From 422268a9d944d186e16658591f95ebe79e1fc68c Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 16:59:57 -0400 Subject: [PATCH 01/17] remove old epi module --- project/epi/__init__.py | 0 project/epi/admin.py | 13 - project/epi/api.py | 29 - project/epi/exports.py | 259 --- project/epi/forms.py | 723 --------- project/epi/lookups.py | 120 -- project/epi/migrations/0001_initial.py | 351 ----- project/epi/migrations/0002_auto_20150629_1327.py | 54 - project/epi/migrations/0003_auto_20150723_1544.py | 25 - project/epi/migrations/__init__.py | 0 project/epi/models.py | 1645 -------------------- project/epi/serializers.py | 192 --- project/epi/urls.py | 164 -- project/epi/views.py | 430 ----- project/hawc/settings/base.py | 1 - project/templates/epi/_epistudy_list.html | 21 - project/templates/epi/_study_population_list.html | 40 - .../epi/assessedoutcome_confirm_delete.html | 15 - .../epi/assessedoutcome_copy_selector.html | 39 - project/templates/epi/assessedoutcome_detail.html | 56 - project/templates/epi/assessedoutcome_form.html | 89 -- project/templates/epi/assessedoutcome_list.html | 47 - .../templates/epi/assessedoutcome_versions.html | 76 - project/templates/epi/exposure_confirm_delete.html | 15 - project/templates/epi/exposure_copy_selector.html | 39 - project/templates/epi/exposure_detail.html | 63 - project/templates/epi/exposure_form.html | 61 - project/templates/epi/factor_form.html | 48 - project/templates/epi/studycriteria_form.html | 48 - .../epi/studypopulation_confirm_delete.html | 15 - .../epi/studypopulation_copy_selector.html | 39 - project/templates/epi/studypopulation_detail.html | 59 - project/templates/epi/studypopulation_form.html | 37 - 33 files changed, 4813 deletions(-) delete mode 100644 project/epi/__init__.py delete mode 100644 project/epi/admin.py delete mode 100644 project/epi/api.py delete mode 100644 project/epi/exports.py delete mode 100644 project/epi/forms.py delete mode 100644 project/epi/lookups.py delete mode 100644 project/epi/migrations/0001_initial.py delete mode 100644 project/epi/migrations/0002_auto_20150629_1327.py delete mode 100644 project/epi/migrations/0003_auto_20150723_1544.py delete mode 100644 project/epi/migrations/__init__.py delete mode 100644 project/epi/models.py delete mode 100644 project/epi/serializers.py delete mode 100644 project/epi/urls.py delete mode 100644 project/epi/views.py delete mode 100644 project/templates/epi/_epistudy_list.html delete mode 100644 project/templates/epi/_study_population_list.html delete mode 100644 project/templates/epi/assessedoutcome_confirm_delete.html delete mode 100644 project/templates/epi/assessedoutcome_copy_selector.html delete mode 100644 project/templates/epi/assessedoutcome_detail.html delete mode 100644 project/templates/epi/assessedoutcome_form.html delete mode 100644 project/templates/epi/assessedoutcome_list.html delete mode 100644 project/templates/epi/assessedoutcome_versions.html delete mode 100644 project/templates/epi/exposure_confirm_delete.html delete mode 100644 project/templates/epi/exposure_copy_selector.html delete mode 100644 project/templates/epi/exposure_detail.html delete mode 100644 project/templates/epi/exposure_form.html delete mode 100644 project/templates/epi/factor_form.html delete mode 100644 project/templates/epi/studycriteria_form.html delete mode 100644 project/templates/epi/studypopulation_confirm_delete.html delete mode 100644 project/templates/epi/studypopulation_copy_selector.html delete mode 100644 project/templates/epi/studypopulation_detail.html delete mode 100644 project/templates/epi/studypopulation_form.html diff --git a/project/epi/__init__.py b/project/epi/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/project/epi/admin.py b/project/epi/admin.py deleted file mode 100644 index 9a77a854..00000000 --- a/project/epi/admin.py +++ /dev/null @@ -1,13 +0,0 @@ -from django.contrib import admin - -from . import models - - -class StatisticalMetricAdmin(admin.ModelAdmin): - list_display = ('metric', 'abbreviation', 'isLog', 'order', ) - - def has_delete_permission(self, request, obj=None): - return False - - -admin.site.register(models.StatisticalMetric, StatisticalMetricAdmin) diff --git a/project/epi/api.py b/project/epi/api.py deleted file mode 100644 index 491be4e5..00000000 --- a/project/epi/api.py +++ /dev/null @@ -1,29 +0,0 @@ -from __future__ import absolute_import - -from assessment.api.views import AssessmentViewset - -from . import models, serializers - - -class MetaResult(AssessmentViewset): - assessment_filter_args = "protocol__study__assessment" - model = models.MetaResult - serializer_class = serializers.MetaResultSerializer - - -class StudyPopulation(AssessmentViewset): - assessment_filter_args = "study__assessment" - model = models.StudyPopulation - serializer_class = serializers.StudyPopulationSerializer - - -class Exposure(AssessmentViewset): - assessment_filter_args = "study_population__study__assessment" - model = models.Exposure - serializer_class = serializers.ExposureVerboseSerializer - - -class AssessedOutcome(AssessmentViewset): - assessment_filter_args = "assessment" - model = models.AssessedOutcome - serializer_class = serializers.AssessedOutcomeSerializer diff --git a/project/epi/exports.py b/project/epi/exports.py deleted file mode 100644 index 5d5f0470..00000000 --- a/project/epi/exports.py +++ /dev/null @@ -1,259 +0,0 @@ -from study.models import Study -from utils.helper import FlatFileExporter -from . import models - - -class AssessedOutcomeFlatComplete(FlatFileExporter): - """ - Returns a complete export of all data required to rebuild the the - epidemiological study type from scratch. - """ - - def _get_header_row(self): - header = [] - header.extend(Study.flat_complete_header_row()) - header.extend(models.StudyPopulation.flat_complete_header_row()) - header.extend(models.Exposure.flat_complete_header_row()) - header.extend(models.AssessedOutcome.flat_complete_header_row()) - header.extend(models.AssessedOutcomeGroup.flat_complete_header_row()) - return header - - def _get_data_rows(self): - rows = [] - for obj in self.queryset: - ser = obj.get_json(json_encode=False) - row = [] - row.extend(Study.flat_complete_data_row(ser['exposure']['study_population']['study'])) - row.extend(models.StudyPopulation.flat_complete_data_row(ser['exposure']['study_population'])) - row.extend(models.Exposure.flat_complete_data_row(ser['exposure'])) - row.extend(models.AssessedOutcome.flat_complete_data_row(ser)) - # build a row for each aog - for aog in ser['groups']: - row_copy = list(row) # clone - row_copy.extend(models.AssessedOutcomeGroup.flat_complete_data_row(aog)) - rows.append(row_copy) - return rows - - -class AssessedOutcomeFlatDataPivot(FlatFileExporter): - """ - Return a subset of frequently-used data for generation of data-pivot - visualizations. - """ - - def _get_header_row(self): - return [ - 'Study', - 'Study URL', - 'Study HAWC ID', - 'Study Published?', - - 'Study Population Name', - 'Study Population Key', - 'Design', - 'Study Population URL', - - 'Exposure', - 'Exposure Key', - 'Exposure Metric', - 'Exposure URL', - 'Dose Units', - - 'Assessed Outcome Name', - 'Assessed Outcome Population Description', - 'Assessed Outcome Key', - 'Diagnostic', - 'Statistical Metric', - 'Statistical Metric Abbreviation', - 'Statistical Metric Description', - 'Outcome Summary', - 'Dose Response', - 'Statistical Power', - 'Support Main Finding', - - 'Exposure Group Name', - 'Exposure Group Comparative Description Name', - 'Exposure Group Order', - 'Exposure Group Numeric', - - 'Row Key', - 'Assessed Outcome Group Primary Key', - 'N', - 'Estimate', - 'Lower CI', - 'Upper CI', - 'CI units', - 'SE', - 'Statistical Significance', - 'Statistical Significance (numeric)', - 'Main Finding' - ] - - def _get_data_rows(self): - rows = [] - for obj in self.queryset: - ser = obj.get_json(json_encode=False) - - row = [ - ser['exposure']['study_population']['study']['short_citation'], - ser['exposure']['study_population']['study']['url'], - ser['exposure']['study_population']['study']['id'], - ser['exposure']['study_population']['study']['published'], - - ser['exposure']['study_population']['name'], - ser['exposure']['study_population']['id'], - ser['exposure']['study_population']['design'], - ser['exposure']['study_population']['url'], - - ser['exposure']['exposure_form_definition'], - ser['exposure']['id'], - ser['exposure']['metric'], - ser['exposure']['url'], - ser['exposure']['metric_units']['name'], - - ser['name'], - ser['population_description'], - ser['id'], - ser['diagnostic'], - ser['statistical_metric']['metric'], - ser['statistical_metric']['abbreviation'], - ser['statistical_metric_description'], - ser['summary'], - ser['dose_response'], - ser['statistical_power'], - ser['main_finding_support'], - ] - - for group in ser['groups']: - row_copy = list(row) # clone - row_copy.extend([ - group['exposure_group']['description'], - group['exposure_group']['comparative_name'], - group['exposure_group']['exposure_group_id'], - group['exposure_group']['exposure_numeric'], - - group['id'], # repeat for data-pivot key - group['id'], - group['n'], - group['estimate'], - group['lower_ci'], - group['upper_ci'], - group['ci_units'], - group['se'], - group['p_value_text'], - group['p_value'], - group['isMainFinding'] - ]) - rows.append(row_copy) - - return rows - - -class MetaResultFlatComplete(FlatFileExporter): - """ - Returns a complete export of all data required to rebuild the the - epidemiological meta-result study type from scratch. - """ - - def _get_header_row(self): - header = [] - header.extend(Study.flat_complete_header_row()) - header.extend(models.MetaProtocol.flat_complete_header_row()) - header.extend(models.MetaResult.flat_complete_header_row()) - header.extend(models.SingleResult.flat_complete_header_row()) - return header - - def _get_data_rows(self): - rows = [] - for obj in self.queryset: - ser = obj.get_json(json_encode=False) - row = [] - row.extend(Study.flat_complete_data_row(ser['protocol']['study'])) - row.extend(models.MetaProtocol.flat_complete_data_row(ser['protocol'])) - row.extend(models.MetaResult.flat_complete_data_row(ser)) - - if len(ser['single_results'])==0: - # print one-row with no single-results - rows.append(row) - else: - # print each single-result as a new row - for sr in ser['single_results']: - row_copy = list(row) # clone - row_copy.extend(models.SingleResult.flat_complete_data_row(sr)) - rows.append(row_copy) - return rows - - -class MetaResultFlatDataPivot(FlatFileExporter): - """ - Return a subset of frequently-used data for generation of data-pivot - visualizations. - """ - - def _get_header_row(self): - return [ - 'Study', - 'Study URL', - 'Study HAWC ID', - 'Study Published?', - - 'Protocol Primary Key', - 'Protocol URL', - 'Protocol Name', - 'Protocol Type', - 'Total References', - 'Identified References', - - 'Row Key', - 'Result Primary Key', - 'Result URL', - 'Result Label', - 'Health Outcome', - 'Exposure', - 'Result References', - 'Statistical Metric', - 'Statistical Metric Abbreviation', - 'N', - 'Estimate', - 'Lower CI', - 'Upper CI', - 'CI units', - 'Heterogeneity' - ] - - def _get_data_rows(self): - rows = [] - for obj in self.queryset: - ser = obj.get_json(json_encode=False) - row = [ - ser['protocol']['study']['short_citation'], - ser['protocol']['study']['url'], - ser['protocol']['study']['id'], - ser['protocol']['study']['published'], - - ser['protocol']['id'], - ser['protocol']['url'], - ser['protocol']['name'], - ser['protocol']['protocol_type'], - ser['protocol']['total_references'], - ser['protocol']['total_studies_identified'], - - ser['id'], # repeat for data-pivot key - ser['id'], - ser['url'], - ser['label'], - ser['health_outcome'], - ser['exposure_name'], - ser['number_studies'], - ser['statistical_metric']['metric'], - ser['statistical_metric']['abbreviation'], - ser['n'], - ser['estimate'], - ser['lower_ci'], - ser['upper_ci'], - ser['ci_units'], - ser['heterogeneity'], - ] - rows.append(row) - - return rows diff --git a/project/epi/forms.py b/project/epi/forms.py deleted file mode 100644 index 8ed34674..00000000 --- a/project/epi/forms.py +++ /dev/null @@ -1,723 +0,0 @@ -from copy import copy - -from django import forms -from django.forms.models import BaseModelFormSet, modelformset_factory -from django.forms.widgets import CheckboxInput, TextInput -from collections import OrderedDict - -from crispy_forms import layout as cfl -from crispy_forms import bootstrap as cfb -from selectable import forms as selectable - -from assessment.lookups import BaseEndpointLookup, EffectTagLookup -from utils.forms import FormsetWithIgnoredFields, anyNull, BaseFormHelper - -from . import models, lookups - - -class StudyPopulationForm(forms.ModelForm): - - inclusion_criteria = selectable.AutoCompleteSelectMultipleField( - lookup_class=lookups.StudyCriteriaLookup, - required=False) - - exclusion_criteria = selectable.AutoCompleteSelectMultipleField( - lookup_class=lookups.StudyCriteriaLookup, - required=False) - - confounding_criteria = selectable.AutoCompleteSelectMultipleField( - lookup_class=lookups.StudyCriteriaLookup, - required=False) - - class Meta: - fields = ('name', 'design', - 'country', 'region', 'state', - 'sex', 'ethnicity', 'fraction_male', 'fraction_male_calculated', - 'n', 'starting_n', - 'age_mean', 'age_mean_type', 'age_calculated', - 'age_description', 'age_sd', 'age_sd_type', - 'age_lower', 'age_lower_type', 'age_upper', 'age_upper_type', - 'inclusion_criteria', - 'exclusion_criteria', - 'confounding_criteria') - model = models.StudyPopulation - exclude = ('study', ) - - def __init__(self, *args, **kwargs): - study = kwargs.pop('parent', None) - super(StudyPopulationForm, self).__init__(*args, **kwargs) - self.fields['region'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.RegionLookup, - allow_new=True) - self.fields['state'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.StateLookup, - allow_new=True) - if study: - self.instance.study = study - self.helper = self.setHelper() - - def setHelper(self): - for fld in ["inclusion_criteria", "exclusion_criteria", "confounding_criteria"]: - self.fields[fld].widget.update_query_parameters({'related': self.instance.study.assessment_id}) - for fld in self.fields.keys(): - widget = self.fields[fld].widget - if type(widget) != forms.CheckboxInput: - if fld in ['inclusion_criteria', 'exclusion_criteria', 'confounding_criteria']: - widget.attrs['class'] = 'span11' - else: - widget.attrs['class'] = 'span12' - - if self.instance.id: - inputs = { - "legend_text": u"Update {}".format(self.instance), - "help_text": u"Update an existing study-population.", - "cancel_url": self.instance.get_absolute_url() - } - else: - inputs = { - "legend_text": u"Create new study-population", - "help_text": u""" - Create a new study population. Each study-population is a - associated with an epidemiology study. There may be - multiple study populations with a single study, - though this is typically unlikely.""", - "cancel_url": self.instance.study.get_absolute_url() - } - - helper = BaseFormHelper(self, **inputs) - helper.form_class = None - helper.add_fluid_row('name', 2, "span6") - helper.add_fluid_row('country', 3, "span4") - helper.add_fluid_row('sex', 4, "span3") - helper.add_fluid_row('n', 2, "span6") - helper.add_fluid_row('age_mean', 3, "span4") - helper.add_fluid_row('age_description', 3, "span4") - helper.add_fluid_row('age_lower', 4, "span3") - - url = '{% url "epi:studycriteria_create" assessment.pk %}' - helper.add_adder("addIncCriteria", "Add new criteria", url) - helper.add_adder("addExcCriteria", "Add new criteria", url) - helper.add_adder("addConCriteria", "Add new criteria", url) - - return helper - - -class ExposureForm(forms.ModelForm): - - class Meta: - model = models.Exposure - exclude = ('study_population', ) - - def __init__(self, *args, **kwargs): - study_population = kwargs.pop('parent', None) - super(ExposureForm, self).__init__(*args, **kwargs) - if study_population: - self.instance.study_population = study_population - self.helper = self.setHelper() - - def setHelper(self): - self.fields['exposure_form_definition'].widget = TextInput() - - for fld in ('metric', 'metric_description', 'analytical_method', - 'control_description'): - self.fields[fld].widget.attrs['rows'] = 3 - - for fld in self.fields.keys(): - widget = self.fields[fld].widget - if type(widget) != forms.CheckboxInput: - widget.attrs['class'] = 'span12' - - if self.instance.id: - inputs = { - "legend_text": u"Update {}".format(self.instance), - "help_text": u"Update an existing exposure.", - "cancel_url": self.instance.get_absolute_url() - } - else: - inputs = { - "legend_text": u"Create new exposure", - "help_text": u""" - Create a new exposure. An exposure is a description of - the metric used to evaluate an individual's exposure. - Each exposure is associated with a particular study - population, and there may be multiple exposure - metrics for that population.""", - "cancel_url": self.instance.study_population.get_absolute_url() - } - - helper = BaseFormHelper(self, **inputs) - helper.form_class = None - helper.add_header("inhalation", "Known exposure routes") - helper.add_header("metric", "Additional exposure information") - helper.add_fluid_row('inhalation', 6, "span2") - helper.add_fluid_row('metric', 3, "span4") - helper.add_fluid_row('analytical_method', 2, "span6") - return helper - - -class ExposureGroupForm(forms.ModelForm): - - class Meta: - fields = ('description', - 'exposure_numeric', - 'comparative_name', - 'sex', - 'ethnicity', - 'fraction_male', - 'fraction_male_calculated', - 'n', - 'starting_n', - 'exposure_n', - 'age_mean', - 'age_mean_type', - 'age_calculated', - 'age_description', - 'age_sd', - 'age_sd_type', - 'age_lower', - 'age_lower_type', - 'age_upper', - 'age_upper_type') - model = models.ExposureGroup - - def __init__(self, *args, **kwargs): - super(ExposureGroupForm, self).__init__(*args, **kwargs) - for key in ('exposure_numeric', 'fraction_male', 'fraction_male_calculated', - 'n', 'starting_n', 'exposure_n', 'age_mean', 'age_mean_type', - 'age_calculated', 'age_description', 'age_sd', - 'age_sd_type', 'age_lower', 'age_lower_type', 'age_upper', - 'age_upper_type'): - self.fields[key].widget.attrs['class'] = 'input-small' - - for key in ('description', 'sex', 'comparative_name'): - self.fields[key].widget.attrs['class'] = 'input-medium' - - -class BaseEGFormSet(BaseModelFormSet): - - def __init__(self, *args, **kwargs): - self.exposure = kwargs.pop('exposure', None) - super(BaseEGFormSet, self).__init__(*args, **kwargs) - - def clean(self): - super(BaseEGFormSet, self).clean() - # check that all descriptions are unique - descriptions = [] - for form in self.forms: - if form.is_valid() and form.clean(): - description = form.cleaned_data['description'] - if description in descriptions: - raise forms.ValidationError("Exposure-groups must have unique descriptions.") - descriptions.append(description) - - # update new forms with exposure_group_id, first get max ID - max_exposure_group_id = -1 - for form in self.forms: - if form.instance.exposure_group_id > max_exposure_group_id: - max_exposure_group_id = form.instance.exposure_group_id - - # now increment - for form in self.extra_forms: - if form.is_valid() and form.clean(): - if self.exposure: - form.instance.exposure = self.exposure - max_exposure_group_id += 1 - form.instance.exposure_group_id = max_exposure_group_id - - # check that there is at least one exposure-group - count = len(filter(lambda f: f.is_valid() and f.clean(), self.forms)) - if count < 1: - raise forms.ValidationError("At least one-exposure group is required.") - - def rebuild_exposure_group_id(self): - # the exposure-group-id must start at zero and continue sequentially; - # this method rebuilds the exposure-groups-ides in increasing order - # properly. Note: cannot add into clean() because has_changed flag - # may not have been set. - deleted_ids = sorted([ - form.instance.exposure_group_id - for form in self. - deleted_forms], reverse=True) - for deleted_id in deleted_ids: - for form in self.forms: - if ((form not in self.deleted_forms) and - (form.instance.exposure_group_id > deleted_id)): - form.instance.exposure_group_id -= 1 - form.instance.save() - - -EGFormSet = modelformset_factory( - models.ExposureGroup, - form=ExposureGroupForm, - formset=BaseEGFormSet, - can_delete=True, - extra=1) - -BlankEGFormSet = modelformset_factory( - models.ExposureGroup, - form=ExposureGroupForm, - formset=BaseEGFormSet, - extra=1) - - -class FactorForm(forms.ModelForm): - - class Meta: - model = models.Factor - exclude = ('assessment', ) - - def __init__(self, *args, **kwargs): - assessment = kwargs.pop('parent', None) - super(FactorForm, self).__init__(*args, **kwargs) - self.fields['description'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.FactorLookup, - allow_new=True) - self.instance.assessment = assessment - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span12' - self.fields['description'].widget.update_query_parameters( - {'related': self.instance.assessment.id}) - - def clean(self): - super(FactorForm, self).clean() - # assessment-description unique-together constraint check must be - # added since assessment is not included on form - pk = getattr(self.instance, 'pk', None) - crits = models.Factor.objects \ - .filter(assessment=self.instance.assessment, - description=self.cleaned_data.get('description', "")) \ - .exclude(pk=pk) - - if crits.count() > 0: - self.add_error("description", "Must be unique for assessment") - - return self.cleaned_data - - -class StudyCriteriaForm(forms.ModelForm): - - class Meta: - model = models.StudyCriteria - exclude = ('assessment', ) - - def __init__(self, *args, **kwargs): - assessment = kwargs.pop('parent', None) - super(StudyCriteriaForm, self).__init__(*args, **kwargs) - self.fields['description'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.StudyCriteriaLookup, - allow_new=True) - self.instance.assessment = assessment - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span12' - self.fields['description'].widget.update_query_parameters( - {'related': self.instance.assessment.id}) - - def clean(self): - super(StudyCriteriaForm, self).clean() - # assessment-description unique-together constraint check must be - # added since assessment is not included on form - pk = getattr(self.instance, 'pk', None) - crits = models.StudyCriteria.objects \ - .filter(assessment=self.instance.assessment, - description=self.cleaned_data.get('description', "")) \ - .exclude(pk=pk) - - if crits.count() > 0: - self.add_error("description", "Must be unique for assessment") - - return self.cleaned_data - - -class AssessedOutcomeForm(forms.ModelForm): - - HELP_TEXT_CREATE = """Create a new assessed outcome. An assessed - outcome is an response measured in an epidemiological study, - associated with an exposure-metric. The overall assessed outcome is - described, and then quantitative differences in response based on - different exposure-metric groups is detailed below. - """ - HELP_TEXT_UPDATE = """Create a new assessed outcome. An assessed - outcome is an response measured in an epidemiological study, - associated with an exposure-metric. The overall assessed outcome is - described, and then quantitative differences in response based on - different exposure-metric groups is detailed below. - """ - - adjustment_factors = selectable.AutoCompleteSelectMultipleField( - help_text="All factors which were included in final model", - lookup_class=lookups.FactorLookup, - required=False) - - confounders_considered = selectable.AutoCompleteSelectMultipleField( - label="Adjustment factors considered", - help_text="All factors which were examined (including those which were included in final model)", - lookup_class=lookups.FactorLookup, - required=False) - - class Meta: - model = models.AssessedOutcome - exclude = ('assessment', 'exposure') - - def __init__(self, *args, **kwargs): - assessment = kwargs.pop('assessment', None) - exposure = kwargs.pop('parent', None) - super(AssessedOutcomeForm, self).__init__(*args, **kwargs) - self.fields['name'].widget = selectable.AutoCompleteWidget( - lookup_class=BaseEndpointLookup, - allow_new=True) - self.fields['effects'].widget = selectable.AutoCompleteSelectMultipleWidget( - lookup_class=EffectTagLookup) - self.fields['effects'].help_text = 'Tags used to help categorize effect description.' - if assessment: - self.instance.assessment = assessment - if exposure: - self.instance.exposure = exposure - - self.fields['adjustment_factors'].widget.update_query_parameters( - {'related': self.instance.assessment.id}) - self.fields['confounders_considered'].widget.update_query_parameters( - {'related': self.instance.assessment.id}) - - self.fields['main_finding'].queryset = self.fields['main_finding']\ - .queryset.filter(exposure=self.instance.exposure) - - self.helper = self.setHelper() - - def setHelper(self): - for fld in ('diagnostic_description', 'summary', 'prevalence_incidence', - 'statistical_power_details', 'dose_response_details', - 'statistical_metric_description'): - self.fields[fld].widget.attrs['rows'] = 3 - - for fld in self.fields.keys(): - widget = self.fields[fld].widget - if type(widget) != forms.CheckboxInput: - if fld in ["adjustment_factors", "confounders_considered", "effects"]: - widget.attrs['class'] = 'span11' - else: - widget.attrs['class'] = 'span12' - - if self.instance.id: - inputs = { - "legend_text": u"Update {}".format(self.instance), - "help_text": self.HELP_TEXT_UPDATE, - "cancel_url": self.instance.get_absolute_url() - } - else: - inputs = { - "legend_text": u"Create new exposure", - "help_text": self.HELP_TEXT_CREATE, - "cancel_url": self.instance.exposure.get_absolute_url() - } - - helper = BaseFormHelper(self, **inputs) - helper.form_class = None - helper.add_fluid_row('effects', 2, "span6") - helper.add_fluid_row('diagnostic', 2, "span6") - helper.add_fluid_row('summary', 2, "span6") - helper.add_fluid_row('adjustment_factors', 2, "span6") - helper.add_fluid_row('dose_response', 2, "span6") - helper.add_fluid_row('statistical_power', 2, "span6") - helper.add_fluid_row('main_finding', 2, "span6") - helper.add_fluid_row('statistical_metric', 2, "span6") - - url = "{% url 'assessment:effect_tag_create' assessment.pk %}" - helper.add_adder("addEffectTags", "Add new effect tag", url) - - url = "{% url 'epi:factor_create' assessment.pk %}" - helper.add_adder("addAdj", "Add new adjustment factor", url) - helper.add_adder("addAdjCons", "Add new adjustment factor", url) - - return helper - - -class AOGForm(forms.ModelForm): - - class Meta: - fields = ('exposure_group', 'n', 'estimate', 'se', 'ci_units', - 'lower_ci', 'upper_ci', 'p_value', 'p_value_qualifier') - exclude = ('assessed_outcome', ) - model = models.AssessedOutcomeGroup - - def __init__(self, *args, **kwargs): - super(AOGForm, self).__init__(*args, **kwargs) - instance = getattr(self, 'instance', None) - self.fields['exposure_group'].widget.attrs['readOnly'] = True - self.fields['exposure_group'].widget.attrs['class'] = 'eg_fields' - for key in ('n', 'estimate', 'se', 'ci_units', 'lower_ci', - 'upper_ci', 'p_value', 'p_value_qualifier'): - self.fields[key].widget.attrs['class'] = 'input-small' - - def clean_exposure_group(self): - instance = getattr(self, 'instance', None) - if instance and instance.pk: - return instance.exposure_group - else: - return self.cleaned_data['exposure_group'] - - -class BaseAOGFormSet(BaseModelFormSet): - pass - - -AOGFormSet = modelformset_factory( - models.AssessedOutcomeGroup, - form=AOGForm, - formset=BaseAOGFormSet, - extra=0) - - -class MetaProtocolForm(forms.ModelForm): - - inclusion_criteria = selectable.AutoCompleteSelectMultipleField( - lookup_class=lookups.StudyCriteriaLookup, - required=False) - - exclusion_criteria = selectable.AutoCompleteSelectMultipleField( - lookup_class=lookups.StudyCriteriaLookup, - required=False) - - class Meta: - model = models.MetaProtocol - exclude = ('study', ) - - def __init__(self, *args, **kwargs): - parent = kwargs.pop('parent', None) - super(MetaProtocolForm, self).__init__(*args, **kwargs) - for fld in self.fields.keys(): - if fld in ('lit_search_notes', 'notes'): - self.fields[fld].widget.attrs['rows'] = 3 - widget = self.fields[fld].widget - if type(widget) != CheckboxInput: - widget.attrs['class'] = 'span12' - if parent: - self.instance.study = parent - self.fields['inclusion_criteria'].widget.update_query_parameters( - {'related': self.instance.study.assessment_id}) - self.fields['exclusion_criteria'].widget.update_query_parameters( - {'related': self.instance.study.assessment_id}) - - -class MetaResultForm(forms.ModelForm): - - adjustment_factors = selectable.AutoCompleteSelectMultipleField( - help_text="All factors which were included in final model", - lookup_class=lookups.FactorLookup, - required=False) - - class Meta: - model = models.MetaResult - exclude = ('protocol', ) - - def __init__(self, *args, **kwargs): - parent = kwargs.pop('parent', None) - assessment_id = kwargs.pop('assessment_id') - super(MetaResultForm, self).__init__(*args, **kwargs) - - self.fields['health_outcome'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.MetaResultHealthOutcomeLookup, - allow_new=True) - - self.fields['exposure_name'].widget = selectable.AutoCompleteWidget( - lookup_class=lookups.MetaResultExposureNameLookup, - allow_new=True) - - for fld in self.fields.keys(): - widget = self.fields[fld].widget - if fld in ('health_outcome_notes', 'statistical_notes', - 'notes', 'exposure_details'): - self.fields[fld].widget.attrs['rows'] = 3 - if type(widget) != CheckboxInput: - widget.attrs['class'] = 'span12' - if parent: - self.instance.protocol = parent - - self.fields['adjustment_factors'].widget.update_query_parameters( - {'related': assessment_id}) - self.fields['health_outcome'].widget.update_query_parameters( - {'related': assessment_id}) - self.fields['exposure_name'].widget.update_query_parameters( - {'related': assessment_id}) - - -class SingleResultForm(forms.ModelForm): - - resultSelector = forms.ChoiceField( - label="Results-data type", - choices=((0, "Add new results"), - (1, "Use existing results")), - initial=0) - - ao = selectable.AutoCompleteSelectField( - lookup_class=lookups.AssessedOutcomeByStudyLookup, - label='Assessed Outcome', - required=False, - widget=selectable.AutoComboboxSelectWidget) - - outcome_group = selectable.AutoCompleteSelectField( - lookup_class=lookups.AssessedOutcomeGroupByAOLookup, - label='Assessed Outcome Group', - required=False, - widget=selectable.AutoComboboxSelectWidget) - - class Meta: - model = models.SingleResult - fields = ('study', 'exposure_name', 'weight', 'outcome_group', - 'n', 'estimate', 'lower_ci', - 'upper_ci', 'ci_units', 'notes') - - def __init__(self, *args, **kwargs): - parent = kwargs.pop("parent", None) - assessment = kwargs.pop("assessment", None) - super(SingleResultForm, self).__init__(*args, **kwargs) - - # re-order with custom-fields: https://djangosnippets.org/snippets/759/ - order = ('resultSelector', 'study', 'ao', 'outcome_group', - 'exposure_name', 'weight', 'n', - 'estimate', 'lower_ci', 'upper_ci', 'ci_units', 'notes') - tmp = copy(self.fields) - self.fields = OrderedDict() - for item in order: - self.fields[item] = tmp[item] - - def updateClasses(fields, cls): - for fld in fields: - self.fields[fld].widget.attrs["class"] = cls - - if assessment: - # used with a single form; not used in formset_factory - return forms.ModelChoiceField( - queryset=self.fields["study"].queryset.filter( - assessment=assessment, study_type=1)) - - for fld in self.fields.keys(): - widget = self.fields[fld].widget - if fld == "notes": - widget.attrs['rows'] = 3 - - updateClasses(("resultSelector", ), "unstyled singleResultType") - updateClasses(("study", "exposure_name", "weight", "notes"), "span12") - updateClasses(("ao", "outcome_group", ), "span11 isAOG") - updateClasses(("n", "estimate", "lower_ci", "upper_ci", 'ci_units'), "span12 isntAOG") - self.fields['study'].widget.attrs["class"] += " studySearch" - self.fields['ao'].widget.attrs["class"] += " aoSearch" - self.fields['outcome_group'].widget.attrs["class"] += " aogSearch" - - if parent: - self.instance.meta_result = parent - - def clean_weight(self): - weight = self.cleaned_data.get('weight') - # todo: removed check, since can't specify instance in formset. - # Ideally would be able to check this. - # if weight is None and self.instance.meta_result.protocol.protocol_type == 0: - # raise forms.ValidationError("For meta-analysis epidemiological protocols, the weight-field is required") - return weight - - def clean(self): - cleaned_data = super(SingleResultForm, self).clean() - - if int(cleaned_data.get('resultSelector')) == 0: - if anyNull(cleaned_data, ('n', 'estimate', 'lower_ci', 'upper_ci')): - raise forms.ValidationError( - "If manually entering single-study data, " - "N, Risk estimate, and upper and lower CI are required.") - else: - if anyNull(cleaned_data, ('study', 'ao', 'outcome_group')): - raise forms.ValidationError( - "If entering single-study data using an Assessed Outcome Group, " - "Study, Assessed-Outcome, and Assessed-Outcome Group are required.") - - return cleaned_data - - -class EmptySingleResultFormset(FormsetWithIgnoredFields): - ignored_fields = ['resultSelector'] - - def get_queryset(self): - return models.SingleResult.objects.none() - - -class LoadedSingleResultFormset(FormsetWithIgnoredFields): - ignored_fields = ['resultSelector'] - - -SingleResultFormset = modelformset_factory( - models.SingleResult, - can_delete=True, - form=SingleResultForm, - formset=LoadedSingleResultFormset, - extra=1) - - -def meta_result_clean_update_formset(formset, assessment): - # cleanup required to get the formset in usable-shape - for form in formset.forms: - form.fields['study'].queryset = form.fields['study'].queryset.filter(assessment=assessment, study_type=1) - if form.instance and form.instance.outcome_group: - form.initial['ao'] = form.instance.outcome_group.assessed_outcome.pk - form.initial['resultSelector'] = 1 - - -class StudyPopulationSelectorForm(forms.Form): - - selector = selectable.AutoCompleteSelectField( - lookup_class=lookups.StudyPopulationByStudyLookup, - label='Study Population', - widget=selectable.AutoComboboxSelectWidget) - - def __init__(self, *args, **kwargs): - study_id = kwargs.pop('study_id') - super(StudyPopulationSelectorForm, self).__init__(*args, **kwargs) - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span11' - self.fields['selector'].widget.update_query_parameters( - {'related': study_id}) - - -class ExposureSelectorForm(forms.Form): - - selector = selectable.AutoCompleteSelectField( - lookup_class=lookups.ExposureByStudyLookup, - label='Exposure', - widget=selectable.AutoComboboxSelectWidget) - - def __init__(self, *args, **kwargs): - study_id = kwargs.pop('study_id') - super(ExposureSelectorForm, self).