def test_format(self):
name_field = DataField.objects.get_by_natural_key(
'tests', 'title', 'name')
salary_field = DataField.objects.get_by_natural_key(
'tests', 'title', 'salary')
boss_field = DataField.objects.get_by_natural_key(
'tests', 'title', 'boss')
concept = DataConcept(name='Title')
concept.save()
DataConceptField(concept=concept, field=name_field, order=1).save()
DataConceptField(concept=concept, field=salary_field, order=2).save()
DataConceptField(concept=concept, field=boss_field, order=3).save()
values = ['CEO', 100000, True]
self.assertEqual(
concept.format(values),
OrderedDict([(u'name', u'CEO'), (u'salary', 100000),
(u'boss', True)]))
self.assertEqual(concept._formatter_cache[0], None)
from avocado.formatters import Formatter, registry as formatters
class HtmlFormatter(Formatter):
def to_html(self, values, **context):
fvalues = self(values, preferred_formats=['string'])
return OrderedDict({
'profile':
'<span>' + '</span><span>'.join(fvalues.values()) +
'</span>'
})
to_html.process_multiple = True
formatters.register(HtmlFormatter, 'HTML')
concept.formatter_name = 'HTML'
self.assertEqual(
concept.format(values, preferred_formats=['html']),
OrderedDict([
('profile',
u'<span>CEO</span><span>100000</span><span>True</span>')
]))
def test_format(self):
name_field = DataField.objects.get_by_natural_key('models', 'title', 'name')
salary_field = DataField.objects.get_by_natural_key('models', 'title', 'salary')
boss_field = DataField.objects.get_by_natural_key('models', 'title', 'boss')
concept = DataConcept(name='Title')
concept.save()
DataConceptField(concept=concept, field=name_field, order=1).save()
DataConceptField(concept=concept, field=salary_field, order=2).save()
DataConceptField(concept=concept, field=boss_field, order=3).save()
values = ['CEO', 100000, True]
self.assertEqual(concept.format(values),
OrderedDict([
(u'name', u'CEO'),
(u'salary', 100000),
(u'boss', True)
]))
self.assertEqual(concept._formatter_cache[0], None)
from avocado.formatters import Formatter, registry as formatters
class HtmlFormatter(Formatter):
def to_html(self, values, **context):
fvalues = self(values, preferred_formats=['string'])
return OrderedDict({
'profile': '<span>' + '</span><span>'.join(fvalues.values()) + '</span>'
})
to_html.process_multiple = True
formatters.register(HtmlFormatter, 'HTML')
concept.formatter_name = 'HTML'
self.assertEqual(concept.format(values, preferred_formats=['html']),
OrderedDict([
('profile', u'<span>CEO</span><span>100000</span><span>True</span>')
]))
def to_html(self, values, **context):
from avocado.models import DataField
test_names = ['plan','pro_adhere']
html_str = ""
for name in test_names:
if getattr(values, name) != None and getattr(values, name) != 'NONE':
data_field = DataField.objects.get_by_natural_key('openmrs', 'pcpdetails', name)
html_str += "<tr><td>{0}</td><td>{1}</td></tr>".format(data_field, getattr(values, name))
if html_str != "":
return "<table class='table table-striped'>{0}</table>".format(html_str)
return ""
class MRNFormatter(Formatter):
def to_html(self, value, **context):
url = reverse('patient-detail', kwargs={'mrn': value})
return '<a href="{0}">{1}</a>'.format(url, value)
registry.register(AgeFormatter, 'Age')
registry.register(GenderFormatter, 'Gender')
registry.register(EncounterAgeFormatter, 'EncounterAge')
registry.register(CbcPanelFormatter, 'CbcPanel')
registry.register(Chem7PanelFormatter, 'Chem7')
registry.register(MiscPanelFormatter, 'MiscLab')
registry.register(SystemsFormatter, 'SystemsReview')
registry.register(HIVDetailFormatter, 'HIVDetail')
registry.register(TBDetailFormatter, 'TBDetail')
registry.register(PCPDetailFormatter, 'PCPDetail')
registry.register(MRNFormatter, 'MRN')
except Pathogenicity.DoesNotExist:
return 'n/a'
return pathogenicity.name
class AssessmentCategory(HTMLFormatter):
def to_html(self, value, **context):
from .models import AssessmentCategory
