rec2 = self.makeIndexRecord(1)
self.makeIndexStage(rec2, 20, 'RT-PCR', 100, '18.5')
self.makeIndexStage(rec2, 20, 'RT-PCR', 200, 'E')
rec3 = self.makeIndexRecord(1)
self.makeIndexStage(rec3, 10, 'Prot-sxn', 100, '18.5')
self.makeIndexStage(rec3, 20, 'RT-PCR', 100, '18.5')
recs = [rec1, rec2, rec3]
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage(recs)
expected = {
'stages': ['18.5', 'E'],
'assays': [{
'indexassay': 'Prot-sxn',
'stages': [2, 1]
}, {
'indexassay': 'RT-PCR',
'stages': [3, 2]
}]
}
self.assertEqual(expected, summary)
def test_genecounts_multiple_records_and_stages_no_gaps(self):
rec1 = self.makeIndexRecord(1)
self.makeIndexStage(rec1, 10, 'Prot-sxn', 100, '18.5')
self.makeIndexStage(rec1, 10, 'Prot-sxn', 200, 'E')
self.makeIndexStage(rec1, 20, 'RT-PCR', 100, '18.5')
self.makeIndexStage(rec1, 20, 'RT-PCR', 200, 'E')
rec2 = self.makeIndexRecord(1)
self.makeIndexStage(rec2, 20, 'RT-PCR', 100, '18.5')
self.makeIndexStage(rec2, 20, 'RT-PCR', 200, 'E')
rec3 = self.makeIndexRecord(1)
self.makeIndexStage(rec3, 10, 'Prot-sxn', 100, '18.5')
self.makeIndexStage(rec3, 20, 'RT-PCR', 100, '18.5')
recs = [rec1, rec2, rec3]
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage(recs)
expected = {'stages':['18.5','E'],
'assays':[{'indexassay':'Prot-sxn', 'stages':[2,1]},
{'indexassay':'RT-PCR', 'stages':[3,2]}]
}
self.assertEqual(expected, summary)
def test_genecounts_manyassays_onestage(self):
rec1 = self.makeIndexRecord(1)
self.makeIndexStage(rec1, 10, 'Prot-sxn', 100, '18.5')
self.makeIndexStage(rec1, 20, 'RT-PCR', 100, '18.5')
self.makeIndexStage(rec1, 30, 'RT-PCR2', 100, '18.5')
recs = [rec1]
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage(recs)
expected = {
'stages': ['18.5'],
'assays': [{
'indexassay': 'Prot-sxn',
'stages': [1]
}, {
'indexassay': 'RT-PCR',
'stages': [1]
}, {
'indexassay': 'RT-PCR2',
'stages': [1]
}]
}
self.assertEqual(expected, summary)
def test_genecounts_onerecord(self):
rec1 = self.makeIndexRecord(1)
self.makeIndexStage(rec1, 10, 'Prot-sxn', 100, '13.5')
recs = [rec1]
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage(recs)
expected = {'stages':['13.5'],
'assays':[{'indexassay':'Prot-sxn', 'stages':[1]}]
}
self.assertEqual(expected, summary)
def renderIndexSummary(form):
# default return values
reference = None
refSortedIndexRecords = None
marker = None
template = "gxdindex_summary"
# gather index records from the DB
indexRecords = form.queryIndexRecords()
# check for truncation by default limits
resultsTruncated = form.index_limit.data and \
(len(indexRecords) >= form.index_limit.data)
# generate age/assay count table
countSummary = gxdindex_aggregator.aggregateGenesByAssayAndStage(indexRecords)
# send to lit-index by reference, if passed a ref ID
if form.refs_id.data:
reference = reference_service.get_by_jnum_id(form.refs_id.data)
template = "gxdindex_summary_by_ref"
# send to lit-index by marker, if passed a marker ID
if form.marker_id.data:
# re-order indexRecords - this page has specific sort
indexRecords.sort(key=lambda r: r.reference.short_citation)
marker = marker_hunter.getMarkerByMGIID(form.marker_id.data)
template = "gxdindex_summary_by_marker"
# send to lit-index by age / assay, if passed age and assay_type
if form.age.data and form.assay_type.data:
template = "gxdindex_summary_by_age_assay"
return render_template("summary/gxdindex/%s.html" % template,
indexRecords=indexRecords,
resultsTruncated=resultsTruncated,
countSummary=countSummary,
reference=reference,
marker=marker,
form=form,
queryString=form.argString())
def renderIndexSummary(form):
# default return values
reference = None
refSortedIndexRecords = None
marker = None
template = "gxdindex_summary"
# gather index records from the DB
indexRecords = form.queryIndexRecords()
# check for truncation by default limits
resultsTruncated = form.index_limit.data and \
(len(indexRecords) >= form.index_limit.data)
# generate age/assay count table
countSummary = gxdindex_aggregator.aggregateGenesByAssayAndStage(indexRecords)
# send to lit-index by reference, if passed a ref ID
if form.refs_id.data:
reference = reference_service.get_by_jnum_id(form.refs_id.data)
template = "gxdindex_summary_by_ref"
# send to lit-index by marker, if passed a marker ID
if form.marker_id.data:
# re-order indexRecords - this page has specific sort
indexRecords.sort(key=lambda r: r.reference.short_citation)
marker = marker_hunter.getMarkerByMGIID(form.marker_id.data)
template = "gxdindex_summary_by_marker"
# send to lit-index by age / assay, if passed age and assay_type
if form.age.data and form.assay_type.data:
template = "gxdindex_summary_by_age_assay"
return render_template("summary/gxdindex/%s.html" % template,
indexRecords=indexRecords,
resultsTruncated=resultsTruncated,
countSummary=countSummary,
reference=reference,
marker=marker,
form=form,
queryString=form.argString())
def test_genecounts_manystages_oneassay(self):
rec1 = self.makeIndexRecord(1)
self.makeIndexStage(rec1, 10, 'Prot-sxn', 100, '13.5')
self.makeIndexStage(rec1, 10, 'Prot-sxn', 200, '15.5')
self.makeIndexStage(rec1, 10, 'Prot-sxn', 300, 'A')
recs = [rec1]
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage(recs)
expected = {
'stages': ['13.5', '15.5', 'A'],
'assays': [{
'indexassay': 'Prot-sxn',
'stages': [1, 1, 1]
}]
}
self.assertEqual(expected, summary)
def test_genecounts_empty(self):
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage([])
self.assertEqual({'stages':[], 'assays':[]}, summary)
def test_genecounts_empty(self):
summary = gxdindex_aggregator.aggregateGenesByAssayAndStage([])
self.assertEqual({'stages': [], 'assays': []}, summary)