__init__(*args, **kwargs) - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span11' - self.fields['selector'].widget.update_query_parameters( - {'related': study_id}) - - -class AssesedOutcomeSelectorForm(forms.Form): - - selector = selectable.AutoCompleteSelectField( - lookup_class=lookups.AssessedOutcomeByStudyLookup, - label='Assessed Outcome', - widget=selectable.AutoComboboxSelectWidget) - - def __init__(self, *args, **kwargs): - study_id = kwargs.pop('study_id') - super(AssesedOutcomeSelectorForm, self).__init__(*args, **kwargs) - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span11' - self.fields['selector'].widget.update_query_parameters( - {'related': study_id}) - - -class MetaResultSelectorForm(forms.Form): - - selector = selectable.AutoCompleteSelectField( - lookup_class=lookups.MetaResultByStudyLookup, - label='Meta Result', - widget=selectable.AutoComboboxSelectWidget) - - def __init__(self, *args, **kwargs): - study_id = kwargs.pop("study_id") - super(MetaResultSelectorForm, self).__init__(*args, **kwargs) - for fld in self.fields.keys(): - self.fields[fld].widget.attrs['class'] = 'span11' - self.fields['selector'].widget.update_query_parameters( - {'related': study_id}) diff --git a/project/epi/lookups.py b/project/epi/lookups.py deleted file mode 100644 index bd96f41e..00000000 --- a/project/epi/lookups.py +++ /dev/null @@ -1,120 +0,0 @@ -from selectable.registry import registry - -from utils.lookups import DistinctStringLookup, RelatedLookup -from . import models - - -class StudyPopulationByStudyLookup(RelatedLookup): - # Return names of study populations available for a particular study - model = models.StudyPopulation - search_fields = ('name__icontains', ) - related_filter = 'study_id' - - -class RegionLookup(DistinctStringLookup): - model = models.StudyPopulation - distinct_field = "region" - - -class StateLookup(DistinctStringLookup): - model = models.StudyPopulation - distinct_field = "state" - - -class StudyCriteriaLookup(RelatedLookup): - model = models.StudyCriteria - search_fields = ('description__icontains', ) - related_filter = 'assessment_id' - - -class ExposureByStudyLookup(StudyPopulationByStudyLookup): - # Return names of exposures available for a particular study - model = models.Exposure - search_fields = ('exposure_form_definition__icontains', ) - related_filter = 'study_population__study_id' - - def get_item_label(self, obj): - return u"{} | {}".format(obj.study_population, obj) - - def get_item_value(self, obj): - return self.get_item_label(obj) - - -class FactorLookup(RelatedLookup): - model = models.Factor - search_fields = ('description__icontains', ) - related_filter = 'assessment__id' - - -class AssessedOutcomeByStudyLookup(StudyPopulationByStudyLookup): - # Return names of assessed outcomes available for a particular study - model = models.AssessedOutcome - search_fields = ( - 'name__icontains', - 'exposure__exposure_form_definition__icontains' - ) - related_filter = 'exposure__study_population__study' - - def get_query(self, request, term): - return super(AssessedOutcomeByStudyLookup, self)\ - .get_query(request, term).order_by('exposure') - - def get_item_label(self, obj): - return u"{} | {} | {}".format(obj.exposure.study_population, obj.exposure, obj) - - def get_item_value(self, obj): - return self.get_item_label(obj) - - -class AssessedOutcomeGroupByAOLookup(RelatedLookup): - model = models.AssessedOutcomeGroup - related_filter = 'assessed_outcome' - - -class MetaResultByStudyLookup(RelatedLookup): - model = models.MetaResult - search_fields = ('label__icontains', ) - related_filter = 'protocol__study' - - -class MetaResultHealthOutcomeLookup(DistinctStringLookup): - model = models.MetaResult - distinct_field = 'health_outcome' - search_fields = ('health_outcome__icontains', ) - - def get_query(self, request, term): - try: - id_ = int(request.GET.get('related', -1)) - except Exception: - id_ = -1 - return self.model.objects.filter( - protocol__study__assessment_id=id_, - health_outcome__icontains=term) - - -class MetaResultExposureNameLookup(DistinctStringLookup): - model = models.MetaResult - distinct_field = 'exposure_name' - search_fields = ('exposure_name__icontains', ) - - def get_query(self, request, term): - try: - id_ = int(request.GET.get('related', -1)) - except Exception: - id_ = -1 - return self.model.objects.filter( - protocol__study__assessment_id=id_, - exposure_name__icontains=term) - - -registry.register(StudyPopulationByStudyLookup) -registry.register(RegionLookup) -registry.register(StateLookup) -registry.register(StudyCriteriaLookup) -registry.register(ExposureByStudyLookup) -registry.register(FactorLookup) -registry.register(AssessedOutcomeByStudyLookup) -registry.register(AssessedOutcomeGroupByAOLookup) -registry.register(MetaResultByStudyLookup) -registry.register(MetaResultHealthOutcomeLookup) -registry.register(MetaResultExposureNameLookup) diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py deleted file mode 100644 index c9f7f81c..00000000 --- a/project/epi/migrations/0001_initial.py +++ /dev/null @@ -1,351 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import unicode_literals - -from django.db import models, migrations -import django.db.models.deletion -import django.core.validators - - -class Migration(migrations.Migration): - - dependencies = [ - ('animal', '0001_initial'), - ('assessment', '0001_initial'), - ('study', '0001_initial'), - ] - - operations = [ - migrations.CreateModel( - name='AssessedOutcome', - fields=[ - ('baseendpoint_ptr', models.OneToOneField(parent_link=True, auto_created=True, primary_key=True, serialize=False, to='assessment.BaseEndpoint')), - ('data_location', models.CharField(help_text=b'Details on where the data are found in the literature (ex: Figure 1, Table 2, etc.)', max_length=128, blank=True)), - ('population_description', models.CharField(help_text=b'Detailed description of the population being studied for this outcome, which may be a subset of the entire study-population. For example, "US (national) NHANES 2003-2008, Hispanic children 6-18 years, \xe2\x99\x82\xe2\x99\x80 (n=797)"', max_length=128, blank=True)), - ('diagnostic', models.PositiveSmallIntegerField(choices=[(0, b'not reported'), (1, b'medical professional or test'), (2, b'medical records'), (3, b'self-reported')])), - ('diagnostic_description', models.TextField()), - ('outcome_n', models.PositiveIntegerField(null=True, verbose_name=b'Outcome N', blank=True)), - ('summary', models.TextField(help_text=b'Summarize main findings of outcome, or describe why no details are presented (for example, "no association (data not shown)")', blank=True)), - ('prevalence_incidence', models.TextField(blank=True)), - ('dose_response', models.PositiveSmallIntegerField(default=0, help_text=b'Was a dose-response trend observed?', verbose_name=b'Dose Response Trend', choices=[(0, b'not-applicable'), (1, b'monotonic'), (2, b'non-monotonic'), (3, b'no trend'), (4, b'not reported')])), - ('dose_response_details', models.TextField(blank=True)), - ('statistical_power', models.PositiveSmallIntegerField(default=0, help_text=b'Is the study sufficiently powered?', choices=[(0, b'not reported or calculated'), (1, b'appears to be adequately powered (sample size met)'), (2, b'somewhat underpowered (sample size is 75% to <100% of recommended)'), (3, b'underpowered (sample size is 50 to <75% required)'), (4, b'severely underpowered (sample size is <50% required)')])), - ('statistical_power_details', models.TextField(blank=True)), - ('main_finding_support', models.PositiveSmallIntegerField(default=1, help_text=b'Are the results supportive of the main-finding?', choices=[(3, b'not-reported'), (2, b'supportive'), (1, b'inconclusive'), (0, b'not-supportive')])), - ('statistical_metric_description', models.TextField(help_text=b'Add additional text describing the statistical metric used, if needed.', blank=True)), - ], - options={ - }, - bases=('assessment.baseendpoint',), - ), - migrations.CreateModel( - name='AssessedOutcomeGroup', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('n', models.PositiveIntegerField(help_text=b'Individuals in group where outcome was measured', null=True, blank=True)), - ('estimate', models.FloatField(help_text=b'Central tendency estimate for group', null=True, blank=True)), - ('se', models.FloatField(help_text=b'Standard error estimate for group', null=True, verbose_name=b'Standard Error (SE)', blank=True)), - ('lower_ci', models.FloatField(help_text=b'Numerical value for lower-confidence interval', null=True, verbose_name=b'Lower CI', blank=True)), - ('upper_ci', models.FloatField(help_text=b'Numerical value for upper-confidence interval', null=True, verbose_name=b'Upper CI', blank=True)), - ('ci_units', models.FloatField(default=0.95, help_text=b'A 95% CI is written as 0.95.', null=True, verbose_name=b'Confidence Interval (CI)', blank=True)), - ('p_value_qualifier', models.CharField(default=b'-', max_length=1, verbose_name=b'p-value qualifier', choices=[(b'<', b'<'), (b'=', b'='), (b'-', b'n.s.')])), - ('p_value', models.FloatField(null=True, verbose_name=b'p-value', blank=True)), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('assessed_outcome', models.ForeignKey(related_name='groups', to='epi.AssessedOutcome')), - ], - options={ - 'ordering': ('exposure_group__exposure_group_id',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='Ethnicity', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('ethnicity', models.CharField(max_length=1, choices=[(b'I', b'American Indian or Alaskan Native'), (b'A', b'Asian'), (b'B', b'Black or African American'), (b'H', b'Hispanic/Latino'), (b'P', b'Native American of Other Pacific Islander'), (b'M', b'Two or More Races'), (b'W', b'White'), (b'O', b'Other'), (b'U', b'Unknown/Unspecified')])), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ], - options={ - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='Exposure', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('inhalation', models.BooleanField(default=False)), - ('dermal', models.BooleanField(default=False)), - ('oral', models.BooleanField(default=False)), - ('in_utero', models.BooleanField(default=False)), - ('iv', models.BooleanField(default=False, verbose_name=b'Intravenous (IV)')), - ('unknown_route', models.BooleanField(default=False)), - ('exposure_form_definition', models.TextField(help_text=b'Name of exposure-route')), - ('metric', models.TextField(verbose_name=b'Measurement Metric')), - ('metric_description', models.TextField(verbose_name=b'Measurement Description')), - ('analytical_method', models.TextField(help_text=b'Include details on the lab-techniques for exposure measurement in samples.')), - ('control_description', models.TextField()), - ('exposure_description', models.CharField(help_text=b'May be used to describe the exposure distribution, for example, "2.05 \xc2\xb5g/g creatinine (urine), geometric mean; 25th percentile = 1.18, 75th percentile = 3.33"', max_length=128, blank=True)), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('metric_units', models.ForeignKey(to='animal.DoseUnits')), - ], - options={ - 'ordering': ('exposure_form_definition',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='ExposureGroup', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('sex', models.CharField(max_length=1, choices=[(b'U', b'Not reported'), (b'M', b'Male'), (b'F', b'Female'), (b'B', b'Male and Female')])), - ('fraction_male', models.FloatField(blank=True, help_text=b'Expects a value between 0 and 1, inclusive (leave blank if unknown)', null=True, validators=[django.core.validators.MinValueValidator(0), django.core.validators.MaxValueValidator(1)])), - ('fraction_male_calculated', models.BooleanField(default=False, help_text=b'Was the fraction-male value calculated/estimated from literature?')), - ('age_mean', models.FloatField(null=True, verbose_name=b'Age central estimate', blank=True)), - ('age_mean_type', models.PositiveSmallIntegerField(default=0, verbose_name=b'Age central estimate type', choices=[(0, None), (1, b'mean'), (2, b'geometric mean'), (3, b'median')])), - ('age_calculated', models.BooleanField(default=False, help_text=b'Were age values calculated/estimated from literature?')), - ('age_description', models.CharField(help_text=b'Age description if numeric ages do not make sense for this study-population (ex: longitudinal studies)', max_length=128, blank=True)), - ('age_sd', models.FloatField(null=True, verbose_name=b'Age variance', blank=True)), - ('age_sd_type', models.PositiveSmallIntegerField(default=0, verbose_name=b'Age variance type', choices=[(0, None), (1, b'SD'), (2, b'SEM')])), - ('age_lower', models.FloatField(null=True, blank=True)), - ('age_lower_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'lower limit')])), - ('age_upper', models.FloatField(null=True, blank=True)), - ('age_upper_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'upper limit')])), - ('n', models.PositiveIntegerField(null=True, blank=True)), - ('starting_n', models.PositiveIntegerField(null=True, blank=True)), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('description', models.CharField(max_length=256)), - ('exposure_numeric', models.FloatField(help_text=b'Should be an exposure-value used for sorting', null=True, verbose_name=b'Low exposure value (sorting)', blank=True)), - ('comparative_name', models.CharField(help_text=b'Should include effect-group and comparative group, for example "1.5-2.5(Q2) vs \xe2\x89\xa41.5(Q1)", or if only one group is available, "4.8\xc2\xb10.2 (mean\xc2\xb1SEM)"', max_length=64, verbose_name=b'Comparative Name', blank=True)), - ('exposure_group_id', models.PositiveSmallIntegerField()), - ('exposure_n', models.PositiveSmallIntegerField(help_text=b'Final N used for exposure group', null=True, blank=True)), - ('ethnicity', models.ManyToManyField(to='epi.Ethnicity', blank=True)), - ('exposure', models.ForeignKey(related_name='groups', to='epi.Exposure')), - ], - options={ - 'ordering': ('exposure_group_id',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='Factor', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('description', models.TextField()), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('assessment', models.ForeignKey(to='assessment.Assessment')), - ], - options={ - 'ordering': ('description',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='MetaProtocol', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('name', models.CharField(max_length=128, verbose_name=b'Protocol name')), - ('protocol_type', models.PositiveSmallIntegerField(default=0, choices=[(0, b'Meta-analysis'), (1, b'Pooled-analysis')])), - ('lit_search_strategy', models.PositiveSmallIntegerField(default=0, verbose_name=b'Literature search strategy', choices=[(0, b'Systematic'), (1, b'Other')])), - ('lit_search_notes', models.TextField(verbose_name=b'Literature search notes', blank=True)), - ('lit_search_start_date', models.DateField(null=True, verbose_name=b'Literature search start-date', blank=True)), - ('lit_search_end_date', models.DateField(null=True, verbose_name=b'Literature search end-date', blank=True)), - ('total_references', models.PositiveIntegerField(help_text=b'References identified through initial literature-search before application of inclusion/exclusion criteria', null=True, verbose_name=b'Total number of references found', blank=True)), - ('total_studies_identified', models.PositiveIntegerField(help_text=b'Total references identified for inclusion after application of literature review and screening criteria', verbose_name=b'Total number of studies identified')), - ('notes', models.TextField(blank=True)), - ], - options={ - 'ordering': ('name',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='MetaResult', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('label', models.CharField(max_length=128)), - ('data_location', models.CharField(help_text=b'Details on where the data are found in the literature (ex: Figure 1, Table 2, etc.)', max_length=128, blank=True)), - ('health_outcome', models.CharField(max_length=128)), - ('health_outcome_notes', models.TextField(blank=True)), - ('exposure_name', models.CharField(max_length=128)), - ('exposure_details', models.TextField(blank=True)), - ('number_studies', models.PositiveSmallIntegerField()), - ('statistical_notes', models.TextField(blank=True)), - ('n', models.PositiveIntegerField(help_text=b'Number of individuals included from all analyses')), - ('estimate', models.FloatField()), - ('lower_ci', models.FloatField(help_text=b'Numerical value for lower-confidence interval', verbose_name=b'Lower CI')), - ('upper_ci', models.FloatField(help_text=b'Numerical value for upper-confidence interval', verbose_name=b'Upper CI')), - ('ci_units', models.FloatField(default=0.95, help_text=b'A 95% CI is written as 0.95.', null=True, verbose_name=b'Confidence Interval (CI)', blank=True)), - ('heterogeneity', models.CharField(max_length=256, blank=True)), - ('notes', models.TextField(blank=True)), - ('adjustment_factors', models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='meta_adjustments', null=True, to='epi.Factor', blank=True)), - ('protocol', models.ForeignKey(related_name='results', to='epi.MetaProtocol')), - ], - options={ - 'ordering': ('label',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='SingleResult', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('exposure_name', models.CharField(help_text=b'Enter a descriptive-name for the single study result (e.g., "Smith et al. 2000, obese-males")', max_length=128)), - ('weight', models.FloatField(blank=True, help_text=b'For meta-analysis, enter the fraction-weight assigned for each result (leave-blank for pooled analyses)', null=True, validators=[django.core.validators.MinValueValidator(0), django.core.validators.MaxValueValidator(1)])), - ('n', models.PositiveIntegerField(help_text=b'Enter the number of observations for this result', null=True, blank=True)), - ('estimate', models.FloatField(help_text=b'Enter the numerical risk-estimate presented for this result', null=True, blank=True)), - ('lower_ci', models.FloatField(help_text=b'Numerical value for lower-confidence interval', null=True, verbose_name=b'Lower CI', blank=True)), - ('upper_ci', models.FloatField(help_text=b'Numerical value for upper-confidence interval', null=True, verbose_name=b'Upper CI', blank=True)), - ('ci_units', models.FloatField(default=0.95, help_text=b'A 95% CI is written as 0.95.', null=True, verbose_name=b'Confidence Interval (CI)', blank=True)), - ('notes', models.TextField(blank=True)), - ('meta_result', models.ForeignKey(related_name='single_results', to='epi.MetaResult')), - ('outcome_group', models.ForeignKey(related_name='single_results', blank=True, to='epi.AssessedOutcomeGroup', null=True)), - ('study', models.ForeignKey(related_name='single_results', blank=True, to='study.Study', null=True)), - ], - options={ - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='StatisticalMetric', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('metric', models.CharField(unique=True, max_length=128)), - ('abbreviation', models.CharField(max_length=32)), - ('isLog', models.BooleanField(default=True, help_text=b'When plotting, use a log base 10 scale', verbose_name=b'Log-results')), - ('order', models.PositiveSmallIntegerField(help_text=b'Order as they appear in option-list')), - ], - options={ - 'ordering': ('order',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='StudyCriteria', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('description', models.TextField()), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('assessment', models.ForeignKey(to='assessment.Assessment')), - ], - options={ - 'ordering': ('description',), - }, - bases=(models.Model,), - ), - migrations.CreateModel( - name='StudyPopulation', - fields=[ - ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), - ('sex', models.CharField(max_length=1, choices=[(b'U', b'Not reported'), (b'M', b'Male'), (b'F', b'Female'), (b'B', b'Male and Female')])), - ('fraction_male', models.FloatField(blank=True, help_text=b'Expects a value between 0 and 1, inclusive (leave blank if unknown)', null=True, validators=[django.core.validators.MinValueValidator(0), django.core.validators.MaxValueValidator(1)])), - ('fraction_male_calculated', models.BooleanField(default=False, help_text=b'Was the fraction-male value calculated/estimated from literature?')), - ('age_mean', models.FloatField(null=True, verbose_name=b'Age central estimate', blank=True)), - ('age_mean_type', models.PositiveSmallIntegerField(default=0, verbose_name=b'Age central estimate type', choices=[(0, None), (1, b'mean'), (2, b'geometric mean'), (3, b'median')])), - ('age_calculated', models.BooleanField(default=False, help_text=b'Were age values calculated/estimated from literature?')), - ('age_description', models.CharField(help_text=b'Age description if numeric ages do not make sense for this study-population (ex: longitudinal studies)', max_length=128, blank=True)), - ('age_sd', models.FloatField(null=True, verbose_name=b'Age variance', blank=True)), - ('age_sd_type', models.PositiveSmallIntegerField(default=0, verbose_name=b'Age variance type', choices=[(0, None), (1, b'SD'), (2, b'SEM')])), - ('age_lower', models.FloatField(null=True, blank=True)), - ('age_lower_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'lower limit')])), - ('age_upper', models.FloatField(null=True, blank=True)), - ('age_upper_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'upper limit')])), - ('n', models.PositiveIntegerField(null=True, blank=True)), - ('starting_n', models.PositiveIntegerField(null=True, blank=True)), - ('created', models.DateTimeField(auto_now_add=True)), - ('last_updated', models.DateTimeField(auto_now=True)), - ('name', models.CharField(max_length=256)), - ('design', models.CharField(max_length=2, choices=[(b'CC', b'Case-control'), (b'CS', b'Cross-sectional'), (b'CP', b'Prospective'), (b'RT', b'Retrospective'), (b'CT', b'Controlled trial'), (b'SE', b'Case-series'), (b'CR', b'Case-report')])), - ('country', models.CharField(max_length=2, choices=[(b'AF', 'Afghanistan'), (b'AX', '\xc5land Islands'), (b'AL', 'Albania'), (b'DZ', 'Algeria'), (b'AS', 'American Samoa'), (b'AD', 'Andorra'), (b'AO', 'Angola'), (b'AI', 'Anguilla'), (b'AQ', 'Antarctica'), (b'AG', 'Antigua And Barbuda'), (b'AR', 'Argentina'), (b'AM', 'Armenia'), (b'AW', 'Aruba'), (b'AU', 'Australia'), (b'AT', 'Austria'), (b'AZ', 'Azerbaijan'), (b'BS', 'Bahamas'), (b'BH', 'Bahrain'), (b'BD', 'Bangladesh'), (b'BB', 'Barbados'), (b'BY', 'Belarus'), (b'BE', 'Belgium'), (b'BZ', 'Belize'), (b'BJ', 'Benin'), (b'BM', 'Bermuda'), (b'BT', 'Bhutan'), (b'BO', 'Bolivia, Plurinational State Of'), (b'BQ', 'Bonaire, Sint Eustatius And Saba'), (b'BA', 'Bosnia And Herzegovina'), (b'BW', 'Botswana'), (b'BV', 'Bouvet Island'), (b'BR', 'Brazil'), (b'IO', 'British Indian Ocean Territory'), (b'BN', 'Brunei Darussalam'), (b'BG', 'Bulgaria'), (b'BF', 'Burkina Faso'), (b'BI', 'Burundi'), (b'KH', 'Cambodia'), (b'CM', 'Cameroon'), (b'CA', 'Canada'), (b'CV', 'Cape Verde'), (b'KY', 'Cayman Islands'), (b'CF', 'Central African Republic'), (b'TD', 'Chad'), (b'CL', 'Chile'), (b'CN', 'China'), (b'CX', 'Christmas Island'), (b'CC', 'Cocos (Keeling) Islands'), (b'CO', 'Colombia'), (b'KM', 'Comoros'), (b'CG', 'Congo'), (b'CD', 'Congo, The Democratic Republic Of The'), (b'CK', 'Cook Islands'), (b'CR', 'Costa Rica'), (b'CI', "C\xf4te D'Ivoire"), (b'HR', 'Croatia'), (b'CU', 'Cuba'), (b'CW', 'Cura\xe7ao'), (b'CY', 'Cyprus'), (b'CZ', 'Czech Republic'), (b'DK', 'Denmark'), (b'DJ', 'Djibouti'), (b'DM', 'Dominica'), (b'DO', 'Dominican Republic'), (b'EC', 'Ecuador'), (b'EG', 'Egypt'), (b'SV', 'El Salvador'), (b'GQ', 'Equatorial Guinea'), (b'ER', 'Eritrea'), (b'EE', 'Estonia'), (b'ET', 'Ethiopia'), (b'FK', 'Falkland Islands (Malvinas)'), (b'FO', 'Faroe Islands'), (b'FJ', 'Fiji'), (b'FI', 'Finland'), (b'FR', 'France'), (b'GF', 'French Guiana'), (b'PF', 'French Polynesia'), (b'TF', 'French Southern Territories'), (b'GA', 'Gabon'), (b'GM', 'Gambia'), (b'GE', 'Georgia'), (b'DE', 'Germany'), (b'GH', 'Ghana'), (b'GI', 'Gibraltar'), (b'GR', 'Greece'), (b'GL', 'Greenland'), (b'GD', 'Grenada'), (b'GP', 'Guadeloupe'), (b'GU', 'Guam'), (b'GT', 'Guatemala'), (b'GG', 'Guernsey'), (b'GN', 'Guinea'), (b'GW', 'Guinea-Bissau'), (b'GY', 'Guyana'), (b'HT', 'Haiti'), (b'HM', 'Heard Island And Mcdonald Islands'), (b'VA', 'Holy See (Vatican City State)'), (b'HN', 'Honduras'), (b'HK', 'Hong Kong'), (b'HU', 'Hungary'), (b'IS', 'Iceland'), (b'IN', 'India'), (b'ID', 'Indonesia'), (b'IR', 'Iran, Islamic Republic Of'), (b'IQ', 'Iraq'), (b'IE', 'Ireland'), (b'IM', 'Isle Of Man'), (b'IL', 'Israel'), (b'IT', 'Italy'), (b'JM', 'Jamaica'), (b'JP', 'Japan'), (b'JE', 'Jersey'), (b'JO', 'Jordan'), (b'KZ', 'Kazakhstan'), (b'KE', 'Kenya'), (b'KI', 'Kiribati'), (b'KP', "Korea, Democratic People's Republic Of"), (b'KR', 'Korea, Republic Of'), (b'KW', 'Kuwait'), (b'KG', 'Kyrgyzstan'), (b'LA', "Lao People's Democratic Republic"), (b'LV', 'Latvia'), (b'LB', 'Lebanon'), (b'LS', 'Lesotho'), (b'LR', 'Liberia'), (b'LY', 'Libya'), (b'LI', 'Liechtenstein'), (b'LT', 'Lithuania'), (b'LU', 'Luxembourg'), (b'MO', 'Macao'), (b'MK', 'Macedonia, The Former Yugoslav Republic Of'), (b'MG', 'Madagascar'), (b'MW', 'Malawi'), (b'MY', 'Malaysia'), (b'MV', 'Maldives'), (b'ML', 'Mali'), (b'MT', 'Malta'), (b'MH', 'Marshall Islands'), (b'MQ', 'Martinique'), (b'MR', 'Mauritania'), (b'MU', 'Mauritius'), (b'YT', 'Mayotte'), (b'MX', 'Mexico'), (b'FM', 'Micronesia, Federated States Of'), (b'MD', 'Moldova, Republic Of'), (b'MC', 'Monaco'), (b'MN', 'Mongolia'), (b'ME', 'Montenegro'), (b'MS', 'Montserrat'), (b'MA', 'Morocco'), (b'MZ', 'Mozambique'), (b'MM', 'Myanmar'), (b'NA', 'Namibia'), (b'NR', 'Nauru'), (b'NP', 'Nepal'), (b'NL', 'Netherlands'), (b'NC', 'New Caledonia'), (b'NZ', 'New Zealand'), (b'NI', 'Nicaragua'), (b'NE', 'Niger'), (b'NG', 'Nigeria'), (b'NU', 'Niue'), (b'NF', 'Norfolk Island'), (b'MP', 'Northern Mariana Islands'), (b'NO', 'Norway'), (b'OM', 'Oman'), (b'PK', 'Pakistan'), (b'PW', 'Palau'), (b'PS', 'Palestine, State Of'), (b'PA', 'Panama'), (b'PG', 'Papua New Guinea'), (b'PY', 'Paraguay'), (b'PE', 'Peru'), (b'PH', 'Philippines'), (b'PN', 'Pitcairn'), (b'PL', 'Poland'), (b'PT', 'Portugal'), (b'PR', 'Puerto Rico'), (b'QA', 'Qatar'), (b'RE', 'R\xe9union'), (b'RO', 'Romania'), (b'RU', 'Russian Federation'), (b'RW', 'Rwanda'), (b'BL', 'Saint Barth\xe9lemy'), (b'SH', 'Saint Helena, Ascension And Tristan Da Cunha'), (b'KN', 'Saint Kitts And Nevis'), (b'LC', 'Saint Lucia'), (b'MF', 'Saint Martin (French Part)'), (b'PM', 'Saint Pierre And Miquelon'), (b'VC', 'Saint Vincent And The Grenadines'), (b'WS', 'Samoa'), (b'SM', 'San Marino'), (b'ST', 'Sao Tome And Principe'), (b'SA', 'Saudi Arabia'), (b'SN', 'Senegal'), (b'RS', 'Serbia'), (b'SC', 'Seychelles'), (b'SL', 'Sierra Leone'), (b'SG', 'Singapore'), (b'SX', 'Sint Maarten (Dutch Part)'), (b'SK', 'Slovakia'), (b'SI', 'Slovenia'), (b'SB', 'Solomon Islands'), (b'SO', 'Somalia'), (b'ZA', 'South Africa'), (b'GS', 'South Georgia And The South Sandwich Islands'), (b'SS', 'South Sudan'), (b'ES', 'Spain'), (b'LK', 'Sri Lanka'), (b'SD', 'Sudan'), (b'SR', 'Suriname'), (b'SJ', 'Svalbard And Jan Mayen'), (b'SZ', 'Swaziland'), (b'SE', 'Sweden'), (b'CH', 'Switzerland'), (b'SY', 'Syrian Arab Republic'), (b'TW', 'Taiwan, Province Of China'), (b'TJ', 'Tajikistan'), (b'TZ', 'Tanzania, United Republic Of'), (b'TH', 'Thailand'), (b'TL', 'Timor-Leste'), (b'TG', 'Togo'), (b'TK', 'Tokelau'), (b'TO', 'Tonga'), (b'TT', 'Trinidad And Tobago'), (b'TN', 'Tunisia'), (b'TR', 'Turkey'), (b'TM', 'Turkmenistan'), (b'TC', 'Turks And Caicos Islands'), (b'TV', 'Tuvalu'), (b'UG', 'Uganda'), (b'UA', 'Ukraine'), (b'AE', 'United Arab Emirates'), (b'GB', 'United Kingdom'), (b'US', 'United States'), (b'UM', 'United States Minor Outlying Islands'), (b'UY', 'Uruguay'), (b'UZ', 'Uzbekistan'), (b'VU', 'Vanuatu'), (b'VE', 'Venezuela, Bolivarian Republic Of'), (b'VN', 'Viet Nam'), (b'VG', 'Virgin Islands, British'), (b'VI', 'Virgin Islands, U.S.'), (b'WF', 'Wallis And Futuna'), (b'EH', 'Western Sahara'), (b'YE', 'Yemen'), (b'ZM', 'Zambia'), (b'ZW', 'Zimbabwe')])), - ('region', models.CharField(max_length=128, blank=True)), - ('state', models.CharField(max_length=128, blank=True)), - ('confounding_criteria', models.ManyToManyField(related_name='confounding_criteria', null=True, to='epi.StudyCriteria', blank=True)), - ('ethnicity', models.ManyToManyField(to='epi.Ethnicity', blank=True)), - ('exclusion_criteria', models.ManyToManyField(related_name='exclusion_criteria', null=True, to='epi.StudyCriteria', blank=True)), - ('inclusion_criteria', models.ManyToManyField(related_name='inclusion_criteria', null=True, to='epi.StudyCriteria', blank=True)), - ('study', models.ForeignKey(related_name='study_populations', to='study.Study')), - ], - options={ - 'ordering': ('name',), - }, - bases=(models.Model,), - ), - migrations.AlterUniqueTogether( - name='studycriteria', - unique_together=set([('assessment', 'description')]), - ), - migrations.AddField( - model_name='metaresult', - name='statistical_metric', - field=models.ForeignKey(to='epi.StatisticalMetric'), - preserve_default=True, - ), - migrations.AddField( - model_name='metaprotocol', - name='exclusion_criteria', - field=models.ManyToManyField(related_name='meta_exclusion_criteria', null=True, to='epi.StudyCriteria', blank=True), - preserve_default=True, - ), - migrations.AddField( - model_name='metaprotocol', - name='inclusion_criteria', - field=models.ManyToManyField(related_name='meta_inclusion_criteria', null=True, to='epi.StudyCriteria', blank=True), - preserve_default=True, - ), - migrations.AddField( - model_name='metaprotocol', - name='study', - field=models.ForeignKey(related_name='meta_protocols', to='study.Study'), - preserve_default=True, - ), - migrations.AlterUniqueTogether( - name='factor', - unique_together=set([('assessment', 'description')]), - ), - migrations.AddField( - model_name='exposure', - name='study_population', - field=models.ForeignKey(related_name='exposures', to='epi.StudyPopulation'), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcomegroup', - name='exposure_group', - field=models.ForeignKey(help_text=b'Exposure-group related to this assessed outcome group', to='epi.ExposureGroup'), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcome', - name='adjustment_factors', - field=models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='adjustments', null=True, to='epi.Factor', blank=True), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcome', - name='confounders_considered', - field=models.ManyToManyField(related_name='confounders', to='epi.Factor', blank=True, help_text=b'All factors which were examined (including those which were included in final model)', null=True, verbose_name=b'Adjustment factors considered'), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcome', - name='exposure', - field=models.ForeignKey(related_name='outcomes', to='epi.Exposure'), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcome', - name='main_finding', - field=models.ForeignKey(on_delete=django.db.models.deletion.SET_NULL, blank=True, to='epi.ExposureGroup', help_text=b'When a study did not report a statistically significant association use the highest exposure group compared with the referent group (e.g., fourth quartile vs. first quartile). When a study reports a statistically significant association use the lowest exposure group with a statistically significant association (e.g., third quartile vs. first quartile). When associations were non-monotonic in nature, select main findings on a case-by-case basis.', null=True, verbose_name=b'Main finding'), - preserve_default=True, - ), - migrations.AddField( - model_name='assessedoutcome', - name='statistical_metric', - field=models.ForeignKey(to='epi.StatisticalMetric'), - preserve_default=True, - ), - ] diff --git a/project/epi/migrations/0002_auto_20150629_1327.py b/project/epi/migrations/0002_auto_20150629_1327.py deleted file mode 100644 index b41e3431..00000000 --- a/project/epi/migrations/0002_auto_20150629_1327.py +++ /dev/null @@ -1,54 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import unicode_literals - -from django.db import models, migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('epi', '0001_initial'), - ] - - operations = [ - migrations.AlterField( - model_name='assessedoutcome', - name='adjustment_factors', - field=models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='adjustments', to='epi.Factor', blank=True), - ), - migrations.AlterField( - model_name='assessedoutcome', - name='confounders_considered', - field=models.ManyToManyField(help_text=b'All factors which were examined (including those which were included in final model)', related_name='confounders', verbose_name=b'Adjustment factors considered', to='epi.Factor', blank=True), - ), - migrations.AlterField( - model_name='metaprotocol', - name='exclusion_criteria', - field=models.ManyToManyField(related_name='meta_exclusion_criteria', to='epi.StudyCriteria', blank=True), - ), - migrations.AlterField( - model_name='metaprotocol', - name='inclusion_criteria', - field=models.ManyToManyField(related_name='meta_inclusion_criteria', to='epi.StudyCriteria', blank=True), - ), - migrations.AlterField( - model_name='metaresult', - name='adjustment_factors', - field=models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='meta_adjustments', to='epi.Factor', blank=True), - ), - migrations.AlterField( - model_name='studypopulation', - name='confounding_criteria', - field=models.ManyToManyField(related_name='confounding_criteria', to='epi.StudyCriteria', blank=True), - ), - migrations.AlterField( - model_name='studypopulation', - name='exclusion_criteria', - field=models.ManyToManyField(related_name='exclusion_criteria', to='epi.StudyCriteria', blank=True), - ), - migrations.AlterField( - model_name='studypopulation', - name='inclusion_criteria', - field=models.ManyToManyField(related_name='inclusion_criteria', to='epi.StudyCriteria', blank=True), - ), - ] diff --git a/project/epi/migrations/0003_auto_20150723_1544.py b/project/epi/migrations/0003_auto_20150723_1544.py deleted file mode 100644 index d8dba4ff..00000000 --- a/project/epi/migrations/0003_auto_20150723_1544.py +++ /dev/null @@ -1,25 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import unicode_literals - -from django.db import models, migrations - - -class Migration(migrations.Migration): - - dependencies = [ - ('epi', '0002_auto_20150629_1327'), - ('animal', '0010_auto_20150723_1536'), - ] - - state_operations = [ - migrations.AlterField( - model_name='exposure', - name='metric_units', - field=models.ForeignKey(to='assessment.DoseUnits'), - ), - ] - - operations = [ - migrations.SeparateDatabaseAndState( - state_operations=state_operations) - ] diff --git a/project/epi/migrations/__init__.py b/project/epi/migrations/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/project/epi/models.py b/project/epi/models.py deleted file mode 100644 index 7be9ba62..00000000 --- a/project/epi/models.py +++ /dev/null @@ -1,1645 