try:
category = AssessmentCategory.objects.get(pk=value)
except AssessmentCategory.DoesNotExist:
return '<span class="muted">n/a</span>'
return category.name
def to_excel(self, value, **context):
from .models import AssessmentCategory
try:
category = AssessmentCategory.objects.get(pk=value)
except AssessmentCategory.DoesNotExist:
return 'n/a'
return category.name
formatters.register(Pathogenicity, 'Pathogenicity')
formatters.register(AssessmentCategory, 'Assessment Category')
href=href, label=values['symbol'])
to_html.process_multiple = True
def to_excel(self, values, **context):
if values['symbol']:
href = self.href.format(values['symbol'])
return '=HYPERLINK("{href}", "{label}")'.format(
href=href, label=values['symbol'])
to_excel.process_multiple = True
class RefSeqTranscript(HTMLFormatter):
href = 'http://www.ncbi.nlm.nih.gov/nuccore/{}'
def to_html(self, value, **context):
if value:
href = self.href.format(value)
return '<a target=_blank href="{href}">{label}</a>'.format(
href=href, label=value)
def to_excel(self, value, **context):
if value:
href = self.href.format(value)
return '=HYPERLINK("{href}", "{label}")'.format(
href=href, label=value)
formatters.register(HGNCGene, 'HGNC Gene')
formatters.register(NCBIGene, 'NCBI Gene')
formatters.register(RefSeqTranscript, 'RefSeq Transcript')
from avocado.formatters import registry
from serrano.formatters import HTMLFormatter
class VaccineFormatter(HTMLFormatter):
def to_html(self, values, **context):
print values
status = values['status']
name = values['name']
if status == 'PREVIOUS IMMUNIZATIONS ADMINISTERED':
status = "(PREVIOUSLY ADMINISTERED)"
return "<strong>" + name + "</strong> " + "<span class='text-info'>" + status + "</span></br>"
elif status == "IMMUNIZATIONS ORDERED":
status = "(ORDERED)"
return "<strong>" + name + "</strong> " + "<span class='text-warning'>" + status + "</span></br>"
return "<h5>" + name + " " + status + "</h5>"
to_html.process_multiple = True
registry.register(VaccineFormatter, 'Vaccine')
from avocado.formatters import registry as formatters
from serrano.formatters import HTMLFormatter
class FowardSlashDelimited(HTMLFormatter):
delimiter = ' / '
class CommaSeparated(HTMLFormatter):
delimiter = ', '
formatters.register(HTMLFormatter, 'HTML')
formatters.register(FowardSlashDelimited, 'Forward-slash Delimited')
formatters.register(CommaSeparated, 'Comma-separated')
to_csv = to_excel
class PolyPhen2Formatter(HTMLFormatter):
alt_keys = ('PolyPhen2 Score', 'PolyPhen2 Prediction')
def _get_values(self, value):
from .models import PolyPhen2
return value, PolyPhen2.get_prediction(value)
def to_html(self, value, **context):
if value is None:
return self.html_map[value]
score, prediction = self._get_values(value)
return '{0} <span class=muted>({1})</span>'.format(prediction, score)
def to_excel(self, value, **context):
score, prediction = self._get_values(value)
return OrderedDict(zip(self.alt_keys, [score, prediction]))
to_csv = to_excel
formatters.register(GenomicCoordinate, 'Genomic Coordinate')
formatters.register(dbSNP, 'dbSNP')
formatters.register(VariantEffect, 'Variant Effect')
formatters.register(AlleleFrequency, 'Allele Frequency')
formatters.register(SiftFormatter, 'Sift')
formatters.register(PolyPhen2Formatter, 'PolyPhen2')
to_csv = to_excel
class PolyPhen2Formatter(HTMLFormatter):
alt_keys = ('PolyPhen2 Score', 'PolyPhen2 Prediction')
def _get_values(self, value):
from vdw.variants.models import PolyPhen2
return value, PolyPhen2.get_prediction(value)
def to_html(self, value, **context):
if value is None:
return self.html_map[value]
score, prediction = self._get_values(value)
return '{0} <span class=muted>({1})</span>'.format(prediction, score)
def to_excel(self, value, **context):
score, prediction = self._get_values(value)
return OrderedDict(zip(self.alt_keys, [score, prediction]))
to_csv = to_excel
formatters.register(GenomicCoordinate, 'Genomic Coordinate')