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf8 -*- - -import hashlib -import json - -from django.db import models -from django.core.urlresolvers import reverse -from django.core.validators import MinValueValidator, MaxValueValidator -from django.db.models.signals import post_save, pre_delete -from django.dispatch import receiver - -import reversion - -from assessment.models import BaseEndpoint -from assessment.serializers import AssessmentSerializer -from utils.helper import HAWCDjangoJSONEncoder, SerializerHelper - - -class StudyCriteria(models.Model): - assessment = models.ForeignKey( - 'assessment.Assessment') - description = models.TextField() - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - class Meta: - ordering = ('description', ) - unique_together = ('assessment', 'description') - - def __unicode__(self): - return self.description - - -class Ethnicity(models.Model): - - # https://www.fsd1.org/powerschool/Documents/PDFs/Federal_Race_Ethnicity_Guidelines.pdf - ETHNICITY_CHOICES = ( - ('I', 'American Indian or Alaskan Native'), - ('A', 'Asian'), - ('B', 'Black or African American'), - ('H', 'Hispanic/Latino'), - ('P', 'Native American of Other Pacific Islander'), - ('M', 'Two or More Races'), - ('W', 'White'), - ('O', 'Other'), - ('U', 'Unknown/Unspecified')) - - ethnicity = models.CharField( - max_length=1, - choices=ETHNICITY_CHOICES) - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - def __unicode__(self): - return self.get_ethnicity_display() - - -class Demographics(models.Model): - - SEX_CHOICES = ( - ("U", "Not reported"), - ("M", "Male"), - ("F", "Female"), - ("B", "Male and Female")) - - MEAN_TYPE_CHOICES = ( - (0, None), - (1, "mean"), - (2, "geometric mean"), - (3, "median")) - - SD_TYPE_CHOICES = ( - (0, None), - (1, "SD"), - (2, "SEM")) - - AGE_LOWER_LIMIT_CHOICES = ( - (0, None), - (1, 'lower limit')) - - AGE_UPPER_LIMIT_CHOICES = ( - (0, None), - (1, 'upper limit')) - - sex = models.CharField( - max_length=1, - choices=SEX_CHOICES) - ethnicity = models.ManyToManyField( - Ethnicity, - blank=True) - fraction_male = models.FloatField( - blank=True, - null=True, - help_text="Expects a value between 0 and 1, inclusive (leave blank if unknown)", - validators=[MinValueValidator(0), MaxValueValidator(1)]) - fraction_male_calculated = models.BooleanField( - default=False, - help_text="Was the fraction-male value calculated/estimated from literature?") - age_mean = models.FloatField( - blank=True, - null=True, - verbose_name='Age central estimate') - age_mean_type = models.PositiveSmallIntegerField( - choices=MEAN_TYPE_CHOICES, - verbose_name="Age central estimate type", - default=0) - age_calculated = models.BooleanField( - default=False, - help_text="Were age values calculated/estimated from literature?") - age_description = models.CharField( - max_length=128, - blank=True, - help_text="Age description if numeric ages do not make sense for this " - "study-population (ex: longitudinal studies)") - age_sd = models.FloatField( - blank=True, - null=True, - verbose_name='Age variance') - age_sd_type = models.PositiveSmallIntegerField( - choices=SD_TYPE_CHOICES, - verbose_name="Age variance type", - default=0) - age_lower = models.FloatField( - blank=True, - null=True) - age_lower_type = models.PositiveSmallIntegerField( - choices=AGE_LOWER_LIMIT_CHOICES, - default=0) - age_upper = models.FloatField( - blank=True, - null=True) - age_upper_type = models.PositiveSmallIntegerField( - choices=AGE_UPPER_LIMIT_CHOICES, - default=0) - n = models.PositiveIntegerField( - blank=True, - null=True) - starting_n = models.PositiveIntegerField( - blank=True, - null=True) - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - class Meta: - abstract = True - - @staticmethod - def flat_complete_header_row(prefix="-"): - return ( - prefix+'sex', - prefix+'ethnicity', - prefix+'fraction_male', - prefix+'fraction_male_calculated', - prefix+'age_mean', - prefix+'age_mean_type', - prefix+'age_calculated', - prefix+'age_description', - prefix+'age_sd', - prefix+'age_sd_type', - prefix+'age_lower', - prefix+'age_lower_type', - prefix+'age_upper', - prefix+'age_upper_type', - prefix+'n' - ) - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['sex'], - '|'.join(ser['ethnicity']), - ser['fraction_male'], - ser['fraction_male_calculated'], - ser['age_mean'], - ser['age_mean_type'], - ser['age_calculated'], - ser['age_description'], - ser['age_sd'], - ser['age_sd_type'], - ser['age_lower'], - ser['age_lower_type'], - ser['age_upper'], - ser['age_upper_type'], - ser['n'] - ) - - def get_ethnicity_list(self): - eths = [] - for eth in self.ethnicity.all(): - eths.append(eth.get_ethnicity_display()) - return ', '.join(eths) - - -class Factor(models.Model): - assessment = models.ForeignKey( - 'assessment.Assessment') - description = models.TextField() - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - class Meta: - unique_together = ('assessment', 'description') - ordering = ('description', ) - - def __unicode__(self): - return self.description - - -class StudyPopulation(Demographics): - - EPI_STUDY_DESIGN_CHOICES = ( - ('CC', 'Case-control'), - ('CS', 'Cross-sectional'), - ('CP', 'Prospective'), - ('RT', 'Retrospective'), - ('CT', 'Controlled trial'), - ('SE', 'Case-series'), - ('CR', 'Case-report')) - - # https://www.iso.org/obp/ui/ - EPI_STUDY_COUNTRY_CHOICES = ( - ("AF", u"Afghanistan"), - ("AX", u"Åland Islands"), - ("AL", u"Albania"), - ("DZ", u"Algeria"), - ("AS", u"American Samoa"), - ("AD", u"Andorra"), - ("AO", u"Angola"), - ("AI", u"Anguilla"), - ("AQ", u"Antarctica"), - ("AG", u"Antigua And Barbuda"), - ("AR", u"Argentina"), - ("AM", u"Armenia"), - ("AW", u"Aruba"), - ("AU", u"Australia"), - ("AT", u"Austria"), - ("AZ", u"Azerbaijan"), - ("BS", u"Bahamas"), - ("BH", u"Bahrain"), - ("BD", u"Bangladesh"), - ("BB", u"Barbados"), - ("BY", u"Belarus"), - ("BE", u"Belgium"), - ("BZ", u"Belize"), - ("BJ", u"Benin"), - ("BM", u"Bermuda"), - ("BT", u"Bhutan"), - ("BO", u"Bolivia, Plurinational State Of"), - ("BQ", u"Bonaire, Sint Eustatius And Saba"), - ("BA", u"Bosnia And Herzegovina"), - ("BW", u"Botswana"), - ("BV", u"Bouvet Island"), - ("BR", u"Brazil"), - ("IO", u"British Indian Ocean Territory"), - ("BN", u"Brunei Darussalam"), - ("BG", u"Bulgaria"), - ("BF", u"Burkina Faso"), - ("BI", u"Burundi"), - ("KH", u"Cambodia"), - ("CM", u"Cameroon"), - ("CA", u"Canada"), - ("CV", u"Cape Verde"), - ("KY", u"Cayman Islands"), - ("CF", u"Central African Republic"), - ("TD", u"Chad"), - ("CL", u"Chile"), - ("CN", u"China"), - ("CX", u"Christmas Island"), - ("CC", u"Cocos (Keeling) Islands"), - ("CO", u"Colombia"), - ("KM", u"Comoros"), - ("CG", u"Congo"), - ("CD", u"Congo, The Democratic Republic Of The"), - ("CK", u"Cook Islands"), - ("CR", u"Costa Rica"), - ("CI", u"Côte D'Ivoire"), - ("HR", u"Croatia"), - ("CU", u"Cuba"), - ("CW", u"Curaçao"), - ("CY", u"Cyprus"), - ("CZ", u"Czech Republic"), - ("DK", u"Denmark"), - ("DJ", u"Djibouti"), - ("DM", u"Dominica"), - ("DO", u"Dominican Republic"), - ("EC", u"Ecuador"), - ("EG", u"Egypt"), - ("SV", u"El Salvador"), - ("GQ", u"Equatorial Guinea"), - ("ER", u"Eritrea"), - ("EE", u"Estonia"), - ("ET", u"Ethiopia"), - ("FK", u"Falkland Islands (Malvinas)"), - ("FO", u"Faroe Islands"), - ("FJ", u"Fiji"), - ("FI", u"Finland"), - ("FR", u"France"), - ("GF", u"French Guiana"), - ("PF", u"French Polynesia"), - ("TF", u"French Southern Territories"), - ("GA", u"Gabon"), - ("GM", u"Gambia"), - ("GE", u"Georgia"), - ("DE", u"Germany"), - ("GH", u"Ghana"), - ("GI", u"Gibraltar"), - ("GR", u"Greece"), - ("GL", u"Greenland"), - ("GD", u"Grenada"), - ("GP", u"Guadeloupe"), - ("GU", u"Guam"), - ("GT", u"Guatemala"), - ("GG", u"Guernsey"), - ("GN", u"Guinea"), - ("GW", u"Guinea-Bissau"), - ("GY", u"Guyana"), - ("HT", u"Haiti"), - ("HM", u"Heard Island And Mcdonald Islands"), - ("VA", u"Holy See (Vatican City State)"), - ("HN", u"Honduras"), - ("HK", u"Hong Kong"), - ("HU", u"Hungary"), - ("IS", u"Iceland"), - ("IN", u"India"), - ("ID", u"Indonesia"), - ("IR", u"Iran, Islamic Republic Of"), - ("IQ", u"Iraq"), - ("IE", u"Ireland"), - ("IM", u"Isle Of Man"), - ("IL", u"Israel"), - ("IT", u"Italy"), - ("JM", u"Jamaica"), - ("JP", u"Japan"), - ("JE", u"Jersey"), - ("JO", u"Jordan"), - ("KZ", u"Kazakhstan"), - ("KE", u"Kenya"), - ("KI", u"Kiribati"), - ("KP", u"Korea, Democratic People's Republic Of"), - ("KR", u"Korea, Republic Of"), - ("KW", u"Kuwait"), - ("KG", u"Kyrgyzstan"), - ("LA", u"Lao People's Democratic Republic"), - ("LV", u"Latvia"), - ("LB", u"Lebanon"), - ("LS", u"Lesotho"), - ("LR", u"Liberia"), - ("LY", u"Libya"), - ("LI", u"Liechtenstein"), - ("LT", u"Lithuania"), - ("LU", u"Luxembourg"), - ("MO", u"Macao"), - ("MK", u"Macedonia, The Former Yugoslav Republic Of"), - ("MG", u"Madagascar"), - ("MW", u"Malawi"), - ("MY", u"Malaysia"), - ("MV", u"Maldives"), - ("ML", u"Mali"), - ("MT", u"Malta"), - ("MH", u"Marshall Islands"), - ("MQ", u"Martinique"), - ("MR", u"Mauritania"), - ("MU", u"Mauritius"), - ("YT", u"Mayotte"), - ("MX", u"Mexico"), - ("FM", u"Micronesia, Federated States Of"), - ("MD", u"Moldova, Republic Of"), - ("MC", u"Monaco"), - ("MN", u"Mongolia"), - ("ME", u"Montenegro"), - ("MS", u"Montserrat"), - ("MA", u"Morocco"), - ("MZ", u"Mozambique"), - ("MM", u"Myanmar"), - ("NA", u"Namibia"), - ("NR", u"Nauru"), - ("NP", u"Nepal"), - ("NL", u"Netherlands"), - ("NC", u"New Caledonia"), - ("NZ", u"New Zealand"), - ("NI", u"Nicaragua"), - ("NE", u"Niger"), - ("NG", u"Nigeria"), - ("NU", u"Niue"), - ("NF", u"Norfolk Island"), - ("MP", u"Northern Mariana Islands"), - ("NO", u"Norway"), - ("OM", u"Oman"), - ("PK", u"Pakistan"), - ("PW", u"Palau"), - ("PS", u"Palestine, State Of"), - ("PA", u"Panama"), - ("PG", u"Papua New Guinea"), - ("PY", u"Paraguay"), - ("PE", u"Peru"), - ("PH", u"Philippines"), - ("PN", u"Pitcairn"), - ("PL", u"Poland"), - ("PT", u"Portugal"), - ("PR", u"Puerto Rico"), - ("QA", u"Qatar"), - ("RE", u"Réunion"), - ("RO", u"Romania"), - ("RU", u"Russian Federation"), - ("RW", u"Rwanda"), - ("BL", u"Saint Barthélemy"), - ("SH", u"Saint Helena, Ascension And Tristan Da Cunha"), - ("KN", u"Saint Kitts And Nevis"), - ("LC", u"Saint Lucia"), - ("MF", u"Saint Martin (French Part)"), - ("PM", u"Saint Pierre And Miquelon"), - ("VC", u"Saint Vincent And The Grenadines"), - ("WS", u"Samoa"), - ("SM", u"San Marino"), - ("ST", u"Sao Tome And Principe"), - ("SA", u"Saudi Arabia"), - ("SN", u"Senegal"), - ("RS", u"Serbia"), - ("SC", u"Seychelles"), - ("SL", u"Sierra Leone"), - ("SG", u"Singapore"), - ("SX", u"Sint Maarten (Dutch Part)"), - ("SK", u"Slovakia"), - ("SI", u"Slovenia"), - ("SB", u"Solomon Islands"), - ("SO", u"Somalia"), - ("ZA", u"South Africa"), - ("GS", u"South Georgia And The South Sandwich Islands"), - ("SS", u"South Sudan"), - ("ES", u"Spain"), - ("LK", u"Sri Lanka"), - ("SD", u"Sudan"), - ("SR", u"Suriname"), - ("SJ", u"Svalbard And Jan Mayen"), - ("SZ", u"Swaziland"), - ("SE", u"Sweden"), - ("CH", u"Switzerland"), - ("SY", u"Syrian Arab Republic"), - ("TW", u"Taiwan, Province Of China"), - ("TJ", u"Tajikistan"), - ("TZ", u"Tanzania, United Republic Of"), - ("TH", u"Thailand"), - ("TL", u"Timor-Leste"), - ("TG", u"Togo"), - ("TK", u"Tokelau"), - ("TO", u"Tonga"), - ("TT", u"Trinidad And Tobago"), - ("TN", u"Tunisia"), - ("TR", u"Turkey"), - ("TM", u"Turkmenistan"), - ("TC", u"Turks And Caicos Islands"), - ("TV", u"Tuvalu"), - ("UG", u"Uganda"), - ("UA", u"Ukraine"), - ("AE", u"United Arab Emirates"), - ("GB", u"United Kingdom"), - ("US", u"United States"), - ("UM", u"United States Minor Outlying Islands"), - ("UY", u"Uruguay"), - ("UZ", u"Uzbekistan"), - ("VU", u"Vanuatu"), - ("VE", u"Venezuela, Bolivarian Republic Of"), - ("VN", u"Viet Nam"), - ("VG", u"Virgin Islands, British"), - ("VI", u"Virgin Islands, U.S."), - ("WF", u"Wallis And Futuna"), - ("EH", u"Western Sahara"), - ("YE", u"Yemen"), - ("ZM", u"Zambia"), - ("ZW", u"Zimbabwe")) - - study = models.ForeignKey( - 'study.Study', - related_name="study_populations") - name = models.CharField( - max_length=256) - design = models.CharField( - max_length=2, - choices=EPI_STUDY_DESIGN_CHOICES) - country = models.CharField( - max_length=2, - choices=EPI_STUDY_COUNTRY_CHOICES) - region = models.CharField( - max_length=128, - blank=True) - state = models.CharField( - max_length=128, - blank=True) - inclusion_criteria = models.ManyToManyField( - StudyCriteria, - related_name='inclusion_criteria', - blank=True) - exclusion_criteria = models.ManyToManyField( - StudyCriteria, - related_name='exclusion_criteria', - blank=True) - confounding_criteria = models.ManyToManyField( - StudyCriteria, - related_name='confounding_criteria', - blank=True) - - class Meta: - ordering = ('name', ) - - def __unicode__(self): - return self.name - - def get_location(self): - loc = "" - if self.country: - loc += self.get_country_display() - if self.state: - loc += " ({s})".format(s=self.state) - if self.region: - loc += " ({r})".format(r=self.region) - return loc - - def get_absolute_url(self): - return reverse('epi:sp_detail', kwargs={'pk': self.pk}) - - def get_assessment(self): - return self.study.get_assessment() - - def get_json(self, json_encode=True): - return SerializerHelper.get_serialized(self, json=json_encode, from_cache=False) - - @staticmethod - def flat_complete_header_row(): - return ( - 'sp-pk', - 'sp-url', - 'sp-name', - 'sp-design', - 'sp-country', - 'sp-region', - 'sp-state', - 'sp-inclusion_criteria', - 'sp-exclusion_criteria', - 'sp-confounding_criteria' - ) + Demographics.flat_complete_header_row(prefix='sp-') - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['url'], - ser['name'], - ser['design'], - ser['country'], - ser['region'], - ser['state'], - '|'.join(ser['inclusion_criteria']), - '|'.join(ser['exclusion_criteria']), - '|'.join(ser['confounding_criteria']) - ) + Demographics.flat_complete_data_row(ser) - - -class Exposure(models.Model): - study_population = models.ForeignKey( - StudyPopulation, - related_name="exposures") - inhalation = models.BooleanField( - default=False) - dermal = models.BooleanField( - default=False) - oral = models.BooleanField( - default=False) - in_utero = models.BooleanField( - default=False) - iv = models.BooleanField( - default=False, - verbose_name="Intravenous (IV)") - unknown_route = models.BooleanField( - default=False) - exposure_form_definition = models.TextField( - help_text='Name of exposure-route') - metric = models.TextField( - verbose_name="Measurement Metric") - metric_units = models.ForeignKey( - 'assessment.DoseUnits') - metric_description = models.TextField( - verbose_name="Measurement Description") - analytical_method = models.TextField( - help_text="Include details on the lab-techniques for exposure measurement in samples.") - control_description = models.TextField() - exposure_description = models.CharField( - max_length=128, - blank=True, - help_text='May be used to describe the exposure distribution, for ' - 'example, "2.05 µg/g creatinine (urine), geometric mean; ' - '25th percentile = 1.18, 75th percentile = 3.33"') - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - class Meta: - ordering = ('exposure_form_definition', ) - - def __unicode__(self): - return self.exposure_form_definition - - def get_absolute_url(self): - return reverse('epi:exposure_detail', kwargs={'pk': self.pk}) - - def get_assessment(self): - return self.study_population.get_assessment() - - @staticmethod - def flat_complete_header_row(): - return ( - 'exposure-pk', - 'exposure-url', - 'exposure-inhalation', - 'exposure-dermal', - 'exposure-oral', - 'exposure-in_utero', - 'exposure-iv', - 'exposure-unknown_route', - 'exposure-exposure_form_definition', - 'exposure-metric', - 'exposure-metric_units', - 'exposure-metric_description', - 'exposure-analytical_method', - 'exposure-control_description', - 'exposure-exposure_description' - ) - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['url'], - ser['inhalation'], - ser['dermal'], - ser['oral'], - ser['in_utero'], - ser['iv'], - ser['unknown_route'], - ser['exposure_form_definition'], - ser['metric'], - ser['metric_units']['name'], - ser['metric_description'], - ser['analytical_method'], - ser['control_description'], - ser['exposure_description'] - ) - - -class StatisticalMetric(models.Model): - metric = models.CharField( - max_length=128, - unique=True) - abbreviation = models.CharField( - max_length=32) - isLog = models.BooleanField( - default=True, - verbose_name="Log-results", - help_text="When plotting, use a log base 10 scale") - order = models.PositiveSmallIntegerField( - help_text="Order as they appear in option-list") - - class Meta: - ordering = ('order', ) - - def __unicode__(self): - return self.metric - - -class AssessedOutcome(BaseEndpoint): - - DIAGNOSTIC_CHOICES = ( - (0, 'not reported'), - (1, 'medical professional or test'), - (2, 'medical records'), - (3, 'self-reported')) - - MAIN_FINDING_CHOICES = ( - (3, "not-reported"), - (2, "supportive"), - (1, "inconclusive"), - (0, "not-supportive")) - - DOSE_RESPONSE_CHOICES = ( - (0, "not-applicable"), - (1, "monotonic"), - (2, "non-monotonic"), - (3, "no trend"), - (4, "not reported")) - - STATISTICAL_POWER_CHOICES = ( - (0, 'not reported or calculated'), - (1, 'appears to be adequately powered (sample size met)'), - (2, 'somewhat underpowered (sample size is 75% to <100% of recommended)'), - (3, 'underpowered (sample size is 50 to <75% required)'), - (4, 'severely underpowered (sample size is <50% required)')) - - exposure = models.ForeignKey( - Exposure, - related_name='outcomes') - data_location = models.CharField( - max_length=128, - blank=True, - help_text="Details on where the data are found in the literature " - "(ex: Figure 1, Table 2, etc.)") - population_description = models.CharField( - max_length=128, - help_text='Detailed description of the population being studied for this outcome, ' - 'which may be a subset of the entire study-population. For example, ' - '"US (national) NHANES 2003-2008, Hispanic children 6-18 years, ♂♀ (n=797)"', - blank=True) - diagnostic = models.PositiveSmallIntegerField( - choices=DIAGNOSTIC_CHOICES) - diagnostic_description = models.TextField() - outcome_n = models.PositiveIntegerField( - blank=True, - null=True, - verbose_name="Outcome N") - summary = models.TextField(blank=True, - help_text='Summarize main findings of outcome, or describe why no ' - 'details are presented (for example, "no association ' - '(data not shown)")') - prevalence_incidence = models.TextField( - blank=True) - adjustment_factors = models.ManyToManyField(Factor, - help_text="All factors which were included in final model", - related_name='adjustments', - blank=True) - confounders_considered = models.ManyToManyField(Factor, - verbose_name= "Adjustment factors considered", - help_text="All factors which were examined " - "(including those which were included in final model)", - related_name='confounders', - blank=True) - dose_response = models.PositiveSmallIntegerField( - verbose_name="Dose Response Trend", - help_text="Was a dose-response trend observed?", - default=0, - choices=DOSE_RESPONSE_CHOICES) - dose_response_details = models.TextField( - blank=True) - statistical_power = models.PositiveSmallIntegerField( - help_text="Is the study sufficiently powered?", - default=0, - choices=STATISTICAL_POWER_CHOICES) - statistical_power_details = models.TextField( - blank=True) - main_finding = models.ForeignKey( - 'epi.ExposureGroup', - blank=True, - null=True, - on_delete=models.SET_NULL, - verbose_name="Main finding", - help_text="When a study did not report a statistically significant " - "association use the highest exposure group compared with " - "the referent group (e.g., fourth quartile vs. first " - "quartile). When a study reports a statistically " - "significant association use the lowest exposure group " - "with a statistically significant association (e.g., " - "third quartile vs. first quartile). When associations " - "were non-monotonic in nature, select main findings " - "on a case-by-case basis.") - main_finding_support = models.PositiveSmallIntegerField( - choices=MAIN_FINDING_CHOICES, - help_text="Are the results supportive of the main-finding?", - default=1) - statistical_metric = models.ForeignKey( - StatisticalMetric) - statistical_metric_description = models.TextField( - blank=True, - help_text="Add additional text describing the statistical metric used, if needed.") - - @classmethod - def delete_caches(cls, ids): - SerializerHelper.delete_caches(cls, ids) - - def get_absolute_url(self): - return reverse('epi:assessedoutcome_detail', kwargs={'pk': self.pk}) - - def get_json(self, json_encode=True): - return SerializerHelper.get_serialized(self, json=json_encode) - - def get_prior_versions_json(self): - """ Get prior versions of object. """ - versions = reversion.get_for_object(self) - versions_json = [] - for version in versions: - fields = version.field_dict - try: - fields['statistical_metric'] = unicode(StatisticalMetric.objects.get(pk=fields['statistical_metric'])) - except Exception: - fields['statistical_metric'] = "-" - return json.dumps(versions_json, cls=HAWCDjangoJSONEncoder) - - @staticmethod - def flat_complete_header_row(): - return ( - 'assessed_outcome-pk', - 'assessed_outcome-url', - 'assessed_outcome-name', - 'assessed_outcome-data_location', - 'assessed_outcome-population_description', - 'assessed_outcome-effects', - 'assessed_outcome-diagnostic', - 'assessed_outcome-diagnostic_description', - 'assessed_outcome-outcome_n', - 'assessed_outcome-summary', - 'assessed_outcome-prevalence_incidence', - 'assessed_outcome-adjustment_factors', - 'assessed_outcome-adjustment_factors_considered', - 'assessed_outcome-main_finding_support', - 'assessed_outcome-dose_response', - 'assessed_outcome-dose_response_details', - 'assessed_outcome-statistical_power', - 'assessed_outcome-statistical_power_details', - 'assessed_outcome-statistical_metric', - 'assessed_outcome-statistical_metric_description' - ) - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['url'], - ser['name'], - ser['data_location'], - ser['population_description'], - '|'.join([unicode(d['name']) for d in ser['effects']]), - ser['diagnostic'], - ser['diagnostic_description'], - ser['outcome_n'], - ser['summary'], - ser['prevalence_incidence'], - '|'.join(ser['adjustment_factors']), - '|'.join(ser['confounders_considered']), - ser['main_finding_support'], - ser['dose_response'], - ser['dose_response_details'], - ser['statistical_power'], - ser['statistical_power_details'], - ser['statistical_metric']['metric'], - ser['statistical_metric_description'] - ) - - @classmethod - def get_docx_template_context(cls, assessment, queryset): - """ - Given a queryset of assessed outcomes, invert the cached results to build - a top-down data hierarchy from study to assessed outcome. We use this - approach since our assessed outcomes are cached, so while it may require - more computation, its close to free on database access. - """ - - def getStatMethods(ao): - v = { - "adjustments_list": ao["adjustments_list"], - "statistical_metric": ao["statistical_metric"]["metric"], - "statistical_metric_description": ao["statistical_metric_description"], - "endpoints": [] - } - k = u"{}|{}|{}".format(v["adjustments_list"], v["statistical_metric"], v["statistical_metric_description"]) - return hashlib.md5(k.encode('UTF-8')).hexdigest(), v - - def getCustomAge(sp): - txt = sp["age_description"] - - rng = sp["age_lower"] is not None and sp["age_upper"] is not None - if rng: - rng = u"{}-{} years".format(sp["age_lower"], sp["age_upper"]) - - if sp["age_mean"] is not None: - txt = u"{} ({})".format(sp["age_mean"], sp["age_mean_type"]) - if rng: - txt += u", from {}".format(rng) - elif rng: - txt = rng - - return txt - - outcomes = [ - SerializerHelper.get_serialized(obj, json=False) - for obj in queryset - ] - studies = {} - - # flip dictionary nesting - for thisAO in outcomes: - thisExp = thisAO["exposure"] - thisSP = thisAO["exposure"]["study_population"] - thisStudy = thisAO["exposure"]["study_population"]["study"] - - study = studies.get(thisStudy["id"]) - if study is None: - study = thisStudy - study["sps"] = {} - studies[study["id"]] = study - - sp = study["sps"].get(thisSP["id"]) - if sp is None: - sp = thisSP - sp["_age"] = getCustomAge(sp) - sp["ethnicities"] = u', '.join(sp["ethnicity"]) - sp["inclusion_list"] = u', '.join(sp["inclusion_criteria"]) - sp["exclusion_list"] = u', '.join(sp["exclusion_criteria"]) - sp["exposures"] = {} - study["sps"][sp["id"]] = sp - - exposure = sp["exposures"].get(thisExp["id"]) - if exposure is None: - exposure = thisExp - exposure["aos"] = {} - exposure["statistical_methods"] = {} - sp["exposures"][exposure["id"]] = exposure - - ao = exposure["aos"].get(thisAO["id"]) - if ao is None: - ao = thisAO - ao["adjustments_list"] = u', '.join(sorted(ao["adjustment_factors"])) - exposure["aos"][ao["id"]] = ao - - key, val = getStatMethods(ao) - stat_methods = exposure['statistical_methods'].get(key) - if not stat_methods: - exposure['statistical_methods'][key] = val - stat_methods = val - stat_methods["endpoints"].append(ao["name"]) - - # convert value dictionaries to lists - studies = sorted( - studies.values(), - key=lambda obj: (obj["short_citation"].lower())) - for study in studies: - study["sps"] = sorted( - study["sps"].values(), - key=lambda obj: (obj["name"].lower())) - for sp in study["sps"]: - sp["exposures"] = sorted( - sp["exposures"].values(), - key=lambda obj: (obj["exposure_form_definition"].lower())) - for exp in sp["exposures"]: - exp["aos"] = sorted( - exp["aos"].values(), - key=lambda obj: (obj["name"].lower())) - for i, ao in enumerate(exp["aos"]): - ao["character"] = chr(65+i) - exp["statistical_methods"] = exp["statistical_methods"].values() - for obj in exp["statistical_methods"]: - obj["endpoints_list"] = u"; ".join(obj["endpoints"]) - - return { - "assessment": AssessmentSerializer().to_representation(assessment), - "studies": studies - } - - -class ExposureGroup(Demographics): - exposure = models.ForeignKey( - Exposure, - related_name='groups') - description = models.CharField( - max_length=256) - exposure_numeric = models.FloatField( - verbose_name='Low exposure value (sorting)', - help_text='Should be an exposure-value used for sorting', - blank=True, null=True) - comparative_name = models.CharField( - max_length=64, - verbose_name="Comparative Name", - help_text='Should include effect-group and comparative group, for example ' - '"1.5-2.5(Q2) vs ≤1.5(Q1)", or if only one group is available, ' - '"4.8±0.2 (mean±SEM)"', - blank=True) - exposure_group_id = models.PositiveSmallIntegerField() - exposure_n = models.PositiveSmallIntegerField( - blank=True, - null=True, - help_text="Final N used for exposure group") - - class Meta: - ordering = ('exposure_group_id', ) - - def __unicode__(self): - return self.description - - def get_assessment(self): - return self.exposure.get_assessment() - - @staticmethod - def flat_complete_header_row(): - return ( - 'exposure_group-pk', - 'exposure_group-description', - 'exposure_group-exposure_numeric', - 'exposure_group-comparative_name', - 'exposure_group-exposure_group_id', - 'exposure_group-exposure_n' - ) + Demographics.flat_complete_header_row(prefix='exposure-group-') - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['description'], - ser['exposure_numeric'], - ser['comparative_name'], - ser['exposure_group_id'], - ser['exposure_n'] - ) + Demographics.flat_complete_data_row(ser) - - -class AssessedOutcomeGroup(models.Model): - - P_VALUE_QUALIFIER_CHOICES = ( - ('<', '<'), - ('=', '='), - ('-', 'n.s.')) - - exposure_group = models.ForeignKey( - ExposureGroup, - help_text="Exposure-group related to this assessed outcome group") - assessed_outcome = models.ForeignKey( - AssessedOutcome, - related_name="groups") - n = models.PositiveIntegerField( - blank=True, - null=True, - help_text="Individuals in group where outcome was measured") - estimate = models.FloatField( - blank=True, - null=True, - help_text="Central tendency estimate for group") - se = models.FloatField( - blank=True, - null=True, - verbose_name='Standard Error (SE)', - help_text="Standard error estimate for group") - lower_ci = models.FloatField( - blank=True, - null=True, - verbose_name='Lower CI', - help_text="Numerical value for lower-confidence interval") - upper_ci = models.FloatField( - blank=True, - null=True, - verbose_name='Upper CI', - help_text="Numerical value for upper-confidence interval") - ci_units = models.FloatField( - blank=True, - null=True, - default=0.95, - verbose_name='Confidence Interval (CI)', - help_text='A 95% CI is written as 0.95.') - p_value_qualifier = models.CharField( - max_length=1, - choices=P_VALUE_QUALIFIER_CHOICES, - default="-", - verbose_name='p-value qualifier') - p_value = models.FloatField( - blank=True, - null=True, - verbose_name='p-value') - created = models.DateTimeField( - auto_now_add=True) - last_updated = models.DateTimeField( - auto_now=True) - - class Meta: - ordering = ('exposure_group__exposure_group_id', ) - - def __unicode__(self): - txt = u"%s: %s" % (self.exposure_group, self.estimate) - if self.se: - txt += u" (SE: %s)" % (self.se) - if self.lower_ci and self.upper_ci: - txt += u" (%s-%s)" % (self.lower_ci, self.upper_ci) - return txt - - @property - def p_value_text(self): - if self.p_value is None: - return "n.s." - txt = self.get_p_value_qualifier_display() - if txt != "n.s.": - txt += str(self.p_value) - return txt - - def get_assessment(self): - return self.assessed_outcome.get_assessment() - - @property - def estimate_formatted(self): - txt = "-" - if self.estimate: - txt = unicode(self.estimate) - if (self.lower_ci is not None and self.upper_ci is not None): - txt += u' ({}, {})'.format(self.lower_ci, self.upper_ci) - return txt - - @property - def isMainFinding(self): - return self.assessed_outcome.main_finding_id == self.exposure_group_id - - @staticmethod - def flat_complete_header_row(): - return ( - 'assessed_outcome_group-pk', - 'assessed_outcome_group-n', - 'assessed_outcome_group-estimate', - 'assessed_outcome_group-se', - 'assessed_outcome_group-lower_ci', - 'assessed_outcome_group-upper_ci', - 'assessed_outcome_group-ci_units', - 'assessed_outcome_group-main_finding', # AssessedOutcome.main_finding - 'assessed_outcome_group-p_value_text' - ) + ExposureGroup.flat_complete_header_row() - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['n'], - ser['estimate'], - ser['se'], - ser['lower_ci'], - ser['upper_ci'], - ser['ci_units'], - ser['isMainFinding'], - ser['p_value_text'] - ) + ExposureGroup.flat_complete_data_row(ser['exposure_group']) - - -class MetaProtocol(models.Model): - - META_PROTOCOL_CHOICES = ( - (0, "Meta-analysis"), - (1, "Pooled-analysis")) - - META_LIT_SEARCH_CHOICES = ( - (0, "Systematic"), - (1, "Other")) - - study = models.ForeignKey('study.Study', - related_name="meta_protocols") - name = models.CharField( - verbose_name="Protocol name", - max_length=128) - protocol_type = models.PositiveSmallIntegerField( - choices=META_PROTOCOL_CHOICES, - default=0) - lit_search_strategy = models.PositiveSmallIntegerField( - verbose_name="Literature search strategy", - choices=META_LIT_SEARCH_CHOICES, - default=0) - lit_search_notes = models.TextField( - verbose_name="Literature search notes", - blank=True) - lit_search_start_date = models.DateField( - verbose_name="Literature search start-date", - blank=True, - null=True) - lit_search_end_date = models.DateField( - verbose_name="Literature search end-date", - blank=True, - null=True) - total_references = models.PositiveIntegerField( - verbose_name="Total number of references found", - help_text="References identified through initial literature-search " - "before application of inclusion/exclusion criteria", - blank=True, - null=True) - inclusion_criteria = models.ManyToManyField( - StudyCriteria, - related_name='meta_inclusion_criteria', - blank=True) - exclusion_criteria = models.ManyToManyField( - StudyCriteria, - related_name='meta_exclusion_criteria', - blank=True) - total_studies_identified = models.PositiveIntegerField( - verbose_name="Total number of studies identified", - help_text="Total references identified for inclusion after application " - "of literature review and screening criteria") - notes = models.TextField(blank=True) - - class Meta: - ordering = ('name', ) - - def __unicode__(self): - return self.name - - def get_assessment(self): - return self.study.get_assessment() - - def get_absolute_url(self): - return reverse('epi:mp_detail', kwargs={'pk': self.pk}) - - def get_json(self, json_encode=True): - return SerializerHelper.get_serialized(self, json=json_encode, from_cache=False) - - @staticmethod - def flat_complete_header_row(): - return ( - 'meta_protocol-pk', - 'meta_protocol-url', - 'meta_protocol-name', - 'meta_protocol-protocol_type', - 'meta_protocol-lit_search_strategy', - 'meta_protocol-lit_search_notes', - 'meta_protocol-lit_search_start_date', - 'meta_protocol-lit_search_end_date', - 'meta_protocol-total_references', - 'meta_protocol-inclusion_criteria', - 'meta_protocol-exclusion_criteria', - 'meta_protocol-total_studies_identified', - 'meta_protocol-notes', - ) - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['url'], - ser['name'], - ser['protocol_type'], - ser['lit_search_strategy'], - ser['lit_search_notes'], - ser['lit_search_start_date'], - ser['lit_search_end_date'], - ser['total_references'], - u'|'.join(ser['inclusion_criteria']), - u'|'.join(ser['exclusion_criteria']), - ser['total_studies_identified'], - ser['notes'] - ) - - -class MetaResult(models.Model): - protocol = models.ForeignKey( - MetaProtocol, - related_name="results") - label = models.CharField( - max_length=128) - data_location = models.CharField( - max_length=128, - blank=True, - help_text="Details on where the data are found in the literature " - "(ex: Figure 1, Table 2, etc.)") - health_outcome = models.CharField( - max_length=128) - health_outcome_notes = models.TextField( - blank=True) - exposure_name = models.CharField( - max_length=128) - exposure_details = models.TextField( - blank=True) - number_studies = models.PositiveSmallIntegerField() - statistical_metric = models.ForeignKey( - StatisticalMetric) - statistical_notes = models.TextField( - blank=True) - n = models.PositiveIntegerField( - help_text="Number of individuals included from all analyses") - estimate = models.FloatField() - lower_ci = models.FloatField( - verbose_name="Lower CI", - help_text="Numerical value for lower-confidence interval") - upper_ci = models.FloatField( - verbose_name="Upper CI", - help_text="Numerical value for upper-confidence interval") - ci_units = models.FloatField( - blank=True, - null=True, - default=0.95, - verbose_name='Confidence Interval (CI)', - help_text='A 95% CI is written as 0.95.') - heterogeneity = models.CharField( - max_length=256, - blank=True) - adjustment_factors = models.ManyToManyField( - Factor, - help_text="All factors which were included in final model", - related_name='meta_adjustments', - blank=True) - notes = models.TextField( - blank=True) - - class Meta: - ordering = ('label', ) - - def __unicode__(self): - return self.label - - def get_assessment(self): - return self.protocol.get_assessment() - - def get_absolute_url(self): - return reverse('epi:mr_detail', kwargs={'pk': self.pk}) - - @property - def estimate_formatted(self): - txt = "-" - if self.estimate: - txt = unicode(self.estimate) - if (self.lower_ci and self.upper_ci): - txt += u' ({}, {})'.format(self.lower_ci, self.upper_ci) - return txt - - @classmethod - def delete_caches(cls, pks): - SerializerHelper.delete_caches(cls, pks) - - def get_json(self, json_encode=True): - return SerializerHelper.get_serialized(self, json=json_encode) - - @staticmethod - def flat_complete_header_row(): - return ( - 'meta_result-pk', - 'meta_result-url', - 'meta_result-label', - 'meta_result-data_location', - 'meta_result-health_outcome', - 'meta_result-health_outcome_notes', - 'meta_result-exposure_name', - 'meta_result-exposure_details', - 'meta_result-number_studies', - 'meta_result-statistical_metric', - 'meta_result-statistical_notes', - 'meta_result-n', - 'meta_result-estimate', - 'meta_result-lower_ci', - 'meta_result-upper_ci', - 'meta_result-ci_units', - 'meta_result-heterogeneity', - 'meta_result-adjustment_factors', - 'meta_result-notes', - ) - - @staticmethod - def flat_complete_data_row(ser): - return ( - ser['id'], - ser['url'], - ser['label'], - ser['data_location'], - ser['health_outcome'], - ser['health_outcome_notes'], - ser['exposure_name'], - ser['exposure_details'], - ser['number_studies'], - ser['statistical_metric']['metric'], - ser['statistical_notes'], - ser['n'], - ser['estimate'], - ser['lower_ci'], - ser['upper_ci'], - ser['ci_units'], - ser['heterogeneity'], - u'|'.join(ser['adjustment_factors']), - ser['notes'], - ) - - @classmethod - def get_docx_template_context(cls, assessment, queryset): - """ - Given a queryset of meta-results, invert the cached results to build - a top-down data hierarchy from study to meta-result. We use this - approach since our meta-results are cached, so while it may require - more computation, its close to free on database access. - """ - - def getStatMethods(mr): - key = u"{}|{}".format( - mr["adjustments_list"], - mr["statistical_notes"] - ) - return key, mr - - results = [ - SerializerHelper.get_serialized(obj, json=False) - for obj in queryset - ] - studies = {} - - # flip dictionary nesting - for thisMr in results: - thisPro = thisMr["protocol"] - thisStudy = thisMr["protocol"]["study"] - - study = studies.get(thisStudy["id"]) - if study is None: - study = thisStudy - study["protocols"] = {} - studies[study["id"]] = study - - pro = study["protocols"].get(thisPro["id"]) - if pro is None: - pro = thisPro - pro["inclusion_list"] = u', '.join(pro["inclusion_criteria"]) - pro["exclusion_list"] = u', '.join(pro["exclusion_criteria"]) - pro["results"] = {} - pro["statistical_methods"] = {} - study["protocols"][pro["id"]] = pro - - mr = pro["results"].get(thisMr["id"]) - if mr is None: - mr = thisMr - mr["ci_percent"] = int(mr["ci_units"]*100.) - mr["adjustments_list"] = u', '.join(sorted(mr["adjustment_factors"])) - pro["results"][mr["id"]] = mr - - statKey, statVal = getStatMethods(thisMr) - stats = pro["statistical_methods"].get(statKey) - if stats is None: - stats = statVal - pro["statistical_methods"][statKey] = statVal - stats["sm_endpoints"] = [] - stats["sm_endpoints"].append(thisMr) - - # convert value dictionaries to lists - studies = sorted( - studies.values(), - key=lambda obj: (obj["short_citation"].lower())) - for study in studies: - study["protocols"] = sorted( - study["protocols"].values(), - key=lambda obj: (obj["name"].lower())) - for pro in study["protocols"]: - pro["results"] = sorted( - pro["results"].values(), - key=lambda obj: (obj["label"].lower())) - pro["statistical_methods"] = pro["statistical_methods"].values() - for obj in pro["statistical_methods"]: - obj["sm_endpoints"] = u"; ".join([ d["label"] for d in obj["sm_endpoints"] ]) - - return { - "assessment": AssessmentSerializer().to_representation(assessment), - "studies": studies - } - - -class SingleResult(models.Model): - meta_result = models.ForeignKey( - MetaResult, - related_name="single_results") - study = models.ForeignKey( - 'study.Study', - related_name="single_results", - blank=True, - null=True) - outcome_group = models.ForeignKey( - AssessedOutcomeGroup, - related_name="single_results", - blank=True, - null=True) - exposure_name = models.CharField( - max_length=128, - help_text='Enter a descriptive-name for the single study result ' - '(e.g., "Smith et al. 2000, obese-males")') - weight = models.FloatField( - blank=True, - null=True, - validators=[MinValueValidator(0),MaxValueValidator(1)], - help_text="For meta-analysis, enter the fraction-weight assigned for " - "each result (leave-blank for pooled analyses)") - n = models.PositiveIntegerField( - blank=True, - null=True, - help_text="Enter the number of observations for this result") - estimate = models.FloatField( - blank=True, - null=True, - help_text="Enter the numerical risk-estimate presented for this result") - lower_ci = models.FloatField( - blank=True, - null=True, - verbose_name="Lower CI", - help_text="Numerical value for lower-confidence interval") - upper_ci = models.FloatField( - blank=True, - null=True, - verbose_name="Upper CI", - help_text="Numerical value for upper-confidence interval") - ci_units = models.FloatField( - blank=True, - null=True, - default=0.95, - verbose_name='Confidence Interval (CI)', - help_text='A 95% CI is written as 0.95.') - notes = models.TextField( - blank=True) - - def __unicode__(self): - return self.exposure_name - - @property - def estimate_formatted(self): - txt = "-" - if self.estimate: - txt = unicode(self.estimate) - if (self.lower_ci and self.upper_ci): - txt += u' ({}, {})'.format(self.lower_ci, self.upper_ci) - return txt - - @staticmethod - def flat_complete_header_row(): - return ( - 'single_result-pk', - 'single_result-study', - 'single_result-outcome_group', - 'single_result-exposure_name', - 'single_result-weight', - 'single_result-n', - 'single_result-estimate', - 'single_result-lower_ci', - 'single_result-upper_ci', - 'single_result-ci_units', - 'single_result-notes', - ) - - @staticmethod - def flat_complete_data_row(ser): - - study = None - try: - study = ser['study']['id'] - except TypeError: - pass - - aog = None - try: - aog = ser['outcome_group']['id'] - except TypeError: - pass - - return ( - ser['id'], - study, - aog, - ser['exposure_name'], - ser['weight'], - ser['n'], - ser['estimate'], - ser['lower_ci'], - ser['upper_ci'], - ser['ci_units'], - ser['notes'], - ) - - -@receiver(post_save, sender=StudyPopulation) -@receiver(pre_delete, sender=StudyPopulation) -@receiver(post_save, sender=Exposure) -@receiver(pre_delete, sender=Exposure) -@receiver(post_save, sender=AssessedOutcome) -@receiver(pre_delete, sender=AssessedOutcome) -@receiver(post_save, sender=ExposureGroup) -@receiver(pre_delete, sender=ExposureGroup) -@receiver(post_save, sender=AssessedOutcomeGroup) -@receiver(pre_delete, sender=AssessedOutcomeGroup) -def invalidate_assessed_outcome_cache(sender, instance, **kwargs): - instance_type = type(instance) - filters = {} - if instance_type is StudyPopulation: - filters["exposure__study_population"] = instance.id - elif instance_type is Exposure: - filters["exposure"] = instance.id - elif instance_type is AssessedOutcome: - ids = [instance.id] - elif instance_type is ExposureGroup: - filters["exposure"] = instance.exposure_id - elif instance_type is AssessedOutcomeGroup: - ids = [instance.assessed_outcome_id] - - if len(filters)>0: - ids = AssessedOutcome.objects.filter(**filters).values_list('id', flat=True) - - AssessedOutcome.delete_caches(ids) - - -@receiver(post_save, sender=ExposureGroup) -def create_new_aogs(sender, instance, created, **kwargs): - # When a new exposure-group is created, create new default assessed-outcome - # group for all assessed-outcomes with the exposure-group's exposure, and - # invalidate old assessed-outcome cache. - if not created: - return - aos = AssessedOutcome.objects\ - .filter(exposure=instance.exposure)\ - .values_list('id', flat=True) - aogs = [] - for ao in aos: - kwargs = { - "exposure_group_id": instance.id, - "assessed_outcome_id": ao - } - aogs.append(AssessedOutcomeGroup(**kwargs)) - AssessedOutcomeGroup.objects.bulk_create(aogs) - AssessedOutcome.delete_caches(aos) - - -@receiver(post_save, sender=MetaProtocol) -@receiver(pre_delete, sender=MetaProtocol) -@receiver(post_save, sender=MetaResult) -@receiver(pre_delete, sender=MetaResult) -@receiver(post_save, sender=SingleResult) -@receiver(pre_delete, sender=SingleResult) -def invalidate_meta_result_cache(sender, instance, **kwargs): - instance_type = type(instance) - filters = {} - if instance_type is MetaProtocol: - filters["protocol"] = instance.id - elif instance_type is MetaResult: - ids = [instance.id] - elif instance_type is SingleResult: - ids = [instance.meta_result_id] - - if len(filters)>0: - ids = MetaResult.objects.filter(**filters).values_list('id', flat=True) - - MetaResult.delete_caches(ids) - - -reversion.register(Ethnicity) -reversion.register(Factor) -reversion.register(StudyPopulation) -reversion.register(StudyCriteria) -reversion.register(Exposure) -reversion.register(AssessedOutcome, - follow=('groups', 'adjustment_factors', 'confounders_considered', 'baseendpoint_ptr')) -reversion.register(ExposureGroup) -reversion.register(AssessedOutcomeGroup, follow=('assessed_outcome', )) -reversion.register(MetaProtocol, - follow=('inclusion_criteria', 'exclusion_criteria')) -reversion.register(MetaResult, follow=('adjustment_factors', )) -reversion.register(SingleResult) diff --git a/project/epi/serializers.py b/project/epi/serializers.py deleted file mode 100644 index ad56e7d9..00000000 --- a/project/epi/serializers.py +++ /dev/null @@ -1,192 +0,0 @@ -from rest_framework import serializers - -from assessment.serializers import EffectTagsSerializer -from study.serializers import StudySerializer - -from utils.helper import SerializerHelper - -from . import models - - -class StudyCriteriaSerializer(serializers.ModelSerializer): - - class Meta: - model = models.StudyCriteria - - -class StatisticalMetricSerializer(serializers.ModelSerializer): - - class Meta: - model = models.StatisticalMetric - - -class StudyPopulationSerializer(serializers.ModelSerializer): - study = StudySerializer() - ethnicity = serializers.StringRelatedField(many=True) - inclusion_criteria = serializers.StringRelatedField(many=True) - exclusion_criteria = serializers.StringRelatedField(many=True) - confounding_criteria = serializers.StringRelatedField(many=True) - - def to_representation(self, instance): - ret = super(StudyPopulationSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - ret['design'] = instance.get_design_display() - ret['country'] = instance.get_country_display() - ret['sex'] = instance.get_sex_display() - ret['age_sd_type'] = instance.get_age_sd_type_display() - ret['age_mean_type'] = instance.get_age_mean_type_display() - ret['age_lower_type'] = instance.get_age_lower_type_display() - ret['age_upper_type'] = instance.get_age_upper_type_display() - return ret - - class Meta: - model = models.StudyPopulation - - -class ExposureSerializer(serializers.ModelSerializer): - study_population = StudyPopulationSerializer() - - def to_representation(self, instance): - ret = super(ExposureSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - return ret - - class Meta: - model = models.Exposure - depth = 1 - - -class ExposureGroupSerializer(serializers.ModelSerializer): - ethnicity = serializers.StringRelatedField(many=True) - - def to_representation(self, instance): - ret = super(ExposureGroupSerializer, self).to_representation(instance) - ret['sex'] = instance.get_sex_display() - ret['age_sd'] = instance.get_age_sd_type_display() - ret['age_mean_type'] = instance.get_age_mean_type_display() - ret['age_lower_type'] = instance.get_age_lower_type_display() - ret['age_upper_type'] = instance.get_age_upper_type_display() - return ret - - class Meta: - model = models.ExposureGroup - - -class ExposureVerboseSerializer(ExposureSerializer): - groups = ExposureGroupSerializer(many=True) - - -class AssessedOutcomeGroupSerializer(serializers.ModelSerializer): - assessed_outcome = serializers.PrimaryKeyRelatedField(read_only=True) - exposure_group = ExposureGroupSerializer() - - def to_representation(self, instance): - ret = super(AssessedOutcomeGroupSerializer, self).to_representation(instance) - ret['p_value_text'] = instance.p_value_text - ret['isMainFinding'] = instance.isMainFinding - ret['estimateFormatted'] = instance.estimate_formatted - if ret['n'] is None: - ret['n'] = ret['exposure_group']['n'] or "-" - return ret - - class Meta: - model = models.AssessedOutcomeGroup - - -class AssessedOutcomeSerializer(serializers.ModelSerializer): - assessment = serializers.PrimaryKeyRelatedField(read_only=True) - main_finding = serializers.PrimaryKeyRelatedField(read_only=True) - exposure = ExposureSerializer() - statistical_metric = StatisticalMetricSerializer() - effects = EffectTagsSerializer() - groups = AssessedOutcomeGroupSerializer(many=True) - adjustment_factors = serializers.StringRelatedField(many=True) - confounders_considered = serializers.StringRelatedField(many=True) - - def to_representation(self, instance): - ret = super(AssessedOutcomeSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - ret['diagnostic'] = instance.get_diagnostic_display() - ret['dose_response'] = instance.get_dose_response_display() - ret['statistical_power'] = instance.get_statistical_power_display() - ret['main_finding_support'] = instance.get_main_finding_support_display() - return ret - - class Meta: - model = models.AssessedOutcome - - -class AssessedOutcomeShallowSerializer(serializers.ModelSerializer): - - def to_representation(self, instance): - ret = super(AssessedOutcomeShallowSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - return ret - - class Meta: - model = models.AssessedOutcome - - -class AssessedOutcomeGroupVerboseSerializer(serializers.ModelSerializer): - assessed_outcome = AssessedOutcomeShallowSerializer() - - def to_representation(self, instance): - ret = super(AssessedOutcomeGroupVerboseSerializer, self).to_representation(instance) - ret['estimateFormatted'] = instance.estimate_formatted - return ret - - class Meta: - model = models.AssessedOutcomeGroup - - -class SingleResultSerializer(serializers.ModelSerializer): - study = StudySerializer() - outcome_group = AssessedOutcomeGroupVerboseSerializer() - meta_result = serializers.PrimaryKeyRelatedField(read_only=True) - - def to_representation(self, instance): - ret = super(SingleResultSerializer, self).to_representation(instance) - if instance.outcome_group is None: - ret['estimateFormatted'] = instance.estimate_formatted - return ret - - class Meta: - model = models.SingleResult - - -class MetaProtocolSerializer(serializers.ModelSerializer): - study = StudySerializer() - inclusion_criteria = serializers.StringRelatedField(many=True) - exclusion_criteria = serializers.StringRelatedField(many=True) - - def to_representation(self, instance): - ret = super(MetaProtocolSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - ret['protocol_type'] = instance.get_protocol_type_display() - ret['lit_search_strategy'] = instance.get_lit_search_strategy_display() - return ret - - class Meta: - model = models.MetaProtocol - - -class MetaResultSerializer(serializers.ModelSerializer): - protocol = MetaProtocolSerializer() - statistical_metric = StatisticalMetricSerializer() - single_results = SingleResultSerializer(many=True) - adjustment_factors = serializers.StringRelatedField(many=True) - - def to_representation(self, instance): - ret = super(MetaResultSerializer, self).to_representation(instance) - ret['url'] = instance.get_absolute_url() - ret['estimateFormatted'] = instance.estimate_formatted - return ret - - class Meta: - model = models.MetaResult - - -SerializerHelper.add_serializer(models.StudyPopulation, StudyPopulationSerializer) -SerializerHelper.add_serializer(models.AssessedOutcome, AssessedOutcomeSerializer) -SerializerHelper.add_serializer(models.MetaProtocol, MetaProtocolSerializer) -SerializerHelper.add_serializer(models.MetaResult, MetaResultSerializer) diff --git a/project/epi/urls.py b/project/epi/urls.py deleted file mode 100644 index e6da3a49..00000000 --- a/project/epi/urls.py +++ /dev/null @@ -1,164 +0,0 @@ -from django.conf.urls import url, include - -from rest_framework.routers import DefaultRouter - -from . import views, api - -router = DefaultRouter() -router.register(r'meta-result', api.MetaResult, base_name="meta-result") -router.register(r'study-population', api.StudyPopulation, base_name="study-population") -router.register(r'exposure', api.Exposure, base_name="exposure") -router.register(r'assessed-outcome', api.AssessedOutcome, base_name="assessed-outcome") - -urlpatterns = [ - - # overall views - url(r'^assessment/(?P\d+)/full-export/$', - views.FullExport.as_view(), - name='export'), - - url(r'^assessment/(?P\d+)/assessed-outcomes/$', - views.AssessedOutcomeList.as_view(), - name='assessedoutcome_list'), - - url(r'^assessment/(?P\d+)/report/$', - views.AssessedOutcomeReport.as_view(), - name='ao_report'), - - url(r'^assessment/(?P\d+)/meta-result-report/$', - views.MetaResultReport.as_view(), - name='mr_report'), - - url(r'^assessment/(?P\d+)/meta-result-full-export/$', - views.MetaResultFullExport.as_view(), - name='mr_export'), - - # study-criteria views - url(r'^assessment/(?P\d+)/study-criteria/create/$', - views.StudyCriteriaCreate.as_view(), - name='studycriteria_create'), - - # study-population views - url(r'^study/(?P\d+)/study-population/create/$', - views.StudyPopulationCreate.as_view(), - name='sp_create'), - - url(r'^study/(?P\d+)/study-population/copy-as-new-selector/$', - views.StudyPopulationCopyAsNewSelector.as_view(), - name='sp_copy_selector'), - - url(r'^study-population/(?P\d+)/$', - views.StudyPopulationDetail.as_view(), - name='sp_detail'), - - url(r'^study-population/(?P\d+)/update/$', - views.StudyPopulationUpdate.as_view(), - name='sp_update'), - - url(r'^study-population/(?P\d+)/delete/$', - views.StudyPopulationDelete.as_view(), - name='sp_delete'), - - # exposure views - url(r'^study-population/(?P\d+)/exposure/create/$', - views.ExposureCreate.as_view(), - name='exposure_create'), - - url(r'^study-population/(?P\d+)/exposure/copy-as-new-selector/$', - views.ExposureCopyAsNewSelector.as_view(), - name='exposure_copy_selector'), - - url(r'^exposure/(?P\d+)/$', - views.ExposureDetail.as_view(), - name='exposure_detail'), - - url(r'^exposure/(?P\d+)/update/$', - views.ExposureUpdate.as_view(), - name='exposure_update'), - - url(r'^exposure/(?P\d+)/delete/$', - views.ExposureDelete.as_view(), - name='exposure_delete'), - - # factor views - url(r'^assessment/(?P\d+)/factors/create/$', - views.FactorCreate.as_view(), - name='factor_create'), - - # assessed-outcome views - url(r'^exposure/(?P\d+)/assessed-outcome/create/$', - views.AssessedOutcomeCreate.as_view(), - name='assessedoutcome_create'), - - url(r'^exposure/(?P\d+)/assessed-outcome/copy-as-new-selector/$', - views.AssessedOutcomeCopyAsNewSelector.as_view(), - name='assessedoutcome_copy_selector'), - - url(r'^assessed-outcome/(?P\d+)/$', - views.AssessedOutcomeDetail.as_view(), - name='assessedoutcome_detail'), - - url(r'^assessed-outcome/(?P\d+)/update/$', - views.AssessedOutcomeUpdate.as_view(), - name='assessedoutcome_update'), - - url(r'^assessed-outcome/(?P\d+)/versions/$', - views.AssessedOutcomeVersions.as_view(), - name='assessedoutcome_versions'), - - url(r'^assessed-outcome/(?P\d+)/delete/$', - views.AssessedOutcomeDelete.as_view(), - name='assessedoutcome_delete'), - - # meta-protocol views - url(r'^study/(?P\d+)/meta-protocol/create/$', - views.MetaProtocolCreate.as_view(), - name='mp_create'), - - url(r'^meta-protocol/(?P\d+)/$', - views.MetaProtocolDetail.as_view(), - name='mp_detail'), - - url(r'^meta-protocol/(?P\d+)/json/$', - views.MetaProtocolJSON.as_view(), - name='mp_json'), - - url(r'^meta-protocol/(?P\d+)/update/$', - views.MetaProtocolUpdate.as_view(), - name='mp_update'), - - url(r'^meta-protocol/(?P\d+)/delete/$', - views.MetaProtocolDelete.as_view(), - name='mp_delete'), - - # meta-result views - url(r'^assessment/(?P\d+)/meta-results/$', - views.MetaResultList.as_view(), - name='metaresult_list'), - - url(r'^meta-protocol/(?P\d+)/meta-result/create/$', - views.MetaResultCreate.as_view(), - name='mr_create'), - - url(r'^meta-protocol/(?P\d+)/meta-result/copy-as-new-selector/$', - views.MetaResultCopyAsNewSelector.as_view(), - name='mr_copy_selector'), - - url(r'^meta-result/(?P\d+)/$', - views.MetaResultDetail.as_view(), - name='mr_detail'), - - url(r'^meta-result/(?P\d+)/json/$', - views.MetaResultJSON.as_view(), - name='mr_json'), - - url(r'^meta-result/(?P\d+)/update/$', - views.MetaResultUpdate.as_view(), - name='mr_update'), - - url(r'^meta-result/(?P\d+)/delete/$', - views.MetaResultDelete.as_view(), - name='mr_delete'), - - url(r'^api/', include(router.urls)), -] diff --git a/project/epi/views.py b/project/epi/views.py deleted file mode 100644 index 16085eb2..00000000 --- a/project/epi/views.py +++ /dev/null @@ -1,430 +0,0 @@ -from django.core.urlresolvers import reverse -from django.forms.models import modelformset_factory -from django.http import HttpResponse - -from assessment.models import Assessment -from utils.views import (BaseDetail, BaseDelete, - BaseVersion, BaseUpdate, BaseCreate, - BaseCreateWithFormset, BaseUpdateWithFormset, - CloseIfSuccessMixin, BaseList, GenerateReport) - -from study.models import Study -from study.views import StudyRead - -from . import forms, models, exports - - -# Study populations -class StudyPopulationCreate(BaseCreate): - success_message = 'Study-population created.' - parent_model = Study - parent_template_name = 'study' - model = models.StudyPopulation - form_class = forms.StudyPopulationForm - - -class StudyPopulationDetail(BaseDetail): - model = models.StudyPopulation - - -class StudyPopulationUpdate(BaseUpdate): - success_message = "Study Population updated." - model = models.StudyPopulation - form_class = forms.StudyPopulationForm - - -class StudyPopulationDelete(BaseDelete): - success_message = "Study Population deleted." - model = models.StudyPopulation - - def get_success_url(self): - self.parent = self.object.study - return reverse("study:detail", kwargs={"pk": self.parent.pk}) - - -class StudyPopulationCopyAsNewSelector(StudyRead): - # Select an existing assessed outcome as a template for a new one - template_name = 'epi/studypopulation_copy_selector.html' - - def get_context_data(self, **kwargs): - context = super(StudyPopulationCopyAsNewSelector, self).get_context_data(**kwargs) - context['form'] = forms.StudyPopulationSelectorForm(study_id=self.object.id) - return context - - -# Exposures -class ExposureCreate(BaseCreateWithFormset): - success_message = 'Exposure created.' - parent_model = models.StudyPopulation - parent_template_name = 'study_population' - model = models.Exposure - form_class = forms.ExposureForm - formset_factory = forms.EGFormSet - - def post_object_save(self, form, formset): - # Bind newly created exposure to exposure-group instance - for i, form in enumerate(formset.forms): - form.instance.exposure_group_id = i - form.instance.exposure = self.object - - def build_initial_formset_factory(self): - return forms.BlankEGFormSet(queryset=models.ExposureGroup.objects.none()) - - -class ExposureDetail(BaseDetail): - model = models.Exposure - - -class ExposureDelete(BaseDelete): - success_message = "Exposure deleted." - model = models.Exposure - - def get_success_url(self): - self.parent = self.object.study_population - return reverse("epi:sp_detail", kwargs={"pk": self.parent.pk}) - - -class ExposureUpdate(BaseUpdateWithFormset): - success_message = "Exposure updated." - model = models.Exposure - form_class = forms.ExposureForm - formset_factory = forms.EGFormSet - - def build_initial_formset_factory(self): - return forms.EGFormSet(queryset=self.object.groups.all() - .order_by('exposure_group_id')) - - def post_object_save(self, form, formset): - for form in formset: - form.instance.exposure = self.object - - def post_formset_save(self, form, formset): - formset.rebuild_exposure_group_id() - - -class ExposureCopyAsNewSelector(StudyPopulationDetail): - # Select an existing assessed outcome as a template for a new one - template_name = 'epi/exposure_copy_selector.html' - - def get_context_data(self, **kwargs): - context = super(ExposureCopyAsNewSelector, self).get_context_data(**kwargs) - context['form'] = forms.ExposureSelectorForm(study_id=self.object.study.id) - return context - - -# Study criteria -class StudyCriteriaCreate(CloseIfSuccessMixin, BaseCreate): - success_message = 'Epidemiology study-population criteria created.' - parent_model = Assessment - parent_template_name = 'assessment' - model = models.StudyCriteria - form_class = forms.StudyCriteriaForm - - -# Factors -class FactorCreate(CloseIfSuccessMixin, BaseCreate): - success_message = 'Factor created.' - parent_model = Assessment - parent_template_name = 'assessment' - model = models.Factor - form_class = forms.FactorForm - - -# Assessed outcomes -class AssessedOutcomeCreate(BaseCreateWithFormset): - success_message = 'Assessed-outcome created.' - parent_model = models.Exposure - parent_template_name = 'object' - model = models.AssessedOutcome - form_class = forms.AssessedOutcomeForm - formset_factory = forms.AOGFormSet - - def get_form_kwargs(self): - kwargs = super(AssessedOutcomeCreate, self).get_form_kwargs() - kwargs['assessment'] = self.assessment - return kwargs - - def post_object_save(self, form, formset): - # Bind newly created assessment outcome to assessment group instances - for form in formset.forms: - form.instance.assessed_outcome = self.object - - def build_initial_formset_factory(self): - initial = self.parent.groups.all().order_by('exposure_group_id').values('pk') - for v in initial: - v['exposure_group'] = v.pop('pk') - AOGFormset = modelformset_factory(models.AssessedOutcomeGroup, - form=forms.AOGForm, - extra=len(initial)) - return AOGFormset(queryset=models.AssessedOutcomeGroup.objects.none(), - initial=initial) - - -class AssessedOutcomeDetail(BaseDetail): - model = models.AssessedOutcome - - -class AssessedOutcomeVersions(BaseVersion): - model = models.AssessedOutcome - template_name = "epi/assessedoutcome_versions.html" - - -class AssessedOutcomeUpdate(BaseUpdateWithFormset): - success_message = "Assessment Outcome updated." - model = models.AssessedOutcome - form_class = forms.AssessedOutcomeForm - formset_factory = forms.AOGFormSet - - def build_initial_formset_factory(self): - return forms.AOGFormSet(queryset=self.object.groups.all() \ - .order_by('exposure_group__exposure_group_id')) - - -class AssessedOutcomeDelete(BaseDelete): - success_message = "Assessment Outcome deleted." - model = models.AssessedOutcome - - def get_success_url(self): - self.parent = self.object.exposure - return reverse("epi:exposure_detail", kwargs={"pk": self.parent.pk}) - - -class AssessedOutcomeReport(GenerateReport): - parent_model = Assessment - model = models.AssessedOutcome - report_type = 3 - - def get_queryset(self): - filters = {"assessment": self.assessment} - perms = super(AssessedOutcomeReport, self).get_obj_perms() - if not perms['edit'] or self.onlyPublished: - filters["exposure__study_population__study__published"] = True - return self.model.objects.filter(**filters) - - def get_filename(self): - return "epidemiology.docx" - - def get_context(self, queryset): - return self.model.get_docx_template_context(self.assessment, queryset) - - -class AssessedOutcomeList(BaseList): - parent_model = Assessment - model = models.AssessedOutcome - - def get_paginate_by(self, qs): - val = 25 - try: - val = int(self.request.GET.get('paginate_by', val)) - except ValueError: - pass - return val - - def get_queryset(self): - filters = {"assessment": self.assessment} - perms = self.get_obj_perms() - if not perms['edit']: - filters["exposure__study_population__study__published"] = True - return self.model.objects.filter(**filters).order_by('name') - - -class FullExport(AssessedOutcomeList): - """ - Full XLS data export for the epidemiology outcome. - """ - def get(self, request, *args, **kwargs): - self.object_list = self.get_queryset() - exporter = exports.AssessedOutcomeFlatComplete( - self.object_list, - export_format="excel", - filename='{}-epi'.format(self.assessment), - sheet_name='epi') - return exporter.build_response() - - -class AssessedOutcomeCopyAsNewSelector(ExposureDetail): - # Select an existing assessed outcome as a template for a new one - template_name = 'epi/assessedoutcome_copy_selector.html' - - def get_context_data(self, **kwargs): - context = super(AssessedOutcomeCopyAsNewSelector, self).get_context_data(**kwargs) - context['form'] = forms.AssesedOutcomeSelectorForm(study_id=self.object.study_population.study.id) - return context - - -# MetaProtocol -class MetaProtocolCreate(BaseCreate): - success_message = 'Meta-protocol created.' - parent_model = Study - parent_template_name = 'study' - model = models.MetaProtocol - form_class = forms.MetaProtocolForm - - -class MetaProtocolDetail(BaseDetail): - model = models.MetaProtocol - - -class MetaProtocolJSON(MetaProtocolDetail): - http_method_names = ('get', ) - - def get(self, request, *args, **kwargs): - self.object = self.get_object() - return HttpResponse(self.object.get_json(json_encode=True), content_type="application/json") - - -class MetaProtocolUpdate(BaseUpdate): - success_message = "Meta-protocol updated." - model = models.MetaProtocol - form_class = forms.MetaProtocolForm - - -class MetaProtocolDelete(BaseDelete): - success_message = "Meta-protocol deleted." - model = models.MetaProtocol - - def get_success_url(self): - self.parent = self.object.study - return reverse("study:detail", kwargs={"pk": self.parent.pk}) - - -# MetaResult -class MetaResultCreate(BaseCreateWithFormset): - success_message = 'Meta-Result created.' - parent_model = models.MetaProtocol - parent_template_name = 'protocol' - model = models.MetaResult - form_class = forms.MetaResultForm - formset_factory = forms.SingleResultFormset - - def post_object_save(self, form, formset): - # Bind newly created single-result outcome to meta-result instance - for form in formset.forms: - form.instance.meta_result = self.object - - def build_initial_formset_factory(self): - - def get_initial_data(field, **kwargs): - formfield = field.formfield(**kwargs) - if field.name == "study": - formfield.queryset = formfield.queryset.filter( - assessment=self.assessment, study_type=1) - return formfield - - return modelformset_factory( - models.SingleResult, - form=forms.SingleResultForm, - formset=forms.EmptySingleResultFormset, - formfield_callback=get_initial_data, - extra=1) - - def get_form_kwargs(self): - kwargs = super(MetaResultCreate, self).get_form_kwargs() - kwargs['assessment_id'] = self.assessment.id - return kwargs - - -class MetaResultCopyAsNewSelector(MetaProtocolDetail): - # Select an existing meta-result as a template for a new one - template_name = 'epi/metaresult_copy_selector.html' - - def get_context_data(self, **kwargs): - context = super(MetaResultCopyAsNewSelector, self).get_context_data(**kwargs) - context['form'] = forms.MetaResultSelectorForm(study_id=self.object.study_id) - return context - - -class MetaResultDetail(BaseDetail): - model = models.MetaResult - - -class MetaResultJSON(MetaResultDetail): - http_method_names = ('get', ) - - def get(self, request, *args, **kwargs): - self.object = self.get_object() - return HttpResponse(self.object.get_json(json_encode=True), content_type="application/json") - - -class MetaResultUpdate(BaseUpdateWithFormset): - success_message = "Meta-Result updated." - model = models.MetaResult - form_class = forms.MetaResultForm - formset_factory = forms.SingleResultFormset - - def build_initial_formset_factory(self): - formset = forms.SingleResultFormset(queryset=self.object.single_results.all().order_by('pk')) - forms.meta_result_clean_update_formset(formset, self.assessment) - return formset - - def get_form_kwargs(self): - kwargs = super(MetaResultUpdate, self).get_form_kwargs() - kwargs['assessment_id'] = self.assessment.id - return kwargs - - def post_object_save(self, form, formset): - # Bind newly single-result outcome to meta-result instance, if adding new - for form in formset.forms: - form.instance.meta_result = self.object - - -class MetaResultDelete(BaseDelete): - success_message = "Meta-Result deleted." - model = models.MetaResult - - def get_success_url(self): - self.parent = self.object.protocol - return reverse("epi:mp_detail", kwargs={"pk": self.parent.pk}) - - -class MetaResultReport(GenerateReport): - parent_model = Assessment - model = models.MetaResult - report_type = 4 - - def get_queryset(self): - filters = {"protocol__study__assessment": self.assessment} - perms = super(MetaResultReport, self).get_obj_perms() - if not perms['edit'] or self.onlyPublished: - filters["protocol__study__published"] = True - return self.model.objects.filter(**filters) - - def get_filename(self): - return "meta-results.docx" - - def get_context(self, queryset): - return self.model.get_docx_template_context(self.assessment, queryset) - - -class MetaResultList(BaseList): - parent_model = Assessment - model = models.MetaResult - - def get_paginate_by(self, qs): - val = 25 - try: - val = int(self.request.GET.get('paginate_by', val)) - except ValueError: - pass - return val - - def get_queryset(self): - filters = {"protocol__study__assessment": self.assessment} - perms = self.get_obj_perms() - if not perms['edit']: - filters["protocol__study__published"] = True - return self.model.objects.filter(**filters).order_by('label') - - -class MetaResultFullExport(MetaResultList): - """ - Full XLS data export for the epidemiology meta-analyses. - """ - def get(self, request, *args, **kwargs): - self.object_list = self.get_queryset() - exporter = exports.MetaResultFlatComplete( - self.object_list, - export_format="excel", - filename='{}-epi-meta-analysis'.format(self.assessment), - sheet_name='epi-meta-analysis') - return exporter.build_response() diff --git a/project/hawc/settings/base.py b/project/hawc/settings/base.py index dbcf8e7d..451663c6 100644 --- a/project/hawc/settings/base.py +++ b/project/hawc/settings/base.py @@ -98,7 +98,6 @@ 'lit', 'study', 'animal', - 'epi', 'epi2', 'epimeta', 'invitro', diff --git a/project/templates/epi/_epistudy_list.html b/project/templates/epi/_epistudy_list.html deleted file mode 100644 index 632f92b6..00000000 --- a/project/templates/epi/_epistudy_list.html +++ /dev/null @@ -1,21 +0,0 @@ -{% if object_list %} - - - - - - - - - - - {% for object in object_list %} - - - - {% endfor %} - -
Short Citation
{{object}}
-{% else %} -