formatters.register(dbSNP, 'dbSNP')
formatters.register(VariantEffect, 'Variant Effect')
formatters.register(AlleleFrequency, 'Allele Frequency')
formatters.register(SiftFormatter, 'Sift')
formatters.register(PolyPhen2Formatter, 'PolyPhen2')
distinct = True
class OtherMedConditionFormatter(SubjectAggregationFormatter):
model = OtherMedCondition
field = 'other_med_condition'
distinct = True
class LimsIDFormatter(SubjectAggregationFormatter):
model = NautilusSubject
field = 'sample_subject_id'
distinct = True
registry.register(PathologyReportFormatter, 'PathologyReportFormatter')
registry.register(OperativeReportFormatter, 'OperativeReportFormatter')
registry.register(AgeDescAggregationFormatter, 'AgeDescAggregationFormatter')
registry.register(AgeAtDiagAggregationFormatter, 'AgeAtDiagAggregationFormatter')
registry.register(AgeYmdAggregationFormatter, 'AgeYmdAggregationFormatter')
registry.register(PatientSummaryFormatter, 'PatientSummaryFormatter')
registry.register(LinkAggFormatter, 'LinkAggFormatter')
registry.register(AliquotAggFormatter, 'AliqAggFormatter')
registry.register(TumorLocFormatter, 'TumorLocFormatter')
registry.register(OtherMedConditionFormatter, 'OtherMedConditionFormatter')
registry.register(PathDiagFormatter, 'PathDiagFormatter')
registry.register(RaceFormatter, 'RaceFormatter')
registry.register(MolecularTestsDoneFormatter, 'MolecularTestsDoneFormatter')
registry.register(DiagnosisTypeListFormatter, 'DiagnosisTypeListFormatter')
registry.register(CancerPredispositionFormatter, 'CancerPredispositionFormatter')
registry.register(RelapseNumberFormatter, 'RelapseNumberFormatter')
for c in cohorts:
output.append((c.name, variants.get(c.pk, 0), c.count))
return output
def to_html(self, value, **context):
variants = self._get_cohort_variants(value, **context)
html = ['<ul class=unstyled>']
for name, af, count in variants:
html.append('<li><small>{0}</small> {1}% <span class=muted>({2})'
'</span></li>'.format(name, str(af * 100), count))
html.append('</ul>')
return ''.join(html)
def to_excel(self, value, **context):
variants = self._get_cohort_variants(value, **context)
output = OrderedDict()
for name, af, count in variants:
key = '{0} Cohort Allele Freq ({1} samples)'.format(name, count)
output[key] = af
return output
to_csv = to_excel
formatters.register(AlamutFormatter, 'Alamut Query Link')
formatters.register(SampleFormatter, 'Sample')
formatters.register(ReadDepthFormatter, 'Read Depth')
formatters.register(CohortsFormatter, 'Cohorts')
test_names = ["plan", "pro_adhere"]
html_str = ""
for name in test_names:
if values[name] != None and values[name] != "NONE":
data_field = DataField.objects.get_by_natural_key("openmrs", "pcpdetails", name)
html_str += "<tr><td>{0}</td><td>{1}</td></tr>".format(data_field, values[name])
if html_str != "":
return "<table class='table table-striped'>{0}</table>".format(html_str)
return ""
to_html.process_multiple = True
class MRNFormatter(HTMLFormatter):
def to_html(self, value, **context):
url = reverse("patient-detail", kwargs={"mrn": value})
return '<a href="{0}">{1}</a>'.format(url, value)
registry.register(AgeFormatter, "Age")
registry.register(GenderFormatter, "Gender")
registry.register(EncounterAgeFormatter, "EncounterAge")
registry.register(CbcPanelFormatter, "CbcPanel")
registry.register(Chem7PanelFormatter, "Chem7")
registry.register(MiscPanelFormatter, "MiscLab")
registry.register(SystemsFormatter, "SystemsReview")
registry.register(HIVDetailFormatter, "HIVDetail")
registry.register(TBDetailFormatter, "TBDetail")
registry.register(PCPDetailFormatter, "PCPDetail")
registry.register(MRNFormatter, "MRN")
from avocado.formatters import Formatter, process_multiple, registry
class HTMLFormatter(Formatter):
delimiter = u' '
html_map = {
None: '<em>n/a</em>'
}
@process_multiple
def to_html(self, values, **context):
toks = []
for value in values.values():