No epidemiology studies are available.

-{% endif %} diff --git a/project/templates/epi/_study_population_list.html b/project/templates/epi/_study_population_list.html deleted file mode 100644 index b27eec80..00000000 --- a/project/templates/epi/_study_population_list.html +++ /dev/null @@ -1,40 +0,0 @@ -{% if object_list %} - - - {%if with_study %} - - - - - {% else %} - - - - {% endif %} - - - - {%if with_study %} - - {% endif %} - - - - - - - {% for object in object_list %} - - {%if with_study %} - - {% endif %} - - - - - {% endfor %} - -
StudyNameDesignLocation
{{object.study}}{{object}}{{object.get_design_display}}{{object.get_location}}
-{% else %} -

No study-populations are available.

-{% endif %} diff --git a/project/templates/epi/assessedoutcome_confirm_delete.html b/project/templates/epi/assessedoutcome_confirm_delete.html deleted file mode 100644 index 553d1413..00000000 --- a/project/templates/epi/assessedoutcome_confirm_delete.html +++ /dev/null @@ -1,15 +0,0 @@ -{% extends 'epi/assessedoutcome_detail.html' %} - -{% block title %} - {{ block.super }} | Delete -{% endblock title %} - -{% block breadcrumbs_self %} -
  • {{object}}/
    • -
  • Delete/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - {{ block.super }} - {% include "hawc/_delete_block.html" with name="assessed outcome" notes="" %} -{% endblock content %} diff --git a/project/templates/epi/assessedoutcome_copy_selector.html b/project/templates/epi/assessedoutcome_copy_selector.html deleted file mode 100644 index 52405388..00000000 --- a/project/templates/epi/assessedoutcome_copy_selector.html +++ /dev/null @@ -1,39 +0,0 @@ -{% extends 'epi/exposure_detail.html' %} - - -{% load add_class %} -{% load selectable_tags %} - -{% block title %} - {{block.super}} | Copy Assessed Outcome -{% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block breadcrumbs_self %} -
  • {{object}}/
    • -
  • Copy outcome/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - - {% include "hawc/_copy_as_new.html" with name="assessed outcome" notes="Select an existing assessed outcome as a template to create a new one." %} - -{% endblock content %} - -{% block extrajs %} - {{ form.media }} - -{% endblock extrajs %} - diff --git a/project/templates/epi/assessedoutcome_detail.html b/project/templates/epi/assessedoutcome_detail.html deleted file mode 100644 index be6a7013..00000000 --- a/project/templates/epi/assessedoutcome_detail.html +++ /dev/null @@ -1,56 +0,0 @@ -{% extends 'portal.html' %} - - -{% block title %}{{assessment}} | {{object.exposure.study_population.study}} | {{object.exposure.study_population}} | {{object.exposure}} | {{object}} {% endblock title %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • -
  • {{object.exposure.study_population.study}}/
    • -
  • {{object.exposure.study_population|truncatechars:40}}/
    • -
  • {{object.exposure}}/
    • - {% block breadcrumbs_self %} -
  • {{object}}/
    • - {% endblock breadcrumbs_self %} -{% endblock %} - -{% block content %} - -

    {{object}} - {% if obj_perms.edit and crud == "Read" %} -
    - Actions - - - -
    - {% endif %} -

    - -

    Assessed outcome description

    -
    - - {% if object.groups.count > 0 %} -

    Results by exposure-group

    -
    -
    -



    - {% endif %} -{% endblock %} - -{% block extrajs %} - -{% endblock %} diff --git a/project/templates/epi/assessedoutcome_form.html b/project/templates/epi/assessedoutcome_form.html deleted file mode 100644 index ff0ef048..00000000 --- a/project/templates/epi/assessedoutcome_form.html +++ /dev/null @@ -1,89 +0,0 @@ -{% extends 'portal.html' %} - -{% load selectable_tags %} -{% load crispy_forms_tags %} - -{% block title %} - {{assessment}} | - {% if crud == "Create" %} - {{object.study_population.study}} | {{object.study_population}} | {{object}} | Create Assessed Outcome - {% elif crud == "Update" %} - {{object.exposure.study_population.study}} | {{object.exposure.study_population}} | {{object.exposure}} | Update {{object}} - {% endif %} -{% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • - {% if crud == "Create" %} -
  • {{object.study_population.study}}/
    • -
  • {{object.study_population|truncatechars:40}}/
    • -
  • {{object}}/
    • -
  • Create Asessed Outcome
    • - {% elif crud == "Update" %} -
  • {{object.exposure.study_population.study}}/
    • -
  • {{object.exposure.study_population|truncatechars:40}}/
    • -
  • {{object.exposure}}/
    • -
  • {{object}}/
    • -
  • Update
    • - {% endif %} -{% endblock %} - -{% block content %} - -
    - {% crispy form %} -
    - -
    - Assessed Outcome Groups -

    - Response data for each individual assessed outcome - (hover over headers for more details). -

    - {% include "hawc/_formset_table_template.html" with showDeleteRow=False %} -
    - -{% endblock %} - -{% block extrajs %} - {{ form.media }} - -{% endblock extrajs %} diff --git a/project/templates/epi/assessedoutcome_list.html b/project/templates/epi/assessedoutcome_list.html deleted file mode 100644 index 946c4253..00000000 --- a/project/templates/epi/assessedoutcome_list.html +++ /dev/null @@ -1,47 +0,0 @@ -{% extends 'portal.html' %} -{% load add_class %} - -{% block title %}{{assessment}} | Assessed outcomes | HAWC {% endblock title %} - -{% block breadcrumbs %} -
  • {{ assessment }}/
    • -
  • Endpoints/
    • -
  • Epidemiological outcomes/
    • -{% endblock %} - -{% block content %} - -

    Assessed outcomes ({{page_obj.paginator.count}} found)

    - -
    -
      - {% for object in object_list %} -
    • {{object}}
      • - {% empty %} -
    • No assessed outcomes are available.
      • - {% endfor %} -
    -
    - - {% if is_paginated %} - - {% endif %} - -{% endblock content %} diff --git a/project/templates/epi/assessedoutcome_versions.html b/project/templates/epi/assessedoutcome_versions.html deleted file mode 100644 index 06301106..00000000 --- a/project/templates/epi/assessedoutcome_versions.html +++ /dev/null @@ -1,76 +0,0 @@ -{% extends 'portal.html' %} - -{% block title %}{{assessment}} | {{object.exposure.study_population.study}} | {{object.exposure.study_population}} | {{object.exposure}} | {{object}} | Versions {% endblock title %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • -
  • {{object.exposure.study_population.study}}/
    • -
  • {{object.exposure.study_population|truncatechars:40}}/
    • -
  • {{object.exposure}}/
    • -
  • {{object}}/
    • -
  • Versions/
    • -{% endblock %} - - -{% block content %} -

    Prior Versions of {{object}}

    - -

    AJS to revise here. First, get just print raw table. Then, get confounder m2m values and add. Finally, get aop values and build table.

    - -
    -
    -

    Comparison

    - - - - - - - - - - - - - - - - - - - - - - -
    FieldCurrent
    Additions to the primary version shown in green.
    Deletions to primary version shown in red.
    Assessed Outcome Name
    Main Findings
    Statistical Metric
    Outcome N
    Diagnostic Description
    Prevalence Incidence
    Date Created
    Last Updated
    -
    -
    -

    Version List

    - - - - - - - - - - -
    {{object}} versions
    - (hover for instructions) -
    Primary version highlighted in blue.
    Secondary version highlighted in red.
    -
    -
    - -{% endblock content %} - -{% block extrajs %} - -{% endblock extrajs %} diff --git a/project/templates/epi/exposure_confirm_delete.html b/project/templates/epi/exposure_confirm_delete.html deleted file mode 100644 index 53147bef..00000000 --- a/project/templates/epi/exposure_confirm_delete.html +++ /dev/null @@ -1,15 +0,0 @@ -{% extends 'epi/exposure_detail.html' %} - -{% block title %} - {{ block.super }} | Delete -{% endblock title %} - -{% block breadcrumbs_self %} -
  • {{object}}/
    • -
  • Delete/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - {{ block.super }} - {% include "hawc/_delete_block.html" with name="exposure" notes="This will remove individual exposure-groups and assessed outcomes related to this exposure." %} -{% endblock content %} diff --git a/project/templates/epi/exposure_copy_selector.html b/project/templates/epi/exposure_copy_selector.html deleted file mode 100644 index 1b8d1870..00000000 --- a/project/templates/epi/exposure_copy_selector.html +++ /dev/null @@ -1,39 +0,0 @@ -{% extends 'epi/studypopulation_detail.html' %} - - -{% load add_class %} -{% load selectable_tags %} - -{% block title %} - {{block.super}} | Copy Exposure -{% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block breadcrumbs_self %} -
  • {{object}}/
    • -
  • Copy outcome/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - - {% include "hawc/_copy_as_new.html" with name="exposure" notes="Select an existing exposure as a template to create a new one." %} - -{% endblock content %} - -{% block extrajs %} - {{ form.media }} - -{% endblock extrajs %} - diff --git a/project/templates/epi/exposure_detail.html b/project/templates/epi/exposure_detail.html deleted file mode 100644 index c9d2957c..00000000 --- a/project/templates/epi/exposure_detail.html +++ /dev/null @@ -1,63 +0,0 @@ -{% extends 'portal.html' %} - - -{% block title %}{{assessment}} | {{object.study_population.study}} | {{object.study_population}} | {{object}} {% endblock title %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • -
  • {{object.study_population.study}}/
    • -
  • {{object.study_population|truncatechars:40}}/
    • - {% block breadcrumbs_self %} -
  • {{object}}/
    • - {% endblock breadcrumbs_self %} -{% endblock %} - -{% block content %} - -

    {{object}} - {% if obj_perms.edit and crud == "Read" %} -
    - Actions - - - -
    - {% endif %} -

    - - {% if crud == "Read" %} -

    Assessed Outcomes

    -
      - {% for ao in object.outcomes.all %} -
    • {{ao}}
      • - {% empty %} -
    • No assessed-outcomes are available for this exposure.
      • - {% endfor %} -
    - {% endif %} - -{% endblock %} - - -{% block extrajs %} - -{% endblock %} diff --git a/project/templates/epi/exposure_form.html b/project/templates/epi/exposure_form.html deleted file mode 100644 index 5587c0f1..00000000 --- a/project/templates/epi/exposure_form.html +++ /dev/null @@ -1,61 +0,0 @@ -{% extends 'portal.html' %} - -{% load crispy_forms_tags %} -{% load add_class %} - -{% block title %} - {{assessment}} | - {% if crud == "Create" %} - {{study_population.study}} | {{study_population}} | Create Exposure - {% elif crud == "Update" %} - {{object.study_population.study}} | {{object.study_population}} | Update {{object}} - {% endif %} -{% endblock title %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • - {% if crud == "Create" %} -
  • {{study_population.study}}/
    • -
  • {{study_population|truncatechars:40}}/
    • -
  • Create Exposure
    • - {% elif crud == "Update" %} -
  • {{object.study_population.study}}/
    • -
  • {{object.study_population|truncatechars:40}}/
    • -
  • {{object}}/
    • -
  • Update
    • - {% endif %} -{% endblock %} - -{% block content %} - -
    - {% crispy form %} -
    - -
    - {# Exposure Group formset #} - Exposure Groups - - - {% if crud == "Create" %} - Exposure-groups are associated with each exposure, and each is a subset of the exposure population. The total number of individuals in all exposure groups should equal the total number of individuals in the exposure-population. For example, exposure-group descriptions may be "quartile 1 (≤1.0)", "quartile 2 (1.0-2.5)", etc.

    - Once created, additional exposure groups cannot be added. It is assumed that the first exposure-group has the lowest exposure, with each subsequent group having a greater exposure. Up to a maximum of eight exposure-groups can be added.
    - {% endif %} - {% include "hawc/_formset_table_template.html" with showDeleteRow=True %} -
    - -{% endblock %} - -{% block extrajs %} - -{% endblock extrajs %} diff --git a/project/templates/epi/factor_form.html b/project/templates/epi/factor_form.html deleted file mode 100644 index ffce549d..00000000 --- a/project/templates/epi/factor_form.html +++ /dev/null @@ -1,48 +0,0 @@ -{% extends 'base.html' %} - -{% load add_class %} -{% load selectable_tags %} - -{% block title %}{{assessment}} | Create Factor {% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block main_content %} - -
    - - {% csrf_token %} - -
    -
    - Create new factor - Create a new factor. Factors can be applied to assessment outcomes as adjustment factors or confounders considered. They are assessment-specific. Please take care not to duplicate existing factors.
    - - {{ form.non_field_errors|add_class:"alert alert-error" }} - - {% for field in form %} -
    - {{field.label_tag|add_class:"control-label"}} -
    - {{field}} - {{field.help_text}} -
    - {{field.errors|add_class:"alert alert-error"}} -
    - {% endfor %} -
    -
    -
    -
    - -
    -
    -
    - -{% endblock main_content %} - -{% block extrajs %} - {{ form.media }} -{% endblock extrajs %} diff --git a/project/templates/epi/studycriteria_form.html b/project/templates/epi/studycriteria_form.html deleted file mode 100644 index 1c91cae1..00000000 --- a/project/templates/epi/studycriteria_form.html +++ /dev/null @@ -1,48 +0,0 @@ -{% extends 'base.html' %} - -{% load add_class %} -{% load selectable_tags %} - -{% block title %}{{assessment}} | {{ crud }} Study Criteria {% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block main_content %} - -
    - - {% csrf_token %} - -
    -
    - Create new study criteria - Create a epidemiology study criteria. Study criteria can be applied to study populations as inclusion criteria, exclusion criteria, or confounding criteria. They are assessment-specific. Please take care not to duplicate existing factors.
    - - {{ form.non_field_errors|add_class:"alert alert-error" }} - - {% for field in form %} -
    - {{field.label_tag|add_class:"control-label"}} -
    - {{field}} - {{field.help_text}} -
    - {{field.errors|add_class:"alert alert-error"}} -
    - {% endfor %} -
    -
    -
    -
    - -
    -
    -
    - -{% endblock main_content %} - -{% block extrajs %} - {{ form.media }} -{% endblock extrajs %} diff --git a/project/templates/epi/studypopulation_confirm_delete.html b/project/templates/epi/studypopulation_confirm_delete.html deleted file mode 100644 index 477d1040..00000000 --- a/project/templates/epi/studypopulation_confirm_delete.html +++ /dev/null @@ -1,15 +0,0 @@ -{% extends 'epi/studypopulation_detail.html' %} - -{% block title %} - {{ block.super }} | Delete -{% endblock title %} - -{% block breadcrumbs_self %} -
  • {{object|truncatechars:40}}/
    • -
  • Delete/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - {{ block.super }} - {% include "hawc/_delete_block.html" with name="study population" notes="This will remove all exposures and assessed outcomes related to this population." %} -{% endblock content %} diff --git a/project/templates/epi/studypopulation_copy_selector.html b/project/templates/epi/studypopulation_copy_selector.html deleted file mode 100644 index b11c83f2..00000000 --- a/project/templates/epi/studypopulation_copy_selector.html +++ /dev/null @@ -1,39 +0,0 @@ -{% extends 'study/study_detail.html' %} - - -{% load add_class %} -{% load selectable_tags %} - -{% block title %} - {{block.super}} | Copy Study Population -{% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block breadcrumbs_self %} -
  • {{object}}/
    • -
  • Copy study population/
    • -{% endblock breadcrumbs_self %} - -{% block content %} - - {% include "hawc/_copy_as_new.html" with name="study population" notes="Select an existing study population as a template to create a new one." %} - -{% endblock content %} - -{% block extrajs %} - {{ form.media }} - -{% endblock extrajs %} - diff --git a/project/templates/epi/studypopulation_detail.html b/project/templates/epi/studypopulation_detail.html deleted file mode 100644 index 2ad008cf..00000000 --- a/project/templates/epi/studypopulation_detail.html +++ /dev/null @@ -1,59 +0,0 @@ -{% extends 'portal.html' %} - -{% block title %}{{assessment}} | {{object.study}} | Study Population {% endblock title %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • -
  • {{object.study}}/
    • - {% block breadcrumbs_self %} -
  • {{object|truncatechars:40}}/
    • - {% endblock breadcrumbs_self %} -{% endblock %} - -{% block content %} - -

    {{object}} - {% if obj_perms.edit and crud == "Read" %} -
    - Actions - - - -
    - {% endif %} -

    - -
    - - {% if crud == "Read" %} -

    Available exposures

    -
      - {% for exposure in object.exposures.all %} -
    • {{exposure}}
      • - {% empty %} -
    • No exposures are available for this study population.
      • - {% endfor %} -
    - {% endif %} - -{% endblock %} - - -{% block extrajs %} - -{% endblock %} diff --git a/project/templates/epi/studypopulation_form.html b/project/templates/epi/studypopulation_form.html deleted file mode 100644 index dc850345..00000000 --- a/project/templates/epi/studypopulation_form.html +++ /dev/null @@ -1,37 +0,0 @@ -{% extends 'portal.html' %} - -{% load selectable_tags %} -{% load crispy_forms_tags %} - -{% block title %} - {{assessment}} | - {% if crud == "Create" %} - {{study}} | Create Study Population - {% elif crud == "Update" %} - {{object.study}} | Update {{object}} - {% endif %} -{% endblock title %} - -{% block extrastyle %} - {% include_ui_theme %} -{% endblock %} - -{% block breadcrumbs %} -
  • {{assessment}}/
    • - {% if crud == "Create" %} -
  • {{study}}/
    • -
  • Create Study Population
    • - {% elif crud == "Update" %} -
  • {{object.study}}/
    • -
  • {{object}}/
    • -
  • Update
    • - {% endif %} -{% endblock %} - -{% block content %} - {% crispy form %} -{% endblock %} - -{% block extrajs %} - {{ form.media }} -{% endblock extrajs %} From 59d87e907449cb5abba756e890a1e186a90cd2ec Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:01:34 -0400 Subject: [PATCH 02/17] rename epi2 to epi --- project/{epi2 => epi}/__init__.py | 0 project/{epi2 => epi}/admin.py | 0 project/{epi2 => epi}/api.py | 0 project/{epi2 => epi}/exports.py | 0 project/{epi2 => epi}/fixtures/countries.json | 0 project/{epi2 => epi}/fixtures/ethnicity.json | 0 project/{epi2 => epi}/fixtures/resultmetric.json | 0 project/{epi2 => epi}/forms.py | 0 project/{epi2 => epi}/lookups.py | 0 project/{epi2 => epi}/migrations/0001_initial.py | 0 project/{epi2 => epi}/migrations/0002_load_fixtures.py | 0 project/{epi2 => epi}/migrations/__init__.py | 0 project/{epi2 => epi}/models.py | 0 project/{epi2 => epi}/serializers.py | 0 project/{epi2 => epi}/urls.py | 0 project/{epi2 => epi}/views.py | 0 project/hawc/settings/base.py | 2 +- project/static/epi/js/{models2.js => models.js} | 0 project/templates/base.html | 2 +- project/templates/{epi2 => epi}/adjustmentfactor_form.html | 0 project/templates/{epi2 => epi}/comparisonset_confirm_delete.html | 0 project/templates/{epi2 => epi}/comparisonset_detail.html | 0 project/templates/{epi2 => epi}/comparisonset_form.html | 0 .../templates/{epi2 => epi}/comparisonset_outcome_copy_selector.html | 0 project/templates/{epi2 => epi}/comparisonset_sp_copy_selector.html | 0 project/templates/{epi2 => epi}/criteria_form.html | 0 project/templates/{epi2 => epi}/exposure2_confirm_delete.html | 0 project/templates/{epi2 => epi}/exposure2_detail.html | 0 project/templates/{epi2 => epi}/exposure2_form.html | 0 project/templates/{epi2 => epi}/exposure_copy_selector.html | 0 project/templates/{epi2 => epi}/group_detail.html | 0 project/templates/{epi2 => epi}/group_form.html | 0 project/templates/{epi2 => epi}/outcome_confirm_delete.html | 0 project/templates/{epi2 => epi}/outcome_copy_selector.html | 0 project/templates/{epi2 => epi}/outcome_detail.html | 0 project/templates/{epi2 => epi}/outcome_form.html | 0 project/templates/{epi2 => epi}/outcome_list.html | 0 project/templates/{epi2 => epi}/result_confirm_delete.html | 0 project/templates/{epi2 => epi}/result_copy_selector.html | 0 project/templates/{epi2 => epi}/result_detail.html | 0 project/templates/{epi2 => epi}/result_form.html | 0 project/templates/{epi2 => epi}/studypopulation_confirm_delete.html | 0 project/templates/{epi2 => epi}/studypopulation_copy_selector.html | 0 project/templates/{epi2 => epi}/studypopulation_detail.html | 0 project/templates/{epi2 => epi}/studypopulation_form.html | 0 45 files changed, 2 insertions(+), 2 deletions(-) rename project/{epi2 => epi}/__init__.py (100%) rename project/{epi2 => epi}/admin.py (100%) rename project/{epi2 => epi}/api.py (100%) rename project/{epi2 => epi}/exports.py (100%) rename project/{epi2 => epi}/fixtures/countries.json (100%) rename project/{epi2 => epi}/fixtures/ethnicity.json (100%) rename project/{epi2 => epi}/fixtures/resultmetric.json (100%) rename project/{epi2 => epi}/forms.py (100%) rename project/{epi2 => epi}/lookups.py (100%) rename project/{epi2 => epi}/migrations/0001_initial.py (100%) rename project/{epi2 => epi}/migrations/0002_load_fixtures.py (100%) rename project/{epi2 => epi}/migrations/__init__.py (100%) rename project/{epi2 => epi}/models.py (100%) rename project/{epi2 => epi}/serializers.py (100%) rename project/{epi2 => epi}/urls.py (100%) rename project/{epi2 => epi}/views.py (100%) rename project/static/epi/js/{models2.js => models.js} (100%) rename project/templates/{epi2 => epi}/adjustmentfactor_form.html (100%) rename project/templates/{epi2 => epi}/comparisonset_confirm_delete.html (100%) rename project/templates/{epi2 => epi}/comparisonset_detail.html (100%) rename project/templates/{epi2 => epi}/comparisonset_form.html (100%) rename project/templates/{epi2 => epi}/comparisonset_outcome_copy_selector.html (100%) rename project/templates/{epi2 => epi}/comparisonset_sp_copy_selector.html (100%) rename project/templates/{epi2 => epi}/criteria_form.html (100%) rename project/templates/{epi2 => epi}/exposure2_confirm_delete.html (100%) rename project/templates/{epi2 => epi}/exposure2_detail.html (100%) rename project/templates/{epi2 => epi}/exposure2_form.html (100%) rename project/templates/{epi2 => epi}/exposure_copy_selector.html (100%) rename project/templates/{epi2 => epi}/group_detail.html (100%) rename project/templates/{epi2 => epi}/group_form.html (100%) rename project/templates/{epi2 => epi}/outcome_confirm_delete.html (100%) rename project/templates/{epi2 => epi}/outcome_copy_selector.html (100%) rename project/templates/{epi2 => epi}/outcome_detail.html (100%) rename project/templates/{epi2 => epi}/outcome_form.html (100%) rename project/templates/{epi2 => epi}/outcome_list.html (100%) rename project/templates/{epi2 => epi}/result_confirm_delete.html (100%) rename project/templates/{epi2 => epi}/result_copy_selector.html (100%) rename project/templates/{epi2 => epi}/result_detail.html (100%) rename project/templates/{epi2 => epi}/result_form.html (100%) rename project/templates/{epi2 => epi}/studypopulation_confirm_delete.html (100%) rename project/templates/{epi2 => epi}/studypopulation_copy_selector.html (100%) rename project/templates/{epi2 => epi}/studypopulation_detail.html (100%) rename project/templates/{epi2 => epi}/studypopulation_form.html (100%) diff --git a/project/epi2/__init__.py b/project/epi/__init__.py similarity index 100% rename from project/epi2/__init__.py rename to project/epi/__init__.py diff --git a/project/epi2/admin.py b/project/epi/admin.py similarity index 100% rename from project/epi2/admin.py rename to project/epi/admin.py diff --git a/project/epi2/api.py b/project/epi/api.py similarity index 100% rename from project/epi2/api.py rename to project/epi/api.py diff --git a/project/epi2/exports.py b/project/epi/exports.py similarity index 100% rename from project/epi2/exports.py rename to project/epi/exports.py diff --git a/project/epi2/fixtures/countries.json b/project/epi/fixtures/countries.json similarity index 100% rename from project/epi2/fixtures/countries.json rename to project/epi/fixtures/countries.json diff --git a/project/epi2/fixtures/ethnicity.json b/project/epi/fixtures/ethnicity.json similarity index 100% rename from project/epi2/fixtures/ethnicity.json rename to project/epi/fixtures/ethnicity.json diff --git a/project/epi2/fixtures/resultmetric.json b/project/epi/fixtures/resultmetric.json similarity index 100% rename from project/epi2/fixtures/resultmetric.json rename to project/epi/fixtures/resultmetric.json diff --git a/project/epi2/forms.py b/project/epi/forms.py similarity index 100% rename from project/epi2/forms.py rename to project/epi/forms.py diff --git a/project/epi2/lookups.py b/project/epi/lookups.py similarity index 100% rename from project/epi2/lookups.py rename to project/epi/lookups.py diff --git a/project/epi2/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py similarity index 100% rename from project/epi2/migrations/0001_initial.py rename to project/epi/migrations/0001_initial.py diff --git a/project/epi2/migrations/0002_load_fixtures.py b/project/epi/migrations/0002_load_fixtures.py similarity index 100% rename from project/epi2/migrations/0002_load_fixtures.py rename to project/epi/migrations/0002_load_fixtures.py diff --git a/project/epi2/migrations/__init__.py b/project/epi/migrations/__init__.py similarity index 100% rename from project/epi2/migrations/__init__.py rename to project/epi/migrations/__init__.py diff --git a/project/epi2/models.py b/project/epi/models.py similarity index 100% rename from project/epi2/models.py rename to project/epi/models.py diff --git a/project/epi2/serializers.py b/project/epi/serializers.py similarity index 100% rename from project/epi2/serializers.py rename to project/epi/serializers.py diff --git a/project/epi2/urls.py b/project/epi/urls.py similarity index 100% rename from project/epi2/urls.py rename to project/epi/urls.py diff --git a/project/epi2/views.py b/project/epi/views.py similarity index 100% rename from project/epi2/views.py rename to project/epi/views.py diff --git a/project/hawc/settings/base.py b/project/hawc/settings/base.py index 451663c6..7e19a848 100644 --- a/project/hawc/settings/base.py +++ b/project/hawc/settings/base.py @@ -98,7 +98,7 @@ 'lit', 'study', 'animal', - 'epi2', + 'epi', 'epimeta', 'invitro', 'bmd', diff --git a/project/static/epi/js/models2.js b/project/static/epi/js/models.js similarity index 100% rename from project/static/epi/js/models2.js rename to project/static/epi/js/models.js diff --git a/project/templates/base.html b/project/templates/base.html index ac0fcdf7..2c902007 100644 --- a/project/templates/base.html +++ b/project/templates/base.html @@ -130,7 +130,7 @@ - + diff --git a/project/templates/epi2/adjustmentfactor_form.html b/project/templates/epi/adjustmentfactor_form.html similarity index 100% rename from project/templates/epi2/adjustmentfactor_form.html rename to project/templates/epi/adjustmentfactor_form.html diff --git a/project/templates/epi2/comparisonset_confirm_delete.html b/project/templates/epi/comparisonset_confirm_delete.html similarity index 100% rename from project/templates/epi2/comparisonset_confirm_delete.html rename to project/templates/epi/comparisonset_confirm_delete.html diff --git a/project/templates/epi2/comparisonset_detail.html b/project/templates/epi/comparisonset_detail.html similarity index 100% rename from project/templates/epi2/comparisonset_detail.html rename to project/templates/epi/comparisonset_detail.html diff --git a/project/templates/epi2/comparisonset_form.html b/project/templates/epi/comparisonset_form.html similarity index 100% rename from project/templates/epi2/comparisonset_form.html rename to project/templates/epi/comparisonset_form.html diff --git a/project/templates/epi2/comparisonset_outcome_copy_selector.html b/project/templates/epi/comparisonset_outcome_copy_selector.html similarity index 100% rename from project/templates/epi2/comparisonset_outcome_copy_selector.html rename to project/templates/epi/comparisonset_outcome_copy_selector.html diff --git a/project/templates/epi2/comparisonset_sp_copy_selector.html b/project/templates/epi/comparisonset_sp_copy_selector.html similarity index 100% rename from project/templates/epi2/comparisonset_sp_copy_selector.html rename to project/templates/epi/comparisonset_sp_copy_selector.html diff --git a/project/templates/epi2/criteria_form.html b/project/templates/epi/criteria_form.html similarity index 100% rename from project/templates/epi2/criteria_form.html rename to project/templates/epi/criteria_form.html diff --git a/project/templates/epi2/exposure2_confirm_delete.html b/project/templates/epi/exposure2_confirm_delete.html similarity index 100% rename from project/templates/epi2/exposure2_confirm_delete.html rename to project/templates/epi/exposure2_confirm_delete.html diff --git a/project/templates/epi2/exposure2_detail.html b/project/templates/epi/exposure2_detail.html similarity index 100% rename from project/templates/epi2/exposure2_detail.html rename to project/templates/epi/exposure2_detail.html diff --git a/project/templates/epi2/exposure2_form.html b/project/templates/epi/exposure2_form.html similarity index 100% rename from project/templates/epi2/exposure2_form.html rename to project/templates/epi/exposure2_form.html diff --git a/project/templates/epi2/exposure_copy_selector.html b/project/templates/epi/exposure_copy_selector.html similarity index 100% rename from project/templates/epi2/exposure_copy_selector.html rename to project/templates/epi/exposure_copy_selector.html diff --git a/project/templates/epi2/group_detail.html b/project/templates/epi/group_detail.html similarity index 100% rename from project/templates/epi2/group_detail.html rename to project/templates/epi/group_detail.html diff --git a/project/templates/epi2/group_form.html b/project/templates/epi/group_form.html similarity index 100% rename from project/templates/epi2/group_form.html rename to project/templates/epi/group_form.html diff --git a/project/templates/epi2/outcome_confirm_delete.html b/project/templates/epi/outcome_confirm_delete.html similarity index 100% rename from project/templates/epi2/outcome_confirm_delete.html rename to project/templates/epi/outcome_confirm_delete.html diff --git a/project/templates/epi2/outcome_copy_selector.html b/project/templates/epi/outcome_copy_selector.html similarity index 100% rename from project/templates/epi2/outcome_copy_selector.html rename to project/templates/epi/outcome_copy_selector.html diff --git a/project/templates/epi2/outcome_detail.html b/project/templates/epi/outcome_detail.html similarity index 100% rename from project/templates/epi2/outcome_detail.html rename to project/templates/epi/outcome_detail.html diff --git a/project/templates/epi2/outcome_form.html b/project/templates/epi/outcome_form.html similarity index 100% rename from project/templates/epi2/outcome_form.html rename to project/templates/epi/outcome_form.html diff --git a/project/templates/epi2/outcome_list.html b/project/templates/epi/outcome_list.html similarity index 100% rename from project/templates/epi2/outcome_list.html rename to project/templates/epi/outcome_list.html diff --git a/project/templates/epi2/result_confirm_delete.html b/project/templates/epi/result_confirm_delete.html similarity index 100% rename from project/templates/epi2/result_confirm_delete.html rename to project/templates/epi/result_confirm_delete.html diff --git a/project/templates/epi2/result_copy_selector.html b/project/templates/epi/result_copy_selector.html similarity index 100% rename from project/templates/epi2/result_copy_selector.html rename to project/templates/epi/result_copy_selector.html diff --git a/project/templates/epi2/result_detail.html b/project/templates/epi/result_detail.html similarity index 100% rename from project/templates/epi2/result_detail.html rename to project/templates/epi/result_detail.html diff --git a/project/templates/epi2/result_form.html b/project/templates/epi/result_form.html similarity index 100% rename from project/templates/epi2/result_form.html rename to project/templates/epi/result_form.html diff --git a/project/templates/epi2/studypopulation_confirm_delete.html b/project/templates/epi/studypopulation_confirm_delete.html similarity index 100% rename from project/templates/epi2/studypopulation_confirm_delete.html rename to project/templates/epi/studypopulation_confirm_delete.html diff --git a/project/templates/epi2/studypopulation_copy_selector.html b/project/templates/epi/studypopulation_copy_selector.html similarity index 100% rename from project/templates/epi2/studypopulation_copy_selector.html rename to project/templates/epi/studypopulation_copy_selector.html diff --git a/project/templates/epi2/studypopulation_detail.html b/project/templates/epi/studypopulation_detail.html similarity index 100% rename from project/templates/epi2/studypopulation_detail.html rename to project/templates/epi/studypopulation_detail.html diff --git a/project/templates/epi2/studypopulation_form.html b/project/templates/epi/studypopulation_form.html similarity index 100% rename from project/templates/epi2/studypopulation_form.html rename to project/templates/epi/studypopulation_form.html From e921c0e2aa5a69115c407eebb62c958ae19f12af Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:08:22 -0400 Subject: [PATCH 03/17] rename Exposure2 to Exposure --- project/epi/api.py | 2 +- project/epi/exports.py | 4 ++-- project/epi/forms.py | 2 +- project/epi/lookups.py | 2 +- project/epi/migrations/0001_initial.py | 4 ++-- project/epi/models.py | 12 ++++++------ project/epi/serializers.py | 6 +++--- project/epi/views.py | 8 ++++---- ...ure2_confirm_delete.html => exposure_confirm_delete.html} | 2 +- .../epi/{exposure2_detail.html => exposure_detail.html} | 0 .../epi/{exposure2_form.html => exposure_form.html} | 0 11 files changed, 21 insertions(+), 21 deletions(-) rename project/templates/epi/{exposure2_confirm_delete.html => exposure_confirm_delete.html} (89%) rename project/templates/epi/{exposure2_detail.html => exposure_detail.html} (100%) rename project/templates/epi/{exposure2_form.html => exposure_form.html} (100%) diff --git a/project/epi/api.py b/project/epi/api.py index a3a9d406..e4b8dc12 100644 --- a/project/epi/api.py +++ b/project/epi/api.py @@ -13,7 +13,7 @@ class StudyPopulation(AssessmentViewset): class Exposure(AssessmentViewset): assessment_filter_args = "study_population__study__assessment" - model = models.Exposure2 + model = models.Exposure serializer_class = serializers.ExposureSerializer diff --git a/project/epi/exports.py b/project/epi/exports.py index fbb1f7f5..4f3e23b5 100644 --- a/project/epi/exports.py +++ b/project/epi/exports.py @@ -11,7 +11,7 @@ def _get_header_row(self): header.extend(Study.flat_complete_header_row()) header.extend(models.StudyPopulation.flat_complete_header_row()) header.extend(models.Outcome.flat_complete_header_row()) - header.extend(models.Exposure2.flat_complete_header_row()) + header.extend(models.Exposure.flat_complete_header_row()) header.extend(models.ComparisonSet.flat_complete_header_row()) header.extend(models.Result.flat_complete_header_row()) header.extend(models.Group.flat_complete_header_row()) @@ -28,7 +28,7 @@ def _get_data_rows(self): row.extend(models.Outcome.flat_complete_data_row(ser)) for res in ser['results']: row_copy = list(row) - row_copy.extend(models.Exposure2.flat_complete_data_row(res["comparison_set"]["exposure"])) + row_copy.extend(models.Exposure.flat_complete_data_row(res["comparison_set"]["exposure"])) row_copy.extend(models.ComparisonSet.flat_complete_data_row(res["comparison_set"])) row_copy.extend(models.Result.flat_complete_data_row(res)) for rg in res['results']: diff --git a/project/epi/forms.py b/project/epi/forms.py index 6caf6fb3..d7ac0086 100644 --- a/project/epi/forms.py +++ b/project/epi/forms.py @@ -272,7 +272,7 @@ class ExposureForm(forms.ModelForm): HELP_TEXT_UPDATE = """Update an existing exposure.""" class Meta: - model = models.Exposure2 + model = models.Exposure exclude = ('study_population', ) def __init__(self, *args, **kwargs): diff --git a/project/epi/lookups.py b/project/epi/lookups.py index b4f7d4b9..3b36d568 100644 --- a/project/epi/lookups.py +++ b/project/epi/lookups.py @@ -44,7 +44,7 @@ class ComparisonSetByOutcomeLookup(ComparisonSetByStudyPopulationLookup): class ExposureByStudyPopulationLookup(RelatedLookup): - model = models.Exposure2 + model = models.Exposure search_fields = ('name__icontains', ) related_filter = 'study_population_id' diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py index dbf5797a..b2102ada 100644 --- a/project/epi/migrations/0001_initial.py +++ b/project/epi/migrations/0001_initial.py @@ -78,7 +78,7 @@ class Migration(migrations.Migration): }, ), migrations.CreateModel( - name='Exposure2', + name='Exposure', fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('name', models.CharField(help_text=b'Name of exposure and exposure-route', max_length=128)), @@ -304,7 +304,7 @@ class Migration(migrations.Migration): migrations.AddField( model_name='comparisonset', name='exposure', - field=models.ForeignKey(related_name='comparison_sets', blank=True, to='epi2.Exposure2', help_text=b'Exposure-group associated with this group', null=True), + field=models.ForeignKey(related_name='comparison_sets', blank=True, to='epi2.Exposure', help_text=b'Exposure-group associated with this group', null=True), ), migrations.AddField( model_name='comparisonset', diff --git a/project/epi/models.py b/project/epi/models.py index bad76be8..cbe7d4c9 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -344,7 +344,7 @@ class ComparisonSet(models.Model): name = models.CharField( max_length=256) exposure = models.ForeignKey( - "Exposure2", + "Exposure", related_name="comparison_sets", help_text="Exposure-group associated with this group", blank=True, @@ -522,7 +522,7 @@ def flat_complete_data_row(ser): ) -class Exposure2(models.Model): +class Exposure(models.Model): study_population = models.ForeignKey( StudyPopulation, related_name='exposures') @@ -1063,8 +1063,8 @@ def flat_complete_data_row(ser): @receiver(pre_delete, sender=StudyPopulation) @receiver(post_save, sender=ComparisonSet) @receiver(pre_delete, sender=ComparisonSet) -@receiver(post_save, sender=Exposure2) -@receiver(pre_delete, sender=Exposure2) +@receiver(post_save, sender=Exposure) +@receiver(pre_delete, sender=Exposure) @receiver(post_save, sender=Group) @receiver(pre_delete, sender=Group) @receiver(post_save, sender=Outcome) @@ -1081,7 +1081,7 @@ def invalidate_outcome_cache(sender, instance, **kwargs): filters["study_population_id"] = instance.id elif instance_type is ComparisonSet: filters["results__comparison_set_id"] = instance.id - elif instance_type is Exposure2: + elif instance_type is Exposure: filters["results__comparison_set__exposure_id"] = instance.id elif instance_type is Group: filters["results__comparison_set__groups"] = instance.id @@ -1106,7 +1106,7 @@ def invalidate_outcome_cache(sender, instance, **kwargs): reversion.register(ResultAdjustmentFactor) reversion.register(StudyPopulation, follow=('country', 'spcriteria')) reversion.register(ComparisonSet) -reversion.register(Exposure2) +reversion.register(Exposure) reversion.register(Outcome, follow=('effects',)) reversion.register(Group, follow=('ethnicities',)) reversion.register(Result, follow=('adjustment_factors', 'resfactors', 'results')) diff --git a/project/epi/serializers.py b/project/epi/serializers.py index c28ffd9e..39eb3849 100644 --- a/project/epi/serializers.py +++ b/project/epi/serializers.py @@ -36,7 +36,7 @@ class ExposureLinkSerializer(serializers.ModelSerializer): url = serializers.CharField(source='get_absolute_url', read_only=True) class Meta: - model = models.Exposure2 + model = models.Exposure fields = ('id', 'name', 'url') @@ -80,7 +80,7 @@ class SimpleExposureSerializer(serializers.ModelSerializer): metric_units = DoseUnitsSerializer() class Meta: - model = models.Exposure2 + model = models.Exposure class ComparisonSetLinkSerializer(serializers.ModelSerializer): @@ -112,7 +112,7 @@ class ExposureSerializer(serializers.ModelSerializer): metric_units = DoseUnitsSerializer() class Meta: - model = models.Exposure2 + model = models.Exposure class GroupResultSerializer(serializers.ModelSerializer): diff --git a/project/epi/views.py b/project/epi/views.py index 1cceb598..0020c5c0 100644 --- a/project/epi/views.py +++ b/project/epi/views.py @@ -69,7 +69,7 @@ class ExposureCreate(BaseCreate): success_message = 'Exposure created.' parent_model = models.StudyPopulation parent_template_name = 'study_population' - model = models.Exposure2 + model = models.Exposure form_class = forms.ExposureForm @@ -83,18 +83,18 @@ def get_context_data(self, **kwargs): class ExposureDetail(BaseDetail): - model = models.Exposure2 + model = models.Exposure class ExposureUpdate(BaseUpdate): success_message = "Study Population updated." - model = models.Exposure2 + model = models.Exposure form_class = forms.ExposureForm class ExposureDelete(BaseDelete): success_message = "Study Population deleted." - model = models.Exposure2 + model = models.Exposure def get_success_url(self): return self.object.study_population.get_absolute_url() diff --git a/project/templates/epi/exposure2_confirm_delete.html b/project/templates/epi/exposure_confirm_delete.html similarity index 89% rename from project/templates/epi/exposure2_confirm_delete.html rename to project/templates/epi/exposure_confirm_delete.html index 5386d473..caefd552 100644 --- a/project/templates/epi/exposure2_confirm_delete.html +++ b/project/templates/epi/exposure_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/exposure2_detail.html' %} +{% extends 'epi2/exposure_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} diff --git a/project/templates/epi/exposure2_detail.html b/project/templates/epi/exposure_detail.html similarity index 100% rename from project/templates/epi/exposure2_detail.html rename to project/templates/epi/exposure_detail.html diff --git a/project/templates/epi/exposure2_form.html b/project/templates/epi/exposure_form.html similarity index 100% rename from project/templates/epi/exposure2_form.html rename to project/templates/epi/exposure_form.html From 73cd019405235ee7217cc6caa7de553b26eb2410 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:11:09 -0400 Subject: [PATCH 04/17] global replace template names --- project/epi/views.py | 12 ++++++------ project/templates/epi/comparisonset_confirm_delete.html | 2 +- .../templates/epi/comparisonset_outcome_copy_selector.html | 2 +- project/templates/epi/comparisonset_sp_copy_selector.html | 2 +- project/templates/epi/exposure_confirm_delete.html | 2 +- project/templates/epi/exposure_copy_selector.html | 2 +- project/templates/epi/outcome_confirm_delete.html | 2 +- project/templates/epi/outcome_copy_selector.html | 2 +- project/templates/epi/result_confirm_delete.html | 2 +- project/templates/epi/result_copy_selector.html | 2 +- project/templates/epi/studypopulation_confirm_delete.html | 2 +- 11 files changed, 16 insertions(+), 16 deletions(-) diff --git a/project/epi/views.py b/project/epi/views.py index 0020c5c0..473285dd 100644 --- a/project/epi/views.py +++ b/project/epi/views.py @@ -29,7 +29,7 @@ class StudyPopulationCreate(BaseCreate): class StudyPopulationCopyAsNewSelector(StudyRead): - template_name = 'epi2/studypopulation_copy_selector.html' + template_name = 'epi/studypopulation_copy_selector.html' def get_context_data(self, **kwargs): context = super(StudyPopulationCopyAsNewSelector, self).get_context_data(**kwargs) @@ -74,7 +74,7 @@ class ExposureCreate(BaseCreate): class ExposureCopyAsNewSelector(StudyPopulationDetail): - template_name = 'epi2/exposure_copy_selector.html' + template_name = 'epi/exposure_copy_selector.html' def get_context_data(self, **kwargs): context = super(ExposureCopyAsNewSelector, self).get_context_data(**kwargs) @@ -149,7 +149,7 @@ def get_form_kwargs(self): class OutcomeCopyAsNewSelector(StudyPopulationDetail): - template_name = 'epi2/outcome_copy_selector.html' + template_name = 'epi/outcome_copy_selector.html' def get_context_data(self, **kwargs): context = super(OutcomeCopyAsNewSelector, self).get_context_data(**kwargs) @@ -201,7 +201,7 @@ def build_initial_formset_factory(self): class ResultCopyAsNewSelector(OutcomeDetail): - template_name = 'epi2/result_copy_selector.html' + template_name = 'epi/result_copy_selector.html' def get_context_data(self, **kwargs): context = super(ResultCopyAsNewSelector, self).get_context_data(**kwargs) @@ -277,7 +277,7 @@ class ComparisonSetOutcomeCreate(ComparisonSetCreate): class ComparisonSetStudyPopCopySelector(StudyPopulationDetail): - template_name = 'epi2/comparisonset_sp_copy_selector.html' + template_name = 'epi/comparisonset_sp_copy_selector.html' def get_context_data(self, **kwargs): context = super(ComparisonSetStudyPopCopySelector, self).get_context_data(**kwargs) @@ -286,7 +286,7 @@ def get_context_data(self, **kwargs): class ComparisonSetOutcomeCopySelector(OutcomeDetail): - template_name = 'epi2/comparisonset_outcome_copy_selector.html' + template_name = 'epi/comparisonset_outcome_copy_selector.html' def get_context_data(self, **kwargs): context = super(ComparisonSetOutcomeCopySelector, self).get_context_data(**kwargs) diff --git a/project/templates/epi/comparisonset_confirm_delete.html b/project/templates/epi/comparisonset_confirm_delete.html index 073b750d..3c9fe15c 100644 --- a/project/templates/epi/comparisonset_confirm_delete.html +++ b/project/templates/epi/comparisonset_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/comparisonset_detail.html' %} +{% extends 'epi/comparisonset_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} diff --git a/project/templates/epi/comparisonset_outcome_copy_selector.html b/project/templates/epi/comparisonset_outcome_copy_selector.html index cdd8b552..d214e8f8 100644 --- a/project/templates/epi/comparisonset_outcome_copy_selector.html +++ b/project/templates/epi/comparisonset_outcome_copy_selector.html @@ -1,4 +1,4 @@ -{% extends 'epi2/outcome_detail.html' %} +{% extends 'epi/outcome_detail.html' %} {% load add_class %} diff --git a/project/templates/epi/comparisonset_sp_copy_selector.html b/project/templates/epi/comparisonset_sp_copy_selector.html index 83a6c9fd..97693a06 100644 --- a/project/templates/epi/comparisonset_sp_copy_selector.html +++ b/project/templates/epi/comparisonset_sp_copy_selector.html @@ -1,4 +1,4 @@ -{% extends 'epi2/studypopulation_detail.html' %} +{% extends 'epi/studypopulation_detail.html' %} {% load add_class %} diff --git a/project/templates/epi/exposure_confirm_delete.html b/project/templates/epi/exposure_confirm_delete.html index caefd552..ddeb80ca 100644 --- a/project/templates/epi/exposure_confirm_delete.html +++ b/project/templates/epi/exposure_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/exposure_detail.html' %} +{% extends 'epi/exposure_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} diff --git a/project/templates/epi/exposure_copy_selector.html b/project/templates/epi/exposure_copy_selector.html index 444dec4d..a59df4b7 100644 --- a/project/templates/epi/exposure_copy_selector.html +++ b/project/templates/epi/exposure_copy_selector.html @@ -1,4 +1,4 @@ -{% extends 'epi2/studypopulation_detail.html' %} +{% extends 'epi/studypopulation_detail.html' %} {% load add_class %} {% load selectable_tags %} diff --git a/project/templates/epi/outcome_confirm_delete.html b/project/templates/epi/outcome_confirm_delete.html index 42a1161b..1096e243 100644 --- a/project/templates/epi/outcome_confirm_delete.html +++ b/project/templates/epi/outcome_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/outcome_detail.html' %} +{% extends 'epi/outcome_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} diff --git a/project/templates/epi/outcome_copy_selector.html b/project/templates/epi/outcome_copy_selector.html index ab978ce6..92b48f22 100644 --- a/project/templates/epi/outcome_copy_selector.html +++ b/project/templates/epi/outcome_copy_selector.html @@ -1,4 +1,4 @@ -{% extends 'epi2/studypopulation_detail.html' %} +{% extends 'epi/studypopulation_detail.html' %} {% load add_class %} diff --git a/project/templates/epi/result_confirm_delete.html b/project/templates/epi/result_confirm_delete.html index 612015b6..e051486c 100644 --- a/project/templates/epi/result_confirm_delete.html +++ b/project/templates/epi/result_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/result_detail.html' %} +{% extends 'epi/result_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} diff --git a/project/templates/epi/result_copy_selector.html b/project/templates/epi/result_copy_selector.html index 5b12a60a..ec4f5300 100644 --- a/project/templates/epi/result_copy_selector.html +++ b/project/templates/epi/result_copy_selector.html @@ -1,4 +1,4 @@ -{% extends 'epi2/studypopulation_detail.html' %} +{% extends 'epi/studypopulation_detail.html' %} {% load add_class %} diff --git a/project/templates/epi/studypopulation_confirm_delete.html b/project/templates/epi/studypopulation_confirm_delete.html index 9b2e3468..d69ff8d1 100644 --- a/project/templates/epi/studypopulation_confirm_delete.html +++ b/project/templates/epi/studypopulation_confirm_delete.html @@ -1,4 +1,4 @@ -{% extends 'epi2/studypopulation_detail.html' %} +{% extends 'epi/studypopulation_detail.html' %} {% block title %} {% include "hawc/siteTitle.html" with crumbs=object.get_crumbs crud=crud %} From d8529a4b60516b379f048ddac974e5743ac7fc33 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:14:52 -0400 Subject: [PATCH 05/17] rename epi urls --- project/epi/forms.py | 4 ++-- project/epi/models.py | 12 ++++++------ project/epimeta/forms.py | 4 ++-- project/templates/assessment/assessment_downloads.html | 2 +- project/templates/assessment/baseendpoint_list.html | 2 +- project/templates/epi/comparisonset_detail.html | 4 ++-- .../epi/comparisonset_outcome_copy_selector.html | 2 +- .../templates/epi/comparisonset_sp_copy_selector.html | 2 +- project/templates/epi/exposure_copy_selector.html | 2 +- project/templates/epi/exposure_detail.html | 4 ++-- project/templates/epi/group_detail.html | 2 +- project/templates/epi/outcome_copy_selector.html | 2 +- project/templates/epi/outcome_detail.html | 12 ++++++------ project/templates/epi/result_copy_selector.html | 2 +- project/templates/epi/result_detail.html | 4 ++-- project/templates/epi/studypopulation_copy_selector.html | 2 +- project/templates/epi/studypopulation_detail.html | 16 ++++++++-------- project/templates/study/study_detail.html | 4 ++-- 18 files changed, 41 insertions(+), 41 deletions(-) diff --git a/project/epi/forms.py b/project/epi/forms.py index d7ac0086..78f0b5f9 100644 --- a/project/epi/forms.py +++ b/project/epi/forms.py @@ -190,7 +190,7 @@ def setHelper(self): helper.add_fluid_row('eligible_n', 3, "span4") helper.add_fluid_row('inclusion_criteria', 3, "span4") - url = reverse('epi2:studycriteria_create', + url = reverse('epi:studycriteria_create', kwargs={'pk': self.instance.study.assessment.pk}) helper.addBtnLayout(helper.layout[6], 0, url, "Create criteria", "span4") helper.addBtnLayout(helper.layout[6], 1, url, "Create criteria", "span4") @@ -680,7 +680,7 @@ def setHelper(self): helper.add_fluid_row('factors_applied', 2, "span6") helper.add_fluid_row('estimate_type', 3, "span4") - url = reverse('epi2:adjustmentfactor_create', + url = reverse('epi:adjustmentfactor_create', kwargs={'pk': self.instance.outcome.assessment_id}) helper.addBtnLayout(helper.layout[8], 0, url, "Add new adjustment factor", "span6") helper.addBtnLayout(helper.layout[8], 1, url, "Add new adjustment factor", "span6") diff --git a/project/epi/models.py b/project/epi/models.py index cbe7d4c9..af3aa03a 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -218,7 +218,7 @@ class Meta: ordering = ('name', ) def get_absolute_url(self): - return reverse('epi2:sp_detail', kwargs={'pk': self.pk}) + return reverse('epi:sp_detail', kwargs={'pk': self.pk}) def get_assessment(self): return self.study.get_assessment() @@ -289,7 +289,7 @@ def delete_caches(cls, ids): SerializerHelper.delete_caches(cls, ids) def get_absolute_url(self): - return reverse('epi2:outcome_detail', kwargs={'pk': self.pk}) + return reverse('epi:outcome_detail', kwargs={'pk': self.pk}) def get_crumbs(self): return get_crumbs(self, self.study_population) @@ -365,7 +365,7 @@ def save(self, *args, **kwargs): super(ComparisonSet, self).save(*args, **kwargs) def get_absolute_url(self): - return reverse('epi2:cs_detail', kwargs={'pk': self.pk}) + return reverse('epi:cs_detail', kwargs={'pk': self.pk}) def get_assessment(self): if self.outcome: @@ -472,7 +472,7 @@ class Meta: ordering = ('comparison_set', 'group_id', ) def get_absolute_url(self): - return reverse('epi2:g_detail', kwargs={'pk': self.pk}) + return reverse('epi:g_detail', kwargs={'pk': self.pk}) def get_assessment(self): return self.comparison_set.get_assessment() @@ -589,7 +589,7 @@ def get_assessment(self): return self.study_population.get_assessment() def get_absolute_url(self): - return reverse('epi2:exp_detail', kwargs={'pk': self.pk}) + return reverse('epi:exp_detail', kwargs={'pk': self.pk}) def get_crumbs(self): return get_crumbs(self, self.study_population) @@ -877,7 +877,7 @@ def get_assessment(self): return self.outcome.get_assessment() def get_absolute_url(self): - return reverse('epi2:result_detail', kwargs={'pk': self.pk}) + return reverse('epi:result_detail', kwargs={'pk': self.pk}) def get_crumbs(self): return get_crumbs(self, self.outcome) diff --git a/project/epimeta/forms.py b/project/epimeta/forms.py index 60fbfe5e..077bb8fb 100644 --- a/project/epimeta/forms.py +++ b/project/epimeta/forms.py @@ -84,7 +84,7 @@ def setHelper(self): helper.add_fluid_row('lit_search_start_date', 3, "span4") helper.add_fluid_row('inclusion_criteria', 2, "span6") - url = reverse('epi2:studycriteria_create', + url = reverse('epi:studycriteria_create', kwargs={'pk': self.instance.study.assessment.pk}) helper.addBtnLayout(helper.layout[5], 0, url, "Create criteria", "span6") helper.addBtnLayout(helper.layout[5], 1, url, "Create criteria", "span6") @@ -172,7 +172,7 @@ def setHelper(self): helper.add_fluid_row('adjustment_factors', 2, "span6") url = reverse( - 'epi2:adjustmentfactor_create', + 'epi:adjustmentfactor_create', kwargs={'pk': self.instance.protocol.study.assessment.pk} ) helper.addBtnLayout(helper.layout[8], 0, url, "Create criteria", "span6") diff --git a/project/templates/assessment/assessment_downloads.html b/project/templates/assessment/assessment_downloads.html index 28f54152..bd12742a 100644 --- a/project/templates/assessment/assessment_downloads.html +++ b/project/templates/assessment/assessment_downloads.html @@ -43,7 +43,7 @@
  • Epidemiology data
    - Download
    + Download