# Check the html_map first
if value in self.html_map:
tok = self.html_map[value]
# Ignore NoneTypes
elif value is None:
continue
# Prettify floats
elif type(value) is float:
tok = filters.floatformat(value)
else:
tok = unicode(value)
toks.append(tok)
return self.delimiter.join(toks)
registry.register(HTMLFormatter, default=True)
for name in test_names:
if getattr(values, name) != None and getattr(values,
name) != 'NONE':
data_field = DataField.objects.get_by_natural_key(
'openmrs', 'pcpdetails', name)
html_str += "<tr><td>{0}</td><td>{1}</td></tr>".format(
data_field, getattr(values, name))
if html_str != "":
return "<table class='table table-striped'>{0}</table>".format(
html_str)
return ""
class MRNFormatter(Formatter):
def to_html(self, value, **context):
url = reverse('patient-detail', kwargs={'mrn': value})
return '<a href="{0}">{1}</a>'.format(url, value)
registry.register(AgeFormatter, 'Age')
registry.register(GenderFormatter, 'Gender')
registry.register(EncounterAgeFormatter, 'EncounterAge')
registry.register(CbcPanelFormatter, 'CbcPanel')
registry.register(Chem7PanelFormatter, 'Chem7')
registry.register(MiscPanelFormatter, 'MiscLab')
registry.register(SystemsFormatter, 'SystemsReview')
registry.register(HIVDetailFormatter, 'HIVDetail')
registry.register(TBDetailFormatter, 'TBDetail')
registry.register(PCPDetailFormatter, 'PCPDetail')
registry.register(MRNFormatter, 'MRN')
pathogenicity = Pathogenicity.objects.get(pk=value)
except Pathogenicity.DoesNotExist:
return 'n/a'
return pathogenicity.name
class AssessmentCategory(HTMLFormatter):
def to_html(self, value, **context):
from vdw.assessments.models import AssessmentCategory
try:
category = AssessmentCategory.objects.get(pk=value)
except AssessmentCategory.DoesNotExist:
return '<span class="muted">n/a</span>'
return category.name
def to_excel(self, value, **context):
from vdw.assessments.models import AssessmentCategory
try:
category = AssessmentCategory.objects.get(pk=value)
except AssessmentCategory.DoesNotExist:
return 'n/a'
return category.name
formatters.register(Pathogenicity, 'Pathogenicity')
formatters.register(AssessmentCategory, 'Assessment Category')
for c in cohorts:
output.append((c.name, variants.get(c.pk, 0), c.count))
return output
def to_html(self, value, **context):
variants = self._get_cohort_variants(value, **context)
html = ['<ul class=unstyled>']
for name, af, count in variants:
html.append('<li><small>{0}</small> {1}% <span class=muted>({2})'
'</span></li>'.format(name, str(af * 100), count))
html.append('</ul>')
return ''.join(html)
def to_excel(self, value, **context):
variants = self._get_cohort_variants(value, **context)
output = OrderedDict()
for name, af, count in variants:
key = '{0} Cohort Allele Freq ({1} samples)'.format(name, count)
output[key] = af
return output
to_csv = to_excel
formatters.register(AlamutFormatter, 'Alamut Query Link')
formatters.register(SampleFormatter, 'Sample')
formatters.register(ReadDepthFormatter, 'Read Depth')
formatters.register(CohortsFormatter, 'Cohorts')
to_csv = to_excel
class PolyPhen2Formatter(HTMLFormatter):
alt_keys = ("PolyPhen2 Score", "PolyPhen2 Prediction")
def _get_values(self, value):
from vdw.variants.models import PolyPhen2
return value, PolyPhen2.get_prediction(value)
def to_html(self, value, **context):
if value is None:
return self.html_map[value]
score, prediction = self._get_values(value)
return "{0} <span class=muted>({1})</span>".format(prediction, score)
def to_excel(self, value, **context):
score, prediction = self._get_values(value)
return OrderedDict(zip(self.alt_keys, [score, prediction]))
to_csv = to_excel
formatters.register(GenomicCoordinate, "Genomic Coordinate")
formatters.register(dbSNP, "dbSNP")
formatters.register(VariantEffect, "Variant Effect")
formatters.register(AlleleFrequency, "Allele Frequency")
formatters.register(SiftFormatter, "Sift")
formatters.register(PolyPhen2Formatter, "PolyPhen2")