    Microsoft Excel spreadsheet

    • diff --git a/project/templates/assessment/baseendpoint_list.html b/project/templates/assessment/baseendpoint_list.html index fff20fe5..e85c24fd 100644 --- a/project/templates/assessment/baseendpoint_list.html +++ b/project/templates/assessment/baseendpoint_list.html @@ -23,7 +23,7 @@ {% endif %} {% if outcomes > 0 %} -
  • +
  • {{outcomes}} epidemiological outcomes assessed
    • {% endif %} diff --git a/project/templates/epi/comparisonset_detail.html b/project/templates/epi/comparisonset_detail.html index 3faaee73..ba2de7bb 100644 --- a/project/templates/epi/comparisonset_detail.html +++ b/project/templates/epi/comparisonset_detail.html @@ -18,8 +18,8 @@ {% endif %} diff --git a/project/templates/epi/comparisonset_outcome_copy_selector.html b/project/templates/epi/comparisonset_outcome_copy_selector.html index d214e8f8..e6149a61 100644 --- a/project/templates/epi/comparisonset_outcome_copy_selector.html +++ b/project/templates/epi/comparisonset_outcome_copy_selector.html @@ -25,7 +25,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:cs_outcome_create' object.pk %}" + "base_url": "{% url 'epi:cs_outcome_create' object.pk %}" }); }); diff --git a/project/templates/epi/comparisonset_sp_copy_selector.html b/project/templates/epi/comparisonset_sp_copy_selector.html index 97693a06..a72870db 100644 --- a/project/templates/epi/comparisonset_sp_copy_selector.html +++ b/project/templates/epi/comparisonset_sp_copy_selector.html @@ -25,7 +25,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:cs_create' object.pk %}" + "base_url": "{% url 'epi:cs_create' object.pk %}" }); }); diff --git a/project/templates/epi/exposure_copy_selector.html b/project/templates/epi/exposure_copy_selector.html index a59df4b7..8981ba95 100644 --- a/project/templates/epi/exposure_copy_selector.html +++ b/project/templates/epi/exposure_copy_selector.html @@ -24,7 +24,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:exp_create' object.pk %}" + "base_url": "{% url 'epi:exp_create' object.pk %}" }); }); diff --git a/project/templates/epi/exposure_detail.html b/project/templates/epi/exposure_detail.html index 6c7805f9..c4c604b1 100644 --- a/project/templates/epi/exposure_detail.html +++ b/project/templates/epi/exposure_detail.html @@ -17,8 +17,8 @@ {% endif %} diff --git a/project/templates/epi/group_detail.html b/project/templates/epi/group_detail.html index 02425484..a3b54cf4 100644 --- a/project/templates/epi/group_detail.html +++ b/project/templates/epi/group_detail.html @@ -17,7 +17,7 @@ {% endif %} diff --git a/project/templates/epi/outcome_copy_selector.html b/project/templates/epi/outcome_copy_selector.html index 92b48f22..701d15db 100644 --- a/project/templates/epi/outcome_copy_selector.html +++ b/project/templates/epi/outcome_copy_selector.html @@ -25,7 +25,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:outcome_create' object.pk %}" + "base_url": "{% url 'epi:outcome_create' object.pk %}" }); }); diff --git a/project/templates/epi/outcome_detail.html b/project/templates/epi/outcome_detail.html index ddd3b073..dba8b7c4 100644 --- a/project/templates/epi/outcome_detail.html +++ b/project/templates/epi/outcome_detail.html @@ -18,15 +18,15 @@ diff --git a/project/templates/epi/result_copy_selector.html b/project/templates/epi/result_copy_selector.html index ec4f5300..47ea03a7 100644 --- a/project/templates/epi/result_copy_selector.html +++ b/project/templates/epi/result_copy_selector.html @@ -25,7 +25,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:result_create' object.pk %}" + "base_url": "{% url 'epi:result_create' object.pk %}" }); }); diff --git a/project/templates/epi/result_detail.html b/project/templates/epi/result_detail.html index df861ba1..47b6d141 100644 --- a/project/templates/epi/result_detail.html +++ b/project/templates/epi/result_detail.html @@ -18,8 +18,8 @@ {% endif %} diff --git a/project/templates/epi/studypopulation_copy_selector.html b/project/templates/epi/studypopulation_copy_selector.html index a57e5c0d..b11c83f2 100644 --- a/project/templates/epi/studypopulation_copy_selector.html +++ b/project/templates/epi/studypopulation_copy_selector.html @@ -30,7 +30,7 @@ new HAWCUtils.InitialForm({ "form": $('form'), - "base_url": "{% url 'epi2:sp_create' object.pk %}" + "base_url": "{% url 'epi:sp_create' object.pk %}" }); }); diff --git a/project/templates/epi/studypopulation_detail.html b/project/templates/epi/studypopulation_detail.html index 88ecc084..ba0c534f 100644 --- a/project/templates/epi/studypopulation_detail.html +++ b/project/templates/epi/studypopulation_detail.html @@ -17,19 +17,19 @@ {% endif %} diff --git a/project/templates/study/study_detail.html b/project/templates/study/study_detail.html index 32b4d29f..31131abe 100644 --- a/project/templates/study/study_detail.html +++ b/project/templates/study/study_detail.html @@ -44,8 +44,8 @@
  • Create new
    • {% elif object.study_type == 1 %}
  • Study Population
    • -
  • Create new
    • -
  • Copy from existing
    • +
  • Create new
    • +
  • Copy from existing
    • {% elif object.study_type == 4 %}
  • Meta-analysis
  • Create new
    • From b689139adeb633f12c0c52429d3bfe7ea6ddd7e5 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:15:10 -0400 Subject: [PATCH 06/17] rename fixtures --- project/epi/fixtures/countries.json | 502 ++++++++++++++++----------------- project/epi/fixtures/ethnicity.json | 18 +- project/epi/fixtures/resultmetric.json | 46 +-- 3 files changed, 283 insertions(+), 283 deletions(-) diff --git a/project/epi/fixtures/countries.json b/project/epi/fixtures/countries.json index fa5ed750..b22ba085 100644 --- a/project/epi/fixtures/countries.json +++ b/project/epi/fixtures/countries.json @@ -4,7 +4,7 @@ "code": "AF", "name": "Afghanistan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 1 }, { @@ -12,7 +12,7 @@ "code": "AX", "name": "Ã…land Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 2 }, { @@ -20,7 +20,7 @@ "code": "AL", "name": "Albania" }, - "model": "epi2.country", + "model": "epi.country", "pk": 3 }, { @@ -28,7 +28,7 @@ "code": "DZ", "name": "Algeria" }, - "model": "epi2.country", + "model": "epi.country", "pk": 4 }, { @@ -36,7 +36,7 @@ "code": "AS", "name": "American Samoa" }, - "model": "epi2.country", + "model": "epi.country", "pk": 5 }, { @@ -44,7 +44,7 @@ "code": "AD", "name": "Andorra" }, - "model": "epi2.country", + "model": "epi.country", "pk": 6 }, { @@ -52,7 +52,7 @@ "code": "AO", "name": "Angola" }, - "model": "epi2.country", + "model": "epi.country", "pk": 7 }, { @@ -60,7 +60,7 @@ "code": "AI", "name": "Anguilla" }, - "model": "epi2.country", + "model": "epi.country", "pk": 8 }, { @@ -68,7 +68,7 @@ "code": "AQ", "name": "Antarctica" }, - "model": "epi2.country", + "model": "epi.country", "pk": 9 }, { @@ -76,7 +76,7 @@ "code": "AG", "name": "Antigua And Barbuda" }, - "model": "epi2.country", + "model": "epi.country", "pk": 10 }, { @@ -84,7 +84,7 @@ "code": "AR", "name": "Argentina" }, - "model": "epi2.country", + "model": "epi.country", "pk": 11 }, { @@ -92,7 +92,7 @@ "code": "AM", "name": "Armenia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 12 }, { @@ -100,7 +100,7 @@ "code": "AW", "name": "Aruba" }, - "model": "epi2.country", + "model": "epi.country", "pk": 13 }, { @@ -108,7 +108,7 @@ "code": "AU", "name": "Australia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 14 }, { @@ -116,7 +116,7 @@ "code": "AT", "name": "Austria" }, - "model": "epi2.country", + "model": "epi.country", "pk": 15 }, { @@ -124,7 +124,7 @@ "code": "AZ", "name": "Azerbaijan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 16 }, { @@ -132,7 +132,7 @@ "code": "BS", "name": "Bahamas" }, - "model": "epi2.country", + "model": "epi.country", "pk": 17 }, { @@ -140,7 +140,7 @@ "code": "BH", "name": "Bahrain" }, - "model": "epi2.country", + "model": "epi.country", "pk": 18 }, { @@ -148,7 +148,7 @@ "code": "BD", "name": "Bangladesh" }, - "model": "epi2.country", + "model": "epi.country", "pk": 19 }, { @@ -156,7 +156,7 @@ "code": "BB", "name": "Barbados" }, - "model": "epi2.country", + "model": "epi.country", "pk": 20 }, { @@ -164,7 +164,7 @@ "code": "BY", "name": "Belarus" }, - "model": "epi2.country", + "model": "epi.country", "pk": 21 }, { @@ -172,7 +172,7 @@ "code": "BE", "name": "Belgium" }, - "model": "epi2.country", + "model": "epi.country", "pk": 22 }, { @@ -180,7 +180,7 @@ "code": "BZ", "name": "Belize" }, - "model": "epi2.country", + "model": "epi.country", "pk": 23 }, { @@ -188,7 +188,7 @@ "code": "BJ", "name": "Benin" }, - "model": "epi2.country", + "model": "epi.country", "pk": 24 }, { @@ -196,7 +196,7 @@ "code": "BM", "name": "Bermuda" }, - "model": "epi2.country", + "model": "epi.country", "pk": 25 }, { @@ -204,7 +204,7 @@ "code": "BT", "name": "Bhutan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 26 }, { @@ -212,7 +212,7 @@ "code": "BO", "name": "Bolivia, Plurinational State Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 27 }, { @@ -220,7 +220,7 @@ "code": "BQ", "name": "Bonaire, Sint Eustatius And Saba" }, - "model": "epi2.country", + "model": "epi.country", "pk": 28 }, { @@ -228,7 +228,7 @@ "code": "BA", "name": "Bosnia And Herzegovina" }, - "model": "epi2.country", + "model": "epi.country", "pk": 29 }, { @@ -236,7 +236,7 @@ "code": "BW", "name": "Botswana" }, - "model": "epi2.country", + "model": "epi.country", "pk": 30 }, { @@ -244,7 +244,7 @@ "code": "BV", "name": "Bouvet Island" }, - "model": "epi2.country", + "model": "epi.country", "pk": 31 }, { @@ -252,7 +252,7 @@ "code": "BR", "name": "Brazil" }, - "model": "epi2.country", + "model": "epi.country", "pk": 32 }, { @@ -260,7 +260,7 @@ "code": "IO", "name": "British Indian Ocean Territory" }, - "model": "epi2.country", + "model": "epi.country", "pk": 33 }, { @@ -268,7 +268,7 @@ "code": "BN", "name": "Brunei Darussalam" }, - "model": "epi2.country", + "model": "epi.country", "pk": 34 }, { @@ -276,7 +276,7 @@ "code": "BG", "name": "Bulgaria" }, - "model": "epi2.country", + "model": "epi.country", "pk": 35 }, { @@ -284,7 +284,7 @@ "code": "BF", "name": "Burkina Faso" }, - "model": "epi2.country", + "model": "epi.country", "pk": 36 }, { @@ -292,7 +292,7 @@ "code": "BI", "name": "Burundi" }, - "model": "epi2.country", + "model": "epi.country", "pk": 37 }, { @@ -300,7 +300,7 @@ "code": "KH", "name": "Cambodia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 38 }, { @@ -308,7 +308,7 @@ "code": "CM", "name": "Cameroon" }, - "model": "epi2.country", + "model": "epi.country", "pk": 39 }, { @@ -316,7 +316,7 @@ "code": "CA", "name": "Canada" }, - "model": "epi2.country", + "model": "epi.country", "pk": 40 }, { @@ -324,7 +324,7 @@ "code": "CV", "name": "Cape Verde" }, - "model": "epi2.country", + "model": "epi.country", "pk": 41 }, { @@ -332,7 +332,7 @@ "code": "KY", "name": "Cayman Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 42 }, { @@ -340,7 +340,7 @@ "code": "CF", "name": "Central African Republic" }, - "model": "epi2.country", + "model": "epi.country", "pk": 43 }, { @@ -348,7 +348,7 @@ "code": "TD", "name": "Chad" }, - "model": "epi2.country", + "model": "epi.country", "pk": 44 }, { @@ -356,7 +356,7 @@ "code": "CL", "name": "Chile" }, - "model": "epi2.country", + "model": "epi.country", "pk": 45 }, { @@ -364,7 +364,7 @@ "code": "CN", "name": "China" }, - "model": "epi2.country", + "model": "epi.country", "pk": 46 }, { @@ -372,7 +372,7 @@ "code": "CX", "name": "Christmas Island" }, - "model": "epi2.country", + "model": "epi.country", "pk": 47 }, { @@ -380,7 +380,7 @@ "code": "CC", "name": "Cocos (Keeling) Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 48 }, { @@ -388,7 +388,7 @@ "code": "CO", "name": "Colombia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 49 }, { @@ -396,7 +396,7 @@ "code": "KM", "name": "Comoros" }, - "model": "epi2.country", + "model": "epi.country", "pk": 50 }, { @@ -404,7 +404,7 @@ "code": "CG", "name": "Congo" }, - "model": "epi2.country", + "model": "epi.country", "pk": 51 }, { @@ -412,7 +412,7 @@ "code": "CD", "name": "Congo, The Democratic Republic Of The" }, - "model": "epi2.country", + "model": "epi.country", "pk": 52 }, { @@ -420,7 +420,7 @@ "code": "CK", "name": "Cook Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 53 }, { @@ -428,7 +428,7 @@ "code": "CR", "name": "Costa Rica" }, - "model": "epi2.country", + "model": "epi.country", "pk": 54 }, { @@ -436,7 +436,7 @@ "code": "CI", "name": "Côte D'Ivoire" }, - "model": "epi2.country", + "model": "epi.country", "pk": 55 }, { @@ -444,7 +444,7 @@ "code": "HR", "name": "Croatia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 56 }, { @@ -452,7 +452,7 @@ "code": "CU", "name": "Cuba" }, - "model": "epi2.country", + "model": "epi.country", "pk": 57 }, { @@ -460,7 +460,7 @@ "code": "CW", "name": "Curaçao" }, - "model": "epi2.country", + "model": "epi.country", "pk": 58 }, { @@ -468,7 +468,7 @@ "code": "CY", "name": "Cyprus" }, - "model": "epi2.country", + "model": "epi.country", "pk": 59 }, { @@ -476,7 +476,7 @@ "code": "CZ", "name": "Czech Republic" }, - "model": "epi2.country", + "model": "epi.country", "pk": 60 }, { @@ -484,7 +484,7 @@ "code": "DK", "name": "Denmark" }, - "model": "epi2.country", + "model": "epi.country", "pk": 61 }, { @@ -492,7 +492,7 @@ "code": "DJ", "name": "Djibouti" }, - "model": "epi2.country", + "model": "epi.country", "pk": 62 }, { @@ -500,7 +500,7 @@ "code": "DM", "name": "Dominica" }, - "model": "epi2.country", + "model": "epi.country", "pk": 63 }, { @@ -508,7 +508,7 @@ "code": "DO", "name": "Dominican Republic" }, - "model": "epi2.country", + "model": "epi.country", "pk": 64 }, { @@ -516,7 +516,7 @@ "code": "EC", "name": "Ecuador" }, - "model": "epi2.country", + "model": "epi.country", "pk": 65 }, { @@ -524,7 +524,7 @@ "code": "EG", "name": "Egypt" }, - "model": "epi2.country", + "model": "epi.country", "pk": 66 }, { @@ -532,7 +532,7 @@ "code": "SV", "name": "El Salvador" }, - "model": "epi2.country", + "model": "epi.country", "pk": 67 }, { @@ -540,7 +540,7 @@ "code": "GQ", "name": "Equatorial Guinea" }, - "model": "epi2.country", + "model": "epi.country", "pk": 68 }, { @@ -548,7 +548,7 @@ "code": "ER", "name": "Eritrea" }, - "model": "epi2.country", + "model": "epi.country", "pk": 69 }, { @@ -556,7 +556,7 @@ "code": "EE", "name": "Estonia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 70 }, { @@ -564,7 +564,7 @@ "code": "ET", "name": "Ethiopia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 71 }, { @@ -572,7 +572,7 @@ "code": "FK", "name": "Falkland Islands (Malvinas)" }, - "model": "epi2.country", + "model": "epi.country", "pk": 72 }, { @@ -580,7 +580,7 @@ "code": "FO", "name": "Faroe Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 73 }, { @@ -588,7 +588,7 @@ "code": "FJ", "name": "Fiji" }, - "model": "epi2.country", + "model": "epi.country", "pk": 74 }, { @@ -596,7 +596,7 @@ "code": "FI", "name": "Finland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 75 }, { @@ -604,7 +604,7 @@ "code": "FR", "name": "France" }, - "model": "epi2.country", + "model": "epi.country", "pk": 76 }, { @@ -612,7 +612,7 @@ "code": "GF", "name": "French Guiana" }, - "model": "epi2.country", + "model": "epi.country", "pk": 77 }, { @@ -620,7 +620,7 @@ "code": "PF", "name": "French Polynesia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 78 }, { @@ -628,7 +628,7 @@ "code": "TF", "name": "French Southern Territories" }, - "model": "epi2.country", + "model": "epi.country", "pk": 79 }, { @@ -636,7 +636,7 @@ "code": "GA", "name": "Gabon" }, - "model": "epi2.country", + "model": "epi.country", "pk": 80 }, { @@ -644,7 +644,7 @@ "code": "GM", "name": "Gambia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 81 }, { @@ -652,7 +652,7 @@ "code": "GE", "name": "Georgia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 82 }, { @@ -660,7 +660,7 @@ "code": "DE", "name": "Germany" }, - "model": "epi2.country", + "model": "epi.country", "pk": 83 }, { @@ -668,7 +668,7 @@ "code": "GH", "name": "Ghana" }, - "model": "epi2.country", + "model": "epi.country", "pk": 84 }, { @@ -676,7 +676,7 @@ "code": "GI", "name": "Gibraltar" }, - "model": "epi2.country", + "model": "epi.country", "pk": 85 }, { @@ -684,7 +684,7 @@ "code": "GR", "name": "Greece" }, - "model": "epi2.country", + "model": "epi.country", "pk": 86 }, { @@ -692,7 +692,7 @@ "code": "GL", "name": "Greenland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 87 }, { @@ -700,7 +700,7 @@ "code": "GD", "name": "Grenada" }, - "model": "epi2.country", + "model": "epi.country", "pk": 88 }, { @@ -708,7 +708,7 @@ "code": "GP", "name": "Guadeloupe" }, - "model": "epi2.country", + "model": "epi.country", "pk": 89 }, { @@ -716,7 +716,7 @@ "code": "GU", "name": "Guam" }, - "model": "epi2.country", + "model": "epi.country", "pk": 90 }, { @@ -724,7 +724,7 @@ "code": "GT", "name": "Guatemala" }, - "model": "epi2.country", + "model": "epi.country", "pk": 91 }, { @@ -732,7 +732,7 @@ "code": "GG", "name": "Guernsey" }, - "model": "epi2.country", + "model": "epi.country", "pk": 92 }, { @@ -740,7 +740,7 @@ "code": "GN", "name": "Guinea" }, - "model": "epi2.country", + "model": "epi.country", "pk": 93 }, { @@ -748,7 +748,7 @@ "code": "GW", "name": "Guinea-Bissau" }, - "model": "epi2.country", + "model": "epi.country", "pk": 94 }, { @@ -756,7 +756,7 @@ "code": "GY", "name": "Guyana" }, - "model": "epi2.country", + "model": "epi.country", "pk": 95 }, { @@ -764,7 +764,7 @@ "code": "HT", "name": "Haiti" }, - "model": "epi2.country", + "model": "epi.country", "pk": 96 }, { @@ -772,7 +772,7 @@ "code": "HM", "name": "Heard Island And Mcdonald Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 97 }, { @@ -780,7 +780,7 @@ "code": "VA", "name": "Holy See (Vatican City State)" }, - "model": "epi2.country", + "model": "epi.country", "pk": 98 }, { @@ -788,7 +788,7 @@ "code": "HN", "name": "Honduras" }, - "model": "epi2.country", + "model": "epi.country", "pk": 99 }, { @@ -796,7 +796,7 @@ "code": "HK", "name": "Hong Kong" }, - "model": "epi2.country", + "model": "epi.country", "pk": 100 }, { @@ -804,7 +804,7 @@ "code": "HU", "name": "Hungary" }, - "model": "epi2.country", + "model": "epi.country", "pk": 101 }, { @@ -812,7 +812,7 @@ "code": "IS", "name": "Iceland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 102 }, { @@ -820,7 +820,7 @@ "code": "IN", "name": "India" }, - "model": "epi2.country", + "model": "epi.country", "pk": 103 }, { @@ -828,7 +828,7 @@ "code": "ID", "name": "Indonesia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 104 }, { @@ -836,7 +836,7 @@ "code": "IR", "name": "Iran, Islamic Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 105 }, { @@ -844,7 +844,7 @@ "code": "IQ", "name": "Iraq" }, - "model": "epi2.country", + "model": "epi.country", "pk": 106 }, { @@ -852,7 +852,7 @@ "code": "IE", "name": "Ireland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 107 }, { @@ -860,7 +860,7 @@ "code": "IM", "name": "Isle Of Man" }, - "model": "epi2.country", + "model": "epi.country", "pk": 108 }, { @@ -868,7 +868,7 @@ "code": "IL", "name": "Israel" }, - "model": "epi2.country", + "model": "epi.country", "pk": 109 }, { @@ -876,7 +876,7 @@ "code": "IT", "name": "Italy" }, - "model": "epi2.country", + "model": "epi.country", "pk": 110 }, { @@ -884,7 +884,7 @@ "code": "JM", "name": "Jamaica" }, - "model": "epi2.country", + "model": "epi.country", "pk": 111 }, { @@ -892,7 +892,7 @@ "code": "JP", "name": "Japan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 112 }, { @@ -900,7 +900,7 @@ "code": "JE", "name": "Jersey" }, - "model": "epi2.country", + "model": "epi.country", "pk": 113 }, { @@ -908,7 +908,7 @@ "code": "JO", "name": "Jordan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 114 }, { @@ -916,7 +916,7 @@ "code": "KZ", "name": "Kazakhstan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 115 }, { @@ -924,7 +924,7 @@ "code": "KE", "name": "Kenya" }, - "model": "epi2.country", + "model": "epi.country", "pk": 116 }, { @@ -932,7 +932,7 @@ "code": "KI", "name": "Kiribati" }, - "model": "epi2.country", + "model": "epi.country", "pk": 117 }, { @@ -940,7 +940,7 @@ "code": "KP", "name": "Korea, Democratic People's Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 118 }, { @@ -948,7 +948,7 @@ "code": "KR", "name": "Korea, Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 119 }, { @@ -956,7 +956,7 @@ "code": "KW", "name": "Kuwait" }, - "model": "epi2.country", + "model": "epi.country", "pk": 120 }, { @@ -964,7 +964,7 @@ "code": "KG", "name": "Kyrgyzstan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 121 }, { @@ -972,7 +972,7 @@ "code": "LA", "name": "Lao People's Democratic Republic" }, - "model": "epi2.country", + "model": "epi.country", "pk": 122 }, { @@ -980,7 +980,7 @@ "code": "LV", "name": "Latvia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 123 }, { @@ -988,7 +988,7 @@ "code": "LB", "name": "Lebanon" }, - "model": "epi2.country", + "model": "epi.country", "pk": 124 }, { @@ -996,7 +996,7 @@ "code": "LS", "name": "Lesotho" }, - "model": "epi2.country", + "model": "epi.country", "pk": 125 }, { @@ -1004,7 +1004,7 @@ "code": "LR", "name": "Liberia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 126 }, { @@ -1012,7 +1012,7 @@ "code": "LY", "name": "Libya" }, - "model": "epi2.country", + "model": "epi.country", "pk": 127 }, { @@ -1020,7 +1020,7 @@ "code": "LI", "name": "Liechtenstein" }, - "model": "epi2.country", + "model": "epi.country", "pk": 128 }, { @@ -1028,7 +1028,7 @@ "code": "LT", "name": "Lithuania" }, - "model": "epi2.country", + "model": "epi.country", "pk": 129 }, { @@ -1036,7 +1036,7 @@ "code": "LU", "name": "Luxembourg" }, - "model": "epi2.country", + "model": "epi.country", "pk": 130 }, { @@ -1044,7 +1044,7 @@ "code": "MO", "name": "Macao" }, - "model": "epi2.country", + "model": "epi.country", "pk": 131 }, { @@ -1052,7 +1052,7 @@ "code": "MK", "name": "Macedonia, The Former Yugoslav Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 132 }, { @@ -1060,7 +1060,7 @@ "code": "MG", "name": "Madagascar" }, - "model": "epi2.country", + "model": "epi.country", "pk": 133 }, { @@ -1068,7 +1068,7 @@ "code": "MW", "name": "Malawi" }, - "model": "epi2.country", + "model": "epi.country", "pk": 134 }, { @@ -1076,7 +1076,7 @@ "code": "MY", "name": "Malaysia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 135 }, { @@ -1084,7 +1084,7 @@ "code": "MV", "name": "Maldives" }, - "model": "epi2.country", + "model": "epi.country", "pk": 136 }, { @@ -1092,7 +1092,7 @@ "code": "ML", "name": "Mali" }, - "model": "epi2.country", + "model": "epi.country", "pk": 137 }, { @@ -1100,7 +1100,7 @@ "code": "MT", "name": "Malta" }, - "model": "epi2.country", + "model": "epi.country", "pk": 138 }, { @@ -1108,7 +1108,7 @@ "code": "MH", "name": "Marshall Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 139 }, { @@ -1116,7 +1116,7 @@ "code": "MQ", "name": "Martinique" }, - "model": "epi2.country", + "model": "epi.country", "pk": 140 }, { @@ -1124,7 +1124,7 @@ "code": "MR", "name": "Mauritania" }, - "model": "epi2.country", + "model": "epi.country", "pk": 141 }, { @@ -1132,7 +1132,7 @@ "code": "MU", "name": "Mauritius" }, - "model": "epi2.country", + "model": "epi.country", "pk": 142 }, { @@ -1140,7 +1140,7 @@ "code": "YT", "name": "Mayotte" }, - "model": "epi2.country", + "model": "epi.country", "pk": 143 }, { @@ -1148,7 +1148,7 @@ "code": "MX", "name": "Mexico" }, - "model": "epi2.country", + "model": "epi.country", "pk": 144 }, { @@ -1156,7 +1156,7 @@ "code": "FM", "name": "Micronesia, Federated States Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 145 }, { @@ -1164,7 +1164,7 @@ "code": "MD", "name": "Moldova, Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 146 }, { @@ -1172,7 +1172,7 @@ "code": "MC", "name": "Monaco" }, - "model": "epi2.country", + "model": "epi.country", "pk": 147 }, { @@ -1180,7 +1180,7 @@ "code": "MN", "name": "Mongolia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 148 }, { @@ -1188,7 +1188,7 @@ "code": "ME", "name": "Montenegro" }, - "model": "epi2.country", + "model": "epi.country", "pk": 149 }, { @@ -1196,7 +1196,7 @@ "code": "MS", "name": "Montserrat" }, - "model": "epi2.country", + "model": "epi.country", "pk": 150 }, { @@ -1204,7 +1204,7 @@ "code": "MA", "name": "Morocco" }, - "model": "epi2.country", + "model": "epi.country", "pk": 151 }, { @@ -1212,7 +1212,7 @@ "code": "MZ", "name": "Mozambique" }, - "model": "epi2.country", + "model": "epi.country", "pk": 152 }, { @@ -1220,7 +1220,7 @@ "code": "MM", "name": "Myanmar" }, - "model": "epi2.country", + "model": "epi.country", "pk": 153 }, { @@ -1228,7 +1228,7 @@ "code": "NA", "name": "Namibia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 154 }, { @@ -1236,7 +1236,7 @@ "code": "NR", "name": "Nauru" }, - "model": "epi2.country", + "model": "epi.country", "pk": 155 }, { @@ -1244,7 +1244,7 @@ "code": "NP", "name": "Nepal" }, - "model": "epi2.country", + "model": "epi.country", "pk": 156 }, { @@ -1252,7 +1252,7 @@ "code": "NL", "name": "Netherlands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 157 }, { @@ -1260,7 +1260,7 @@ "code": "NC", "name": "New Caledonia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 158 }, { @@ -1268,7 +1268,7 @@ "code": "NZ", "name": "New Zealand" }, - "model": "epi2.country", + "model": "epi.country", "pk": 159 }, { @@ -1276,7 +1276,7 @@ "code": "NI", "name": "Nicaragua" }, - "model": "epi2.country", + "model": "epi.country", "pk": 160 }, { @@ -1284,7 +1284,7 @@ "code": "NE", "name": "Niger" }, - "model": "epi2.country", + "model": "epi.country", "pk": 161 }, { @@ -1292,7 +1292,7 @@ "code": "NG", "name": "Nigeria" }, - "model": "epi2.country", + "model": "epi.country", "pk": 162 }, { @@ -1300,7 +1300,7 @@ "code": "NU", "name": "Niue" }, - "model": "epi2.country", + "model": "epi.country", "pk": 163 }, { @@ -1308,7 +1308,7 @@ "code": "NF", "name": "Norfolk Island" }, - "model": "epi2.country", + "model": "epi.country", "pk": 164 }, { @@ -1316,7 +1316,7 @@ "code": "MP", "name": "Northern Mariana Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 165 }, { @@ -1324,7 +1324,7 @@ "code": "NO", "name": "Norway" }, - "model": "epi2.country", + "model": "epi.country", "pk": 166 }, { @@ -1332,7 +1332,7 @@ "code": "OM", "name": "Oman" }, - "model": "epi2.country", + "model": "epi.country", "pk": 167 }, { @@ -1340,7 +1340,7 @@ "code": "PK", "name": "Pakistan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 168 }, { @@ -1348,7 +1348,7 @@ "code": "PW", "name": "Palau" }, - "model": "epi2.country", + "model": "epi.country", "pk": 169 }, { @@ -1356,7 +1356,7 @@ "code": "PS", "name": "Palestine, State Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 170 }, { @@ -1364,7 +1364,7 @@ "code": "PA", "name": "Panama" }, - "model": "epi2.country", + "model": "epi.country", "pk": 171 }, { @@ -1372,7 +1372,7 @@ "code": "PG", "name": "Papua New Guinea" }, - "model": "epi2.country", + "model": "epi.country", "pk": 172 }, { @@ -1380,7 +1380,7 @@ "code": "PY", "name": "Paraguay" }, - "model": "epi2.country", + "model": "epi.country", "pk": 173 }, { @@ -1388,7 +1388,7 @@ "code": "PE", "name": "Peru" }, - "model": "epi2.country", + "model": "epi.country", "pk": 174 }, { @@ -1396,7 +1396,7 @@ "code": "PH", "name": "Philippines" }, - "model": "epi2.country", + "model": "epi.country", "pk": 175 }, { @@ -1404,7 +1404,7 @@ "code": "PN", "name": "Pitcairn" }, - "model": "epi2.country", + "model": "epi.country", "pk": 176 }, { @@ -1412,7 +1412,7 @@ "code": "PL", "name": "Poland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 177 }, { @@ -1420,7 +1420,7 @@ "code": "PT", "name": "Portugal" }, - "model": "epi2.country", + "model": "epi.country", "pk": 178 }, { @@ -1428,7 +1428,7 @@ "code": "PR", "name": "Puerto Rico" }, - "model": "epi2.country", + "model": "epi.country", "pk": 179 }, { @@ -1436,7 +1436,7 @@ "code": "QA", "name": "Qatar" }, - "model": "epi2.country", + "model": "epi.country", "pk": 180 }, { @@ -1444,7 +1444,7 @@ "code": "RE", "name": "Réunion" }, - "model": "epi2.country", + "model": "epi.country", "pk": 181 }, { @@ -1452,7 +1452,7 @@ "code": "RO", "name": "Romania" }, - "model": "epi2.country", + "model": "epi.country", "pk": 182 }, { @@ -1460,7 +1460,7 @@ "code": "RU", "name": "Russian Federation" }, - "model": "epi2.country", + "model": "epi.country", "pk": 183 }, { @@ -1468,7 +1468,7 @@ "code": "RW", "name": "Rwanda" }, - "model": "epi2.country", + "model": "epi.country", "pk": 184 }, { @@ -1476,7 +1476,7 @@ "code": "BL", "name": "Saint Barthélemy" }, - "model": "epi2.country", + "model": "epi.country", "pk": 185 }, { @@ -1484,7 +1484,7 @@ "code": "SH", "name": "Saint Helena, Ascension And Tristan Da Cunha" }, - "model": "epi2.country", + "model": "epi.country", "pk": 186 }, { @@ -1492,7 +1492,7 @@ "code": "KN", "name": "Saint Kitts And Nevis" }, - "model": "epi2.country", + "model": "epi.country", "pk": 187 }, { @@ -1500,7 +1500,7 @@ "code": "LC", "name": "Saint Lucia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 188 }, { @@ -1508,7 +1508,7 @@ "code": "MF", "name": "Saint Martin (French Part)" }, - "model": "epi2.country", + "model": "epi.country", "pk": 189 }, { @@ -1516,7 +1516,7 @@ "code": "PM", "name": "Saint Pierre And Miquelon" }, - "model": "epi2.country", + "model": "epi.country", "pk": 190 }, { @@ -1524,7 +1524,7 @@ "code": "VC", "name": "Saint Vincent And The Grenadines" }, - "model": "epi2.country", + "model": "epi.country", "pk": 191 }, { @@ -1532,7 +1532,7 @@ "code": "WS", "name": "Samoa" }, - "model": "epi2.country", + "model": "epi.country", "pk": 192 }, { @@ -1540,7 +1540,7 @@ "code": "SM", "name": "San Marino" }, - "model": "epi2.country", + "model": "epi.country", "pk": 193 }, { @@ -1548,7 +1548,7 @@ "code": "ST", "name": "Sao Tome And Principe" }, - "model": "epi2.country", + "model": "epi.country", "pk": 194 }, { @@ -1556,7 +1556,7 @@ "code": "SA", "name": "Saudi Arabia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 195 }, { @@ -1564,7 +1564,7 @@ "code": "SN", "name": "Senegal" }, - "model": "epi2.country", + "model": "epi.country", "pk": 196 }, { @@ -1572,7 +1572,7 @@ "code": "RS", "name": "Serbia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 197 }, { @@ -1580,7 +1580,7 @@ "code": "SC", "name": "Seychelles" }, - "model": "epi2.country", + "model": "epi.country", "pk": 198 }, { @@ -1588,7 +1588,7 @@ "code": "SL", "name": "Sierra Leone" }, - "model": "epi2.country", + "model": "epi.country", "pk": 199 }, { @@ -1596,7 +1596,7 @@ "code": "SG", "name": "Singapore" }, - "model": "epi2.country", + "model": "epi.country", "pk": 200 }, { @@ -1604,7 +1604,7 @@ "code": "SX", "name": "Sint Maarten (Dutch Part)" }, - "model": "epi2.country", + "model": "epi.country", "pk": 201 }, { @@ -1612,7 +1612,7 @@ "code": "SK", "name": "Slovakia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 202 }, { @@ -1620,7 +1620,7 @@ "code": "SI", "name": "Slovenia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 203 }, { @@ -1628,7 +1628,7 @@ "code": "SB", "name": "Solomon Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 204 }, { @@ -1636,7 +1636,7 @@ "code": "SO", "name": "Somalia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 205 }, { @@ -1644,7 +1644,7 @@ "code": "ZA", "name": "South Africa" }, - "model": "epi2.country", + "model": "epi.country", "pk": 206 }, { @@ -1652,7 +1652,7 @@ "code": "GS", "name": "South Georgia And The South Sandwich Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 207 }, { @@ -1660,7 +1660,7 @@ "code": "SS", "name": "South Sudan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 208 }, { @@ -1668,7 +1668,7 @@ "code": "ES", "name": "Spain" }, - "model": "epi2.country", + "model": "epi.country", "pk": 209 }, { @@ -1676,7 +1676,7 @@ "code": "LK", "name": "Sri Lanka" }, - "model": "epi2.country", + "model": "epi.country", "pk": 210 }, { @@ -1684,7 +1684,7 @@ "code": "SD", "name": "Sudan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 211 }, { @@ -1692,7 +1692,7 @@ "code": "SR", "name": "Suriname" }, - "model": "epi2.country", + "model": "epi.country", "pk": 212 }, { @@ -1700,7 +1700,7 @@ "code": "SJ", "name": "Svalbard And Jan Mayen" }, - "model": "epi2.country", + "model": "epi.country", "pk": 213 }, { @@ -1708,7 +1708,7 @@ "code": "SZ", "name": "Swaziland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 214 }, { @@ -1716,7 +1716,7 @@ "code": "SE", "name": "Sweden" }, - "model": "epi2.country", + "model": "epi.country", "pk": 215 }, { @@ -1724,7 +1724,7 @@ "code": "CH", "name": "Switzerland" }, - "model": "epi2.country", + "model": "epi.country", "pk": 216 }, { @@ -1732,7 +1732,7 @@ "code": "SY", "name": "Syrian Arab Republic" }, - "model": "epi2.country", + "model": "epi.country", "pk": 217 }, { @@ -1740,7 +1740,7 @@ "code": "TW", "name": "Taiwan, Province Of China" }, - "model": "epi2.country", + "model": "epi.country", "pk": 218 }, { @@ -1748,7 +1748,7 @@ "code": "TJ", "name": "Tajikistan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 219 }, { @@ -1756,7 +1756,7 @@ "code": "TZ", "name": "Tanzania, United Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 220 }, { @@ -1764,7 +1764,7 @@ "code": "TH", "name": "Thailand" }, - "model": "epi2.country", + "model": "epi.country", "pk": 221 }, { @@ -1772,7 +1772,7 @@ "code": "TL", "name": "Timor-Leste" }, - "model": "epi2.country", + "model": "epi.country", "pk": 222 }, { @@ -1780,7 +1780,7 @@ "code": "TG", "name": "Togo" }, - "model": "epi2.country", + "model": "epi.country", "pk": 223 }, { @@ -1788,7 +1788,7 @@ "code": "TK", "name": "Tokelau" }, - "model": "epi2.country", + "model": "epi.country", "pk": 224 }, { @@ -1796,7 +1796,7 @@ "code": "TO", "name": "Tonga" }, - "model": "epi2.country", + "model": "epi.country", "pk": 225 }, { @@ -1804,7 +1804,7 @@ "code": "TT", "name": "Trinidad And Tobago" }, - "model": "epi2.country", + "model": "epi.country", "pk": 226 }, { @@ -1812,7 +1812,7 @@ "code": "TN", "name": "Tunisia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 227 }, { @@ -1820,7 +1820,7 @@ "code": "TR", "name": "Turkey" }, - "model": "epi2.country", + "model": "epi.country", "pk": 228 }, { @@ -1828,7 +1828,7 @@ "code": "TM", "name": "Turkmenistan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 229 }, { @@ -1836,7 +1836,7 @@ "code": "TC", "name": "Turks And Caicos Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 230 }, { @@ -1844,7 +1844,7 @@ "code": "TV", "name": "Tuvalu" }, - "model": "epi2.country", + "model": "epi.country", "pk": 231 }, { @@ -1852,7 +1852,7 @@ "code": "UG", "name": "Uganda" }, - "model": "epi2.country", + "model": "epi.country", "pk": 232 }, { @@ -1860,7 +1860,7 @@ "code": "UA", "name": "Ukraine" }, - "model": "epi2.country", + "model": "epi.country", "pk": 233 }, { @@ -1868,7 +1868,7 @@ "code": "AE", "name": "United Arab Emirates" }, - "model": "epi2.country", + "model": "epi.country", "pk": 234 }, { @@ -1876,7 +1876,7 @@ "code": "GB", "name": "United Kingdom" }, - "model": "epi2.country", + "model": "epi.country", "pk": 235 }, { @@ -1884,7 +1884,7 @@ "code": "US", "name": "United States" }, - "model": "epi2.country", + "model": "epi.country", "pk": 236 }, { @@ -1892,7 +1892,7 @@ "code": "UM", "name": "United States Minor Outlying Islands" }, - "model": "epi2.country", + "model": "epi.country", "pk": 237 }, { @@ -1900,7 +1900,7 @@ "code": "UY", "name": "Uruguay" }, - "model": "epi2.country", + "model": "epi.country", "pk": 238 }, { @@ -1908,7 +1908,7 @@ "code": "UZ", "name": "Uzbekistan" }, - "model": "epi2.country", + "model": "epi.country", "pk": 239 }, { @@ -1916,7 +1916,7 @@ "code": "VU", "name": "Vanuatu" }, - "model": "epi2.country", + "model": "epi.country", "pk": 240 }, { @@ -1924,7 +1924,7 @@ "code": "VE", "name": "Venezuela, Bolivarian Republic Of" }, - "model": "epi2.country", + "model": "epi.country", "pk": 241 }, { @@ -1932,7 +1932,7 @@ "code": "VN", "name": "Viet Nam" }, - "model": "epi2.country", + "model": "epi.country", "pk": 242 }, { @@ -1940,7 +1940,7 @@ "code": "VG", "name": "Virgin Islands, British" }, - "model": "epi2.country", + "model": "epi.country", "pk": 243 }, { @@ -1948,7 +1948,7 @@ "code": "VI", "name": "Virgin Islands, U.S." }, - "model": "epi2.country", + "model": "epi.country", "pk": 244 }, { @@ -1956,7 +1956,7 @@ "code": "WF", "name": "Wallis And Futuna" }, - "model": "epi2.country", + "model": "epi.country", "pk": 245 }, { @@ -1964,7 +1964,7 @@ "code": "EH", "name": "Western Sahara" }, - "model": "epi2.country", + "model": "epi.country", "pk": 246 }, { @@ -1972,7 +1972,7 @@ "code": "YE", "name": "Yemen" }, - "model": "epi2.country", + "model": "epi.country", "pk": 247 }, { @@ -1980,7 +1980,7 @@ "code": "ZM", "name": "Zambia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 248 }, { @@ -1988,7 +1988,7 @@ "code": "ZW", "name": "Zimbabwe" }, - "model": "epi2.country", + "model": "epi.country", "pk": 249 }, { @@ -1996,7 +1996,7 @@ "code": "", "name": "Unknown/Unspecified" }, - "model": "epi2.country", + "model": "epi.country", "pk": 250 }, { @@ -2004,7 +2004,7 @@ "code": "", "name": "Socialist Federal Republic of Yugoslavia" }, - "model": "epi2.country", + "model": "epi.country", "pk": 251 } ] diff --git a/project/epi/fixtures/ethnicity.json b/project/epi/fixtures/ethnicity.json index 01f48e77..9f02035f 100644 --- a/project/epi/fixtures/ethnicity.json +++ b/project/epi/fixtures/ethnicity.json @@ -5,7 +5,7 @@ "name": "American Indian or Alaskan Native", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 1 }, { @@ -14,7 +14,7 @@ "name": "Asian", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 2 }, { @@ -23,7 +23,7 @@ "name": "Black or African American", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 3 }, { @@ -32,7 +32,7 @@ "name": "Hispanic/Latino", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 4 }, { @@ -41,7 +41,7 @@ "name": "Native American of Other Pacific Islander", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 5 }, { @@ -50,7 +50,7 @@ "name": "Two or More Races", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 6 }, { @@ -59,7 +59,7 @@ "name": "White", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 7 }, { @@ -68,7 +68,7 @@ "name": "Unknown/Unspecified", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 8 }, { @@ -77,7 +77,7 @@ "name": "Other", "created": "2013-02-16T14:30:00.001Z" }, - "model": "epi2.ethnicity", + "model": "epi.ethnicity", "pk": 9 } ] diff --git a/project/epi/fixtures/resultmetric.json b/project/epi/fixtures/resultmetric.json index 8245d797..10f38447 100644 --- a/project/epi/fixtures/resultmetric.json +++ b/project/epi/fixtures/resultmetric.json @@ -8,7 +8,7 @@ "order": 0, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 1 }, { @@ -20,7 +20,7 @@ "order": 1, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 2 }, { @@ -32,7 +32,7 @@ "order": 2, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 3 }, { @@ -44,7 +44,7 @@ "order": 3, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 4 }, { @@ -56,7 +56,7 @@ "order": 4, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 5 }, { @@ -68,7 +68,7 @@ "order": 5, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 6 }, { @@ -80,7 +80,7 @@ "order": 6, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 7 }, { @@ -92,7 +92,7 @@ "order": 7, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 8 }, { @@ -104,7 +104,7 @@ "order": 8, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 9 }, { @@ -116,7 +116,7 @@ "order": 9, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 10 }, { @@ -128,7 +128,7 @@ "order": 10, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 11 }, { @@ -140,7 +140,7 @@ "order": 11, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 12 }, { @@ -152,7 +152,7 @@ "order": 12, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 13 }, { @@ -164,7 +164,7 @@ "order": 13, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 14 }, { @@ -176,7 +176,7 @@ "order": 14, "reference_value": 0 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 15 }, { @@ -188,7 +188,7 @@ "order": 15, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 16 }, { @@ -200,7 +200,7 @@ "order": 16, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 17 }, { @@ -212,7 +212,7 @@ "order": 50, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 18 }, { @@ -224,7 +224,7 @@ "order": 17, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 19 }, { @@ -236,7 +236,7 @@ "order": 18, "reference_value": null }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 20 }, { @@ -248,7 +248,7 @@ "order": 19, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 21 }, { @@ -260,7 +260,7 @@ "order": 20, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 22 }, { @@ -272,7 +272,7 @@ "order": 21, "reference_value": 1 }, - "model": "epi2.ResultMetric", + "model": "epi.ResultMetric", "pk": 23 } ] From 452f959ba950a046b22f411fb8379c06b52da6a3 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:17:01 -0400 Subject: [PATCH 07/17] fix related name study_population --- project/epi/migrations/0001_initial.py | 2 +- project/epi/models.py | 2 +- project/templates/study/study_detail.html | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py index b2102ada..97f925a5 100644 --- a/project/epi/migrations/0001_initial.py +++ b/project/epi/migrations/0001_initial.py @@ -264,7 +264,7 @@ class Migration(migrations.Migration): migrations.AddField( model_name='studypopulation', name='study', - field=models.ForeignKey(related_name='study_populations2', to='study.Study'), + field=models.ForeignKey(related_name='study_populations', to='study.Study'), ), migrations.AddField( model_name='result', diff --git a/project/epi/models.py b/project/epi/models.py index af3aa03a..9e8c4236 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -113,7 +113,7 @@ class StudyPopulation(models.Model): study = models.ForeignKey( 'study.Study', - related_name="study_populations2") + related_name="study_populations") name = models.CharField( max_length=256) design = models.CharField( diff --git a/project/templates/study/study_detail.html b/project/templates/study/study_detail.html index 31131abe..d8354206 100644 --- a/project/templates/study/study_detail.html +++ b/project/templates/study/study_detail.html @@ -76,7 +76,7 @@ {% elif study.study_type == 1 %}

    Available study populations

      - {% for obj in object.study_populations2.all %} + {% for obj in object.study_populations.all %}
    • {{obj}}
      • {% endfor %}
    From 92297c0d608770c2cddc3ba90e54def92cd2481d Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:18:01 -0400 Subject: [PATCH 08/17] rename migrations --- project/epi/migrations/0001_initial.py | 42 ++++++++++++++-------------- project/epi/migrations/0002_load_fixtures.py | 14 +++++----- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py index 97f925a5..4853a067 100644 --- a/project/epi/migrations/0001_initial.py +++ b/project/epi/migrations/0001_initial.py @@ -122,8 +122,8 @@ class Migration(migrations.Migration): ('comments', models.TextField(help_text=b'Any other comments related to this group', blank=True)), ('created', models.DateTimeField(auto_now_add=True)), ('last_updated', models.DateTimeField(auto_now=True)), - ('comparison_set', models.ForeignKey(related_name='groups', to='epi2.ComparisonSet')), - ('ethnicities', models.ManyToManyField(to='epi2.Ethnicity', blank=True)), + ('comparison_set', models.ForeignKey(related_name='groups', to='epi.ComparisonSet')), + ('ethnicities', models.ManyToManyField(to='epi.Ethnicity', blank=True)), ], options={ 'ordering': ('comparison_set', 'group_id'), @@ -143,7 +143,7 @@ class Migration(migrations.Migration): ('lower_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'lower limit'), (2, b'5% CI'), (3, b'other')])), ('upper', models.FloatField(null=True, blank=True)), ('upper_type', models.PositiveSmallIntegerField(default=0, choices=[(0, None), (1, b'upper limit'), (2, b'95% CI'), (3, b'other')])), - ('group', models.ForeignKey(related_name='descriptions', to='epi2.Group')), + ('group', models.ForeignKey(related_name='descriptions', to='epi.Group')), ], ), migrations.CreateModel( @@ -161,7 +161,7 @@ class Migration(migrations.Migration): ('main_finding_support', models.PositiveSmallIntegerField(default=1, help_text=b'Are the results supportive of the main-finding?', choices=[(3, b'not-reported'), (2, b'supportive'), (1, b'inconclusive'), (0, b'not-supportive')])), ('created', models.DateTimeField(auto_now_add=True)), ('last_updated', models.DateTimeField(auto_now=True)), - ('group', models.ForeignKey(related_name='results', to='epi2.Group')), + ('group', models.ForeignKey(related_name='results', to='epi.Group')), ], options={ 'ordering': ('result', 'group__comparison_set_id'), @@ -206,8 +206,8 @@ class Migration(migrations.Migration): fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('included_in_final_model', models.BooleanField(default=True)), - ('adjustment_factor', models.ForeignKey(related_name='resfactors', to='epi2.AdjustmentFactor')), - ('result', models.ForeignKey(related_name='resfactors', to='epi2.Result')), + ('adjustment_factor', models.ForeignKey(related_name='resfactors', to='epi.AdjustmentFactor')), + ('result', models.ForeignKey(related_name='resfactors', to='epi.Result')), ], ), migrations.CreateModel( @@ -241,7 +241,7 @@ class Migration(migrations.Migration): ('comments', models.TextField(help_text=b'Note matching criteria, etc.', blank=True)), ('created', models.DateTimeField(auto_now_add=True)), ('last_updated', models.DateTimeField(auto_now=True)), - ('country', models.ForeignKey(to='epi2.Country')), + ('country', models.ForeignKey(to='epi.Country')), ], options={ 'ordering': ('name',), @@ -252,14 +252,14 @@ class Migration(migrations.Migration): fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('criteria_type', models.CharField(max_length=1, choices=[(b'I', b'Inclusion'), (b'E', b'Exclusion'), (b'C', b'Confounding')])), - ('criteria', models.ForeignKey(related_name='spcriteria', to='epi2.Criteria')), - ('study_population', models.ForeignKey(related_name='spcriteria', to='epi2.StudyPopulation')), + ('criteria', models.ForeignKey(related_name='spcriteria', to='epi.Criteria')), + ('study_population', models.ForeignKey(related_name='spcriteria', to='epi.StudyPopulation')), ], ), migrations.AddField( model_name='studypopulation', name='criteria', - field=models.ManyToManyField(related_name='populations', through='epi2.StudyPopulationCriteria', to='epi2.Criteria'), + field=models.ManyToManyField(related_name='populations', through='epi.StudyPopulationCriteria', to='epi.Criteria'), ), migrations.AddField( model_name='studypopulation', @@ -269,52 +269,52 @@ class Migration(migrations.Migration): migrations.AddField( model_name='result', name='adjustment_factors', - field=models.ManyToManyField(related_name='outcomes', through='epi2.ResultAdjustmentFactor', to='epi2.AdjustmentFactor', blank=True), + field=models.ManyToManyField(related_name='outcomes', through='epi.ResultAdjustmentFactor', to='epi.AdjustmentFactor', blank=True), ), migrations.AddField( model_name='result', name='comparison_set', - field=models.ForeignKey(related_name='results', to='epi2.ComparisonSet'), + field=models.ForeignKey(related_name='results', to='epi.ComparisonSet'), ), migrations.AddField( model_name='result', name='metric', - field=models.ForeignKey(related_name='results', to='epi2.ResultMetric', help_text=b' '), + field=models.ForeignKey(related_name='results', to='epi.ResultMetric', help_text=b' '), ), migrations.AddField( model_name='result', name='outcome', - field=models.ForeignKey(related_name='results', to='epi2.Outcome'), + field=models.ForeignKey(related_name='results', to='epi.Outcome'), ), migrations.AddField( model_name='outcome', name='study_population', - field=models.ForeignKey(related_name='outcomes', to='epi2.StudyPopulation'), + field=models.ForeignKey(related_name='outcomes', to='epi.StudyPopulation'), ), migrations.AddField( model_name='groupresult', name='result', - field=models.ForeignKey(related_name='results', to='epi2.Result'), + field=models.ForeignKey(related_name='results', to='epi.Result'), ), migrations.AddField( - model_name='exposure2', + model_name='Exposure', name='study_population', - field=models.ForeignKey(related_name='exposures', to='epi2.StudyPopulation'), + field=models.ForeignKey(related_name='exposures', to='epi.StudyPopulation'), ), migrations.AddField( model_name='comparisonset', name='exposure', - field=models.ForeignKey(related_name='comparison_sets', blank=True, to='epi2.Exposure', help_text=b'Exposure-group associated with this group', null=True), + field=models.ForeignKey(related_name='comparison_sets', blank=True, to='epi.Exposure', help_text=b'Exposure-group associated with this group', null=True), ), migrations.AddField( model_name='comparisonset', name='outcome', - field=models.ForeignKey(related_name='comparison_sets', to='epi2.Outcome', null=True), + field=models.ForeignKey(related_name='comparison_sets', to='epi.Outcome', null=True), ), migrations.AddField( model_name='comparisonset', name='study_population', - field=models.ForeignKey(related_name='comparison_sets', to='epi2.StudyPopulation', null=True), + field=models.ForeignKey(related_name='comparison_sets', to='epi.StudyPopulation', null=True), ), migrations.AlterUniqueTogether( name='criteria', diff --git a/project/epi/migrations/0002_load_fixtures.py b/project/epi/migrations/0002_load_fixtures.py index f54a0c13..b4998c0a 100644 --- a/project/epi/migrations/0002_load_fixtures.py +++ b/project/epi/migrations/0002_load_fixtures.py @@ -16,27 +16,27 @@ def load_fixture(apps, schema_editor): call_command( 'loaddata', os.path.join(fixture_dir, 'ethnicity.json'), - app_label='epi2') + app_label='epi') call_command( 'loaddata', os.path.join(fixture_dir, 'countries.json'), - app_label='epi2') + app_label='epi') call_command( 'loaddata', os.path.join(fixture_dir, 'resultmetric.json'), - app_label='epi2') + app_label='epi') def unload_fixture(apps, schema_editor): - apps.get_model("epi2", "Ethnicity").objects.all().delete() - apps.get_model("epi2", "Country").objects.all().delete() - apps.get_model("epi2", "ResultMetric").objects.all().delete() + apps.get_model("epi", "Ethnicity").objects.all().delete() + apps.get_model("epi", "Country").objects.all().delete() + apps.get_model("epi", "ResultMetric").objects.all().delete() class Migration(migrations.Migration): dependencies = [ - ('epi2', '0001_initial'), + ('epi', '0001_initial'), ] operations = [ From 09417c24e3e30fcd858d8fa1ec6833f115a7f396 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:18:52 -0400 Subject: [PATCH 09/17] rename epi2 models in other models --- project/epimeta/forms.py | 2 +- project/epimeta/models.py | 2 +- project/epimeta/serializers.py | 2 +- project/summary/models.py | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/project/epimeta/forms.py b/project/epimeta/forms.py index 077bb8fb..34190ce9 100644 --- a/project/epimeta/forms.py +++ b/project/epimeta/forms.py @@ -6,7 +6,7 @@ from selectable import forms as selectable from utils.forms import BaseFormHelper -from epi2.lookups import AdjustmentFactorLookup, CriteriaLookup +from epi.lookups import AdjustmentFactorLookup, CriteriaLookup from . import models, lookups diff --git a/project/epimeta/models.py b/project/epimeta/models.py index c39d440f..0df008f6 100644 --- a/project/epimeta/models.py +++ b/project/epimeta/models.py @@ -10,7 +10,7 @@ import reversion from assessment.serializers import AssessmentSerializer -from epi2.models import Criteria, ResultMetric, AdjustmentFactor +from epi.models import Criteria, ResultMetric, AdjustmentFactor from utils.helper import SerializerHelper from utils.models import get_crumbs diff --git a/project/epimeta/serializers.py b/project/epimeta/serializers.py index a26e14a8..c307af55 100644 --- a/project/epimeta/serializers.py +++ b/project/epimeta/serializers.py @@ -1,6 +1,6 @@ from rest_framework import serializers -from epi2.serializers import ResultMetricSerializer +from epi.serializers import ResultMetricSerializer from study.serializers import StudySerializer from utils.helper import SerializerHelper diff --git a/project/summary/models.py b/project/summary/models.py index 2e439cb0..0593600d 100644 --- a/project/summary/models.py +++ b/project/summary/models.py @@ -8,13 +8,13 @@ from study.models import Study from animal.models import Endpoint -from epi2.models import Outcome +from epi.models import Outcome from epimeta.models import MetaResult from invitro.models import IVEndpoint from comments.models import Comment from animal.exports import EndpointFlatDataPivot -from epi2.exports import OutcomeDataPivot +from epi.exports import OutcomeDataPivot from epimeta.exports import MetaResultFlatDataPivot from invitro.exports import IVEndpointFlatDataPivot From 5ac60a6b05496ee10e2f042b0b8509f8aacd42e1 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:21:31 -0400 Subject: [PATCH 10/17] remove various old epi2 calls --- project/epimeta/migrations/0001_initial.py | 10 +++++----- project/hawc/urls.py | 2 -- project/static/epi/js/models.js | 12 ++++++------ project/templates/epi/result_form.html | 2 +- 4 files changed, 12 insertions(+), 14 deletions(-) diff --git a/project/epimeta/migrations/0001_initial.py b/project/epimeta/migrations/0001_initial.py index d16262bf..0f5e76b8 100644 --- a/project/epimeta/migrations/0001_initial.py +++ b/project/epimeta/migrations/0001_initial.py @@ -9,7 +9,7 @@ class Migration(migrations.Migration): dependencies = [ ('study', '0001_initial'), - ('epi2', '0001_initial'), + ('epi', '0001_initial'), ] operations = [ @@ -26,8 +26,8 @@ class Migration(migrations.Migration): ('total_references', models.PositiveIntegerField(help_text=b'References identified through initial literature-search before application of inclusion/exclusion criteria', null=True, verbose_name=b'Total number of references found', blank=True)), ('total_studies_identified', models.PositiveIntegerField(help_text=b'Total references identified for inclusion after application of literature review and screening criteria', verbose_name=b'Total number of studies identified')), ('notes', models.TextField(blank=True)), - ('exclusion_criteria', models.ManyToManyField(related_name='meta_exclusion_criteria', to='epi2.Criteria', blank=True)), - ('inclusion_criteria', models.ManyToManyField(related_name='meta_inclusion_criteria', to='epi2.Criteria', blank=True)), + ('exclusion_criteria', models.ManyToManyField(related_name='meta_exclusion_criteria', to='epi.Criteria', blank=True)), + ('inclusion_criteria', models.ManyToManyField(related_name='meta_inclusion_criteria', to='epi.Criteria', blank=True)), ('study', models.ForeignKey(related_name='meta_protocols2', to='study.Study')), ], options={ @@ -53,8 +53,8 @@ class Migration(migrations.Migration): ('upper_ci', models.FloatField(help_text=b'Numerical value for upper-confidence interval', verbose_name=b'Upper CI')), ('ci_units', models.FloatField(default=0.95, help_text=b'A 95% CI is written as 0.95.', null=True, verbose_name=b'Confidence Interval (CI)', blank=True)), ('notes', models.TextField(blank=True)), - ('adjustment_factors', models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='meta_adjustments', to='epi2.AdjustmentFactor', blank=True)), - ('metric', models.ForeignKey(to='epi2.ResultMetric')), + ('adjustment_factors', models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='meta_adjustments', to='epi.AdjustmentFactor', blank=True)), + ('metric', models.ForeignKey(to='epi.ResultMetric')), ('protocol', models.ForeignKey(related_name='results2', to='epimeta.MetaProtocol')), ], options={ diff --git a/project/hawc/urls.py b/project/hawc/urls.py index 6dd01cca..be218ab0 100644 --- a/project/hawc/urls.py +++ b/project/hawc/urls.py @@ -31,8 +31,6 @@ include('animal.urls', namespace='animal')), url(r'^epi/', include('epi.urls', namespace='epi')), - url(r'^epi2/', - include('epi2.urls', namespace='epi2')), url(r'^epi-meta/', include('epimeta.urls', namespace='meta')), url(r'^in-vitro/', diff --git a/project/static/epi/js/models.js b/project/static/epi/js/models.js index 46eda9ec..620fc998 100644 --- a/project/static/epi/js/models.js +++ b/project/static/epi/js/models.js @@ -6,7 +6,7 @@ var StudyPopulation = function(data){ }; _.extend(StudyPopulation, { get_object: function(id, cb){ - $.get('/epi2/api/study-population/{0}/'.printf(id), function(d){ + $.get('/epi/api/study-population/{0}/'.printf(id), function(d){ cb(new StudyPopulation(d)); }); }, @@ -98,7 +98,7 @@ var Exposure = function(data){ }; _.extend(Exposure, { get_object: function(id, cb){ - $.get('/epi2/api/exposure/{0}/'.printf(id), function(d){ + $.get('/epi/api/exposure/{0}/'.printf(id), function(d){ cb(new Exposure(d)); }); }, @@ -187,7 +187,7 @@ var ComparisonSet = function(data){ }; _.extend(ComparisonSet, { get_object: function(id, cb){ - $.get('/epi2/api/comparison-set/{0}/'.printf(id), function(d){ + $.get('/epi/api/comparison-set/{0}/'.printf(id), function(d){ cb(new ComparisonSet(d)); }); }, @@ -293,7 +293,7 @@ var Group = function(data){ }; _.extend(Group, { get_object: function(id, cb){ - $.get('/epi2/api/group/{0}/'.printf(id), function(d){ + $.get('/epi/api/group/{0}/'.printf(id), function(d){ cb(new Group(d)); }); }, @@ -510,7 +510,7 @@ var Outcome = function(data){ }; _.extend(Outcome, { get_object: function(id, cb){ - $.get('/epi2/api/outcome/{0}/'.printf(id), function(d){ + $.get('/epi/api/outcome/{0}/'.printf(id), function(d){ cb(new Outcome(d)); }); }, @@ -635,7 +635,7 @@ var Result = function(data){ }; _.extend(Result, { get_object: function(id, cb){ - $.get('/epi2/api/result/{0}/'.printf(id), function(d){ + $.get('/epi/api/result/{0}/'.printf(id), function(d){ cb(new Result(d)); }); }, diff --git a/project/templates/epi/result_form.html b/project/templates/epi/result_form.html index b91e384a..22a356fc 100644 --- a/project/templates/epi/result_form.html +++ b/project/templates/epi/result_form.html @@ -83,7 +83,7 @@ // bind formset change to group-change $('#id_comparison_set').change(function(){ var val = parseInt(this.value), - url = "/epi2/api/comparison-set/{0}/".printf(val); + url = "/epi/api/comparison-set/{0}/".printf(val); if (_.isNaN(val)){ updateFormset(); } else if (val !== comparison_set_id || isNew){ From 18ac98e5be7c40c8641a9efee2e4585bdc102f9e Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:26:02 -0400 Subject: [PATCH 11/17] rename epimeta related_names --- project/epimeta/exports.py | 4 ++-- project/epimeta/migrations/0001_initial.py | 8 ++++---- project/epimeta/models.py | 10 +++++----- project/epimeta/serializers.py | 4 ++-- project/epimeta/views.py | 2 +- project/static/epimeta/js/models.js | 6 +++--- project/templates/study/study_detail.html | 2 +- 7 files changed, 18 insertions(+), 18 deletions(-) diff --git a/project/epimeta/exports.py b/project/epimeta/exports.py index 90affb93..bacf35bf 100644 --- a/project/epimeta/exports.py +++ b/project/epimeta/exports.py @@ -27,12 +27,12 @@ def _get_data_rows(self): row.extend(models.MetaProtocol.flat_complete_data_row(ser['protocol'])) row.extend(models.MetaResult.flat_complete_data_row(ser)) - if len(ser['single_results2']) == 0: + if len(ser['single_results']) == 0: # print one-row with no single-results rows.append(row) else: # print each single-result as a new row - for sr in ser['single_results2']: + for sr in ser['single_results']: row_copy = list(row) # clone row_copy.extend(models.SingleResult.flat_complete_data_row(sr)) rows.append(row_copy) diff --git a/project/epimeta/migrations/0001_initial.py b/project/epimeta/migrations/0001_initial.py index 0f5e76b8..98112463 100644 --- a/project/epimeta/migrations/0001_initial.py +++ b/project/epimeta/migrations/0001_initial.py @@ -28,7 +28,7 @@ class Migration(migrations.Migration): ('notes', models.TextField(blank=True)), ('exclusion_criteria', models.ManyToManyField(related_name='meta_exclusion_criteria', to='epi.Criteria', blank=True)), ('inclusion_criteria', models.ManyToManyField(related_name='meta_inclusion_criteria', to='epi.Criteria', blank=True)), - ('study', models.ForeignKey(related_name='meta_protocols2', to='study.Study')), + ('study', models.ForeignKey(related_name='meta_protocols', to='study.Study')), ], options={ 'ordering': ('name',), @@ -55,7 +55,7 @@ class Migration(migrations.Migration): ('notes', models.TextField(blank=True)), ('adjustment_factors', models.ManyToManyField(help_text=b'All factors which were included in final model', related_name='meta_adjustments', to='epi.AdjustmentFactor', blank=True)), ('metric', models.ForeignKey(to='epi.ResultMetric')), - ('protocol', models.ForeignKey(related_name='results2', to='epimeta.MetaProtocol')), + ('protocol', models.ForeignKey(related_name='results', to='epimeta.MetaProtocol')), ], options={ 'ordering': ('label',), @@ -73,8 +73,8 @@ class Migration(migrations.Migration): ('upper_ci', models.FloatField(help_text=b'Numerical value for upper-confidence interval', null=True, verbose_name=b'Upper CI', blank=True)), ('ci_units', models.FloatField(default=0.95, help_text=b'A 95% CI is written as 0.95.', null=True, verbose_name=b'Confidence Interval (CI)', blank=True)), ('notes', models.TextField(blank=True)), - ('meta_result', models.ForeignKey(related_name='single_results2', to='epimeta.MetaResult')), - ('study', models.ForeignKey(related_name='single_results2', blank=True, to='study.Study', null=True)), + ('meta_result', models.ForeignKey(related_name='single_results', to='epimeta.MetaResult')), + ('study', models.ForeignKey(related_name='single_results', blank=True, to='study.Study', null=True)), ], ), ] diff --git a/project/epimeta/models.py b/project/epimeta/models.py index 0df008f6..93fa9f38 100644 --- a/project/epimeta/models.py +++ b/project/epimeta/models.py @@ -26,7 +26,7 @@ class MetaProtocol(models.Model): (1, "Other")) study = models.ForeignKey('study.Study', - related_name="meta_protocols2") + related_name="meta_protocols") name = models.CharField( verbose_name="Protocol name", max_length=128) @@ -126,7 +126,7 @@ def flat_complete_data_row(ser): class MetaResult(models.Model): protocol = models.ForeignKey( MetaProtocol, - related_name="results2") + related_name="results") label = models.CharField( max_length=128) data_location = models.CharField( @@ -337,10 +337,10 @@ def getStatMethods(mr): class SingleResult(models.Model): meta_result = models.ForeignKey( MetaResult, - related_name="single_results2") + related_name="single_results") study = models.ForeignKey( 'study.Study', - related_name="single_results2", + related_name="single_results", blank=True, null=True) exposure_name = models.CharField( @@ -458,7 +458,7 @@ def invalidate_meta_result_cache(sender, instance, **kwargs): ) reversion.register( MetaResult, - follow=('adjustment_factors', 'single_results2') + follow=('adjustment_factors', 'single_results') ) reversion.register( SingleResult diff --git a/project/epimeta/serializers.py b/project/epimeta/serializers.py index c307af55..f4900f1d 100644 --- a/project/epimeta/serializers.py +++ b/project/epimeta/serializers.py @@ -35,7 +35,7 @@ class MetaProtocolSerializer(serializers.ModelSerializer): url = serializers.ReadOnlyField(source="get_absolute_url") protocol_type = serializers.ReadOnlyField(source="get_protocol_type_display") lit_search_strategy = serializers.ReadOnlyField(source="get_lit_search_strategy_display") - results2 = MetaResultLinkSerializer(many=True) + results = MetaResultLinkSerializer(many=True) class Meta: model = models.MetaProtocol @@ -46,7 +46,7 @@ class MetaResultSerializer(serializers.ModelSerializer): url = serializers.ReadOnlyField(source="get_absolute_url") metric = ResultMetricSerializer() adjustment_factors = serializers.StringRelatedField(many=True) - single_results2 = SingleResultSerializer(many=True) + single_results = SingleResultSerializer(many=True) def to_representation(self, instance): ret = super(MetaResultSerializer, self).to_representation(instance) diff --git a/project/epimeta/views.py b/project/epimeta/views.py index 8c1ae76c..eae9bbee 100644 --- a/project/epimeta/views.py +++ b/project/epimeta/views.py @@ -88,7 +88,7 @@ def get_formset_kwargs(self): def build_initial_formset_factory(self): return forms.SingleResultFormset( - queryset=self.object.single_results2.all().order_by('pk'), + queryset=self.object.single_results.all().order_by('pk'), **self.get_formset_kwargs()) def get_form_kwargs(self): diff --git a/project/static/epimeta/js/models.js b/project/static/epimeta/js/models.js index 28f86952..13aa446b 100644 --- a/project/static/epimeta/js/models.js +++ b/project/static/epimeta/js/models.js @@ -62,8 +62,8 @@ MetaProtocol.prototype = { }; $el.append("

    Results

    "); - if (this.data.results2.length>0){ - $el.append(HAWCUtils.buildUL(this.data.results2, liFunc)); + if (this.data.results.length>0){ + $el.append(HAWCUtils.buildUL(this.data.results, liFunc)); } else { $el.append("

    No results are available for this protocol.

    "); } @@ -94,7 +94,7 @@ _.extend(MetaResult, { MetaResult.prototype = { _unpack_single_results: function(){ var single_results = this.single_results; - this.data.single_results2.forEach(function(v,i){ + this.data.single_results.forEach(function(v,i){ single_results.push(new SingleStudyResult(v)); }); this.data.single_results = []; diff --git a/project/templates/study/study_detail.html b/project/templates/study/study_detail.html index d8354206..4d6f80a4 100644 --- a/project/templates/study/study_detail.html +++ b/project/templates/study/study_detail.html @@ -85,7 +85,7 @@ {% include "invitro/_experiment_list.html" with object_list=object.ivexperiments.all %} {% elif study.study_type == 4 %}

    Available epidemiological meta-analyses

    - {% include "epimeta/_metaprotocol_list.html" with object_list=object.meta_protocols2.all %} + {% include "epimeta/_metaprotocol_list.html" with object_list=object.meta_protocols.all %} {% endif %}
    From e9de1da8ba6d7375286a8d495276ca50fcfe6aec Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:50:49 -0400 Subject: [PATCH 12/17] changed other references to old epi module --- project/animal/migrations/0011_auto_20150723_1600.py | 2 +- project/assessment/models.py | 4 ++-- project/assessment/views.py | 14 ++++---------- project/study/models.py | 6 +++--- 4 files changed, 10 insertions(+), 16 deletions(-) diff --git a/project/animal/migrations/0011_auto_20150723_1600.py b/project/animal/migrations/0011_auto_20150723_1600.py index a96c2979..1a9a0a60 100644 --- a/project/animal/migrations/0011_auto_20150723_1600.py +++ b/project/animal/migrations/0011_auto_20150723_1600.py @@ -9,7 +9,7 @@ class Migration(migrations.Migration): dependencies = [ ('animal', '0010_auto_20150723_1536'), ('bmd', '0002_auto_20150723_1557'), - ('epi', '0003_auto_20150723_1544'), + ('epi', '0001_initial'), ('invitro', '0002_auto_20150723_1542'), ('summary', '0003_auto_20150723_1557'), ] diff --git a/project/assessment/models.py b/project/assessment/models.py index a66194b4..27c41977 100644 --- a/project/assessment/models.py +++ b/project/assessment/models.py @@ -473,8 +473,8 @@ def get_json(self, *args, **kwargs): return an empty object. """ d = {} - if hasattr(self, 'assessedoutcome'): - d = self.assessedoutcome.get_json(*args, **kwargs) + if hasattr(self, 'outcome'): + d = self.outcome.get_json(*args, **kwargs) elif hasattr(self, 'endpoint'): d = self.endpoint.d_response(*args, **kwargs) elif hasattr(self, 'ivendpoint'): diff --git a/project/assessment/views.py b/project/assessment/views.py index cf628092..bec1d80d 100644 --- a/project/assessment/views.py +++ b/project/assessment/views.py @@ -325,17 +325,12 @@ def get_context_data(self, **kwargs): .filter(assessment_id=self.assessment.id)\ .count() - aos = self.model.assessedoutcome\ + os = self.model.outcome\ .related.related_model.objects\ .filter(assessment_id=self.assessment.id)\ .count() - aos2 = self.model.outcome\ - .related.related_model.objects\ - .filter(assessment_id=self.assessment.id)\ - .count() - - mrs = get_model('epi', 'metaresult')\ + mrs = get_model('epimeta', 'metaresult')\ .objects\ .filter(protocol__study__assessment_id=self.assessment.id)\ .count() @@ -345,13 +340,12 @@ def get_context_data(self, **kwargs): .filter(assessment_id=self.assessment.id)\ .count() - alleps = eps + aos + aos2 + mrs + iveps + alleps = eps + os + mrs + iveps context.update({ "ivendpoints": iveps, "endpoints": eps, - "assessed_outcomes": aos, - "outcomes": aos2, + "outcomes": os, "meta_results": mrs, "total_endpoints": alleps }) diff --git a/project/study/models.py b/project/study/models.py index 475c00ae..9add0211 100644 --- a/project/study/models.py +++ b/project/study/models.py @@ -434,10 +434,10 @@ def invalidate_caches_study(sender, instance, **kwargs): Model = get_model('animal', 'Endpoint') filters["animal_group__experiment__study"] = instance.id elif instance.study_type == 1: - Model = get_model('epi', 'AssessedOutcome') - filters["exposure__study_population__study"] = instance.id + Model = get_model('epi', 'Outcome') + filters["study_population__study"] = instance.id elif instance.study_type == 4: - Model = get_model('epi', 'MetaResult') + Model = get_model('epimeta', 'MetaResult') filters["protocol__study"] = instance.id Study.delete_caches([instance.id]) From 3fb8789fead5f748428206dc84e0b560e47839f7 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Mon, 5 Oct 2015 17:51:27 -0400 Subject: [PATCH 13/17] use hyphenated version of cross-sectional --- project/epi/migrations/0001_initial.py | 2 +- project/epi/models.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py index 4853a067..bbe2c808 100644 --- a/project/epi/migrations/0001_initial.py +++ b/project/epi/migrations/0001_initial.py @@ -230,7 +230,7 @@ class Migration(migrations.Migration): fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('name', models.CharField(max_length=256)), - ('design', models.CharField(max_length=2, choices=[(b'CO', b'Cohort'), (b'CC', b'Case-control'), (b'NC', b'Nested case-control'), (b'CR', b'Case report'), (b'SE', b'Case series'), (b'CT', b'Controlled trial'), (b'CS', b'Cross sectional')])), + ('design', models.CharField(max_length=2, choices=[(b'CO', b'Cohort'), (b'CC', b'Case-control'), (b'NC', b'Nested case-control'), (b'CR', b'Case report'), (b'SE', b'Case series'), (b'CT', b'Controlled trial'), (b'CS', b'Cross-sectional')])), ('age_profile', models.CharField(help_text=b'Age profile of population (ex: adults, children, pregnant women, etc.)', max_length=128, blank=True)), ('source', models.CharField(help_text=b'Population source (ex: general population, environmental exposure, occupational cohort)', max_length=128, blank=True)), ('region', models.CharField(max_length=128, blank=True)), diff --git a/project/epi/models.py b/project/epi/models.py index 9e8c4236..ec45d475 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -108,7 +108,7 @@ class StudyPopulation(models.Model): ('CR', 'Case report'), ('SE', 'Case series'), ('CT', 'Controlled trial'), - ('CS', 'Cross sectional'), + ('CS', 'Cross-sectional'), ) study = models.ForeignKey( From 02a546636201677cff5e128ea825a8f7d69d2623 Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Tue, 6 Oct 2015 12:23:37 -0400 Subject: [PATCH 14/17] add back cohort subtype designs --- project/epi/migrations/0001_initial.py | 2 +- project/epi/models.py | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/project/epi/migrations/0001_initial.py b/project/epi/migrations/0001_initial.py index bbe2c808..589b7fc4 100644 --- a/project/epi/migrations/0001_initial.py +++ b/project/epi/migrations/0001_initial.py @@ -230,7 +230,7 @@ class Migration(migrations.Migration): fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('name', models.CharField(max_length=256)), - ('design', models.CharField(max_length=2, choices=[(b'CO', b'Cohort'), (b'CC', b'Case-control'), (b'NC', b'Nested case-control'), (b'CR', b'Case report'), (b'SE', b'Case series'), (b'CT', b'Controlled trial'), (b'CS', b'Cross-sectional')])), + ('design', models.CharField(max_length=2, choices=[(b'CO', b'Cohort'), (b'CX', b'Cohort (Retrospective)'), (b'CY', b'Cohort (Prospective)'), (b'CC', b'Case-control'), (b'NC', b'Nested case-control'), (b'CR', b'Case report'), (b'SE', b'Case series'), (b'CT', b'Controlled trial'), (b'CS', b'Cross-sectional')])), ('age_profile', models.CharField(help_text=b'Age profile of population (ex: adults, children, pregnant women, etc.)', max_length=128, blank=True)), ('source', models.CharField(help_text=b'Population source (ex: general population, environmental exposure, occupational cohort)', max_length=128, blank=True)), ('region', models.CharField(max_length=128, blank=True)), diff --git a/project/epi/models.py b/project/epi/models.py index ec45d475..290c357d 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -103,6 +103,8 @@ class StudyPopulation(models.Model): DESIGN_CHOICES = ( ('CO', 'Cohort'), + ('CX', 'Cohort (Retrospective)'), + ('CY', 'Cohort (Prospective)'), ('CC', 'Case-control'), ('NC', 'Nested case-control'), ('CR', 'Case report'), @@ -111,6 +113,8 @@ class StudyPopulation(models.Model): ('CS', 'Cross-sectional'), ) + OUTCOME_GROUP_DESIGNS = ("CC", "NC") + study = models.ForeignKey( 'study.Study', related_name="study_populations") @@ -242,7 +246,7 @@ def get_crumbs(self): return get_crumbs(self, self.study) def can_create_sets(self): - return self.design not in ("CC", "NC") + return self.design not in self.OUTCOME_GROUP_DESIGNS class Outcome(BaseEndpoint): From 2e805e2d960f54fcac3fb2b61eedb537505582cc Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Thu, 8 Oct 2015 14:52:03 -0400 Subject: [PATCH 15/17] rebuild data-pivot exports and fix data-pivot extensions logic --- project/animal/exports.py | 54 +++---- project/epi/exports.py | 100 ++++++------- project/epimeta/exports.py | 48 +++--- project/invitro/exports.py | 68 ++++----- project/static/summary/js/data_pivot.js | 258 +++++++++++++++++--------------- 5 files changed, 259 insertions(+), 269 deletions(-) diff --git a/project/animal/exports.py b/project/animal/exports.py index 22f86f64..adb4bac1 100644 --- a/project/animal/exports.py +++ b/project/animal/exports.py @@ -89,19 +89,16 @@ class EndpointFlatDataPivot(FlatFileExporter): def _get_header_row(self): return [ - 'study', - 'study_url', - 'Study HAWC ID', - 'Study Published', - - 'Experiment ID', - 'experiment', - 'experiment_url', + 'study id', + 'study name', + 'study published', + + 'experiment id', + 'experiment name', 'chemical', - 'Animal Group ID', - 'animal_group', - 'animal_group_url', + 'animal group id', + 'animal group name', 'lifestage exposed', 'lifestage assessed', 'species', @@ -114,20 +111,19 @@ def _get_header_row(self): 'treatment period', 'duration exposure', - 'endpoint_name', - 'endpoint_url', + 'endpoint id', + 'endpoint name', 'system', 'organ', 'effect', 'effect subtype', 'diagnostic', 'tags', - 'observation_time', - 'data_type', + 'observation time', + 'data type', 'doses', - 'dose_units', - 'response_units', - 'Endpoint Key', + 'dose units', + 'response units', 'low_dose', 'NOEL', @@ -141,16 +137,16 @@ def _get_header_row(self): 'BMDU', 'CSF', - 'Row Key', - 'dose_index', + 'key', + 'dose index', 'dose', - 'n', + 'N', 'incidence', 'response', - 'stdev', - 'percentControlMean', - 'percentControlLow', - 'percentControlHigh' + 'variance', + 'percent control mean', + 'percent control low', + 'percent control high' ] def _get_data_rows(self): @@ -201,19 +197,16 @@ def get_tags(e): # build endpoint-group independent data row = [ - ser['animal_group']['experiment']['study']['short_citation'], - ser['animal_group']['experiment']['study']['url'], ser['animal_group']['experiment']['study']['id'], + ser['animal_group']['experiment']['study']['short_citation'], ser['animal_group']['experiment']['study']['published'], ser['animal_group']['experiment']['id'], ser['animal_group']['experiment']['name'], - ser['animal_group']['experiment']['url'], ser['animal_group']['experiment']['chemical'], ser['animal_group']['id'], ser['animal_group']['name'], - ser['animal_group']['url'], ser['animal_group']['lifestage_exposed'], ser['animal_group']['lifestage_assessed'], ser['animal_group']['species'], @@ -227,8 +220,8 @@ def get_tags(e): ser['animal_group']['dosing_regime']), ser['animal_group']['dosing_regime']['duration_exposure_text'], + ser['id'], ser['name'], - ser['url'], ser['system'], ser['organ'], ser['effect'], @@ -240,7 +233,6 @@ def get_tags(e): get_doses_str(doses), get_dose_units(doses), ser['response_units'], - ser['id'] ] # dose-group specific information diff --git a/project/epi/exports.py b/project/epi/exports.py index 4f3e23b5..f6759c5a 100644 --- a/project/epi/exports.py +++ b/project/epi/exports.py @@ -43,55 +43,52 @@ class OutcomeDataPivot(FlatFileExporter): def _get_header_row(self): return [ - 'Study', - 'Study URL', - 'Study HAWC ID', - 'Study Published?', - - 'Study Population Name', - 'Study Population Key', - 'Design', - 'Study Population URL', - - 'Assessed Outcome Key', - 'Assessed Outcome Name', - 'Diagnostic', - - 'Comparison Set ID', - 'Comparison Set name', - - 'Exposure', - 'Exposure Key', - 'Exposure Metric', - 'Exposure URL', - 'Dose Units', - - 'Result ID', - 'Assessed Outcome Population Description', - 'Statistical Metric', - 'Statistical Metric Abbreviation', - 'Statistical Metric Description', - 'Outcome Summary', - 'Dose Response', - 'Statistical Power', + 'study id', + 'study name', + 'study published', + + 'study population id', + 'study population name', + 'design', + + 'outcome id', + 'outcome name', + 'diagnostic', + + 'comparison set id', + 'comparison set name', + + 'exposure id', + 'exposure name', + 'exposure metric', + 'dose units', + + 'result id', + 'result population description', + 'statistical metric', + 'statistical metric abbreviation', + 'statistical metric description', + 'result summary', + 'dose response', + 'statistical power', 'CI units', - 'Exposure Group Name', - 'Exposure Group Comparative Description Name', - 'Exposure Group Order', - 'Exposure Group Numeric', + 'exposure group order', + 'exposure group name', + 'exposure group comparison name', + 'exposure group numeric', - 'Row Key', - 'Assessed Outcome Group Primary Key', + 'key', + 'result group id', 'N', - 'Estimate', - 'Lower CI', - 'Upper CI', - 'SE', - 'Statistical Significance', - 'Statistical Significance (numeric)', - 'Main Finding', - 'Support Main Finding', + 'estimate', + 'lower CI', + 'upper CI', + 'variance', + 'statistical significance', + 'statistical significance (numeric)', + 'main finding', + 'main finding support', ] def _get_data_rows(self): @@ -99,15 +96,13 @@ def _get_data_rows(self): for obj in self.queryset: ser = obj.get_json(json_encode=False) row = [ - ser['study_population']['study']['short_citation'], - ser['study_population']['study']['url'], ser['study_population']['study']['id'], + ser['study_population']['study']['short_citation'], ser['study_population']['study']['published'], - ser['study_population']['name'], ser['study_population']['id'], + ser['study_population']['name'], ser['study_population']['design'], - ser['study_population']['url'], ser['id'], ser['name'], @@ -119,10 +114,9 @@ def _get_data_rows(self): res["comparison_set"]["id"], res["comparison_set"]["name"], - res["comparison_set"]["exposure"]["name"], res["comparison_set"]["exposure"]["id"], + res["comparison_set"]["exposure"]["name"], res["comparison_set"]["exposure"]["metric"], - res["comparison_set"]["exposure"]["url"], res["comparison_set"]["exposure"]["metric_units"]["name"], res['id'], @@ -138,13 +132,13 @@ def _get_data_rows(self): for rg in res['results']: row_copy2 = list(row_copy) row_copy2.extend([ + rg['group']['group_id'], rg['group']['name'], rg['group']['comparative_name'], - rg['group']['group_id'], rg['group']['numeric'], - rg['id'], # repeat for data-pivot key rg['id'], + rg['id'], # repeat for data-pivot key rg['n'], rg['estimate'], rg['lower_ci'], diff --git a/project/epimeta/exports.py b/project/epimeta/exports.py index bacf35bf..02c01385 100644 --- a/project/epimeta/exports.py +++ b/project/epimeta/exports.py @@ -47,33 +47,30 @@ class MetaResultFlatDataPivot(FlatFileExporter): def _get_header_row(self): return [ - 'Study', - 'Study URL', - 'Study HAWC ID', - 'Study Published?', + 'study id', + 'study name', + 'study published', - 'Protocol Primary Key', - 'Protocol URL', - 'Protocol Name', - 'Protocol Type', - 'Total References', - 'Identified References', + 'protocol id', + 'protocol name', + 'protocol type', + 'total references', + 'identified references', - 'Row Key', - 'Result Primary Key', - 'Result URL', - 'Result Label', - 'Health Outcome', - 'Exposure', - 'Result References', - 'Statistical Metric', - 'Statistical Metric Abbreviation', + 'key', + 'meta result id', + 'meta result label', + 'health outcome', + 'exposure', + 'result references', + 'statistical metric', + 'statistical metric abbreviation', 'N', - 'Estimate', - 'Lower CI', - 'Upper CI', + 'estimate', + 'lower CI', + 'upper CI', 'CI units', - 'Heterogeneity' + 'heterogeneity' ] def _get_data_rows(self): @@ -81,13 +78,11 @@ def _get_data_rows(self): for obj in self.queryset: ser = obj.get_json(json_encode=False) row = [ - ser['protocol']['study']['short_citation'], - ser['protocol']['study']['url'], ser['protocol']['study']['id'], + ser['protocol']['study']['short_citation'], ser['protocol']['study']['published'], ser['protocol']['id'], - ser['protocol']['url'], ser['protocol']['name'], ser['protocol']['protocol_type'], ser['protocol']['total_references'], @@ -95,7 +90,6 @@ def _get_data_rows(self): ser['id'], # repeat for data-pivot key ser['id'], - ser['url'], ser['label'], ser['health_outcome'], ser['exposure_name'], diff --git a/project/invitro/exports.py b/project/invitro/exports.py index acfb9359..ac43aa91 100644 --- a/project/invitro/exports.py +++ b/project/invitro/exports.py @@ -7,45 +7,43 @@ class IVEndpointFlatDataPivot(FlatFileExporter): def _get_header_row(self): header = [ - 'Study', - 'Study HAWC ID', - 'Study identifier', - 'Study URL', - 'Study Published', - - 'Chemical name', - 'Chemical HAWC ID', - 'Chemical CAS', - 'Chemical purity', - - 'IVExperiment HAWC ID', - 'IVExperiment URL', - 'Cell species', - 'Cell sex', - 'Cell type', - 'Cell tissue', + 'study id', + 'study name', + 'study identifier', + 'study published', + + 'chemical id', + 'chemical name', + 'chemical CAS', + 'chemical purity', + + 'IVExperiment id', + 'cell species', + 'cell sex', + 'cell type', + 'cell tissue', 'Dose units', 'Metabolic activation', 'Transfection', + 'key', + 'IVEndpoint id', 'IVEndpoint name', - 'IVEndpoint HAWC ID', - 'IVEndpoint URL', 'IVEndpoint description tags', - 'Assay type', - 'Endpoint description', - 'Endpoint response units', - 'Observation time', - 'Observation time units', + 'assay type', + 'endpoint description', + 'endpoint response units', + 'observation time', + 'observation time units', 'NOEL', 'LOEL', - 'Monotonicity', - 'Overall pattern', - 'Trend test result', - 'Minimum dose', - 'Maximum dose', - 'Number of doses' + 'monotonicity', + 'overall pattern', + 'trend test result', + 'minimum dose', + 'maximum dose', + 'number of doses', ] num_cats = 0 @@ -107,19 +105,17 @@ def getDose(ser, tag): bm_values = [bm["value"] for bm in ser["benchmarks"]] row = [ - ser['experiment']['study']['short_citation'], ser['experiment']['study']['id'], + ser['experiment']['study']['short_citation'], ser['experiment']['study']['study_identifier'], - ser['experiment']['study']['url'], ser['experiment']['study']['published'], - ser['chemical']['name'], ser['chemical']['id'], + ser['chemical']['name'], ser['chemical']['cas'], ser['chemical']['purity'], ser['experiment']['id'], - ser['experiment']['url'], ser['experiment']['cell_type']['species'], ser['experiment']['cell_type']['sex'], ser['experiment']['cell_type']['cell_type'], @@ -129,9 +125,9 @@ def getDose(ser, tag): ser['experiment']['metabolic_activation'], ser['experiment']['transfection'], - ser['name'], + ser['id'], # repeat for data-pivot key ser['id'], - ser['url'], + ser['name'], '|'.join([d['name'] for d in ser['effects']]), ser['assay_type'], ser['short_description'], diff --git a/project/static/summary/js/data_pivot.js b/project/static/summary/js/data_pivot.js index e31d5b8b..5e788754 100644 --- a/project/static/summary/js/data_pivot.js +++ b/project/static/summary/js/data_pivot.js @@ -179,7 +179,7 @@ _.extend(DataPivot, { // add data-pivot row-level key and index row._dp_y = i; - row._dp_pk = row['Row Key'] || i; + row._dp_pk = row['key'] || i; return row; }, @@ -303,7 +303,7 @@ DataPivot.prototype = { this.data_headers = data_headers; }, build_settings: function(){ - + this.dpe_options = DataPivotExtension.get_options(this); var self = this, build_description_tab = function(){ var tab = $('
    '), @@ -1348,7 +1348,7 @@ var _DataPivot_settings_description = function(data_pivot, values){ "header_style": this.data_pivot.style_manager.add_select("texts", values.header_style), "text_style": this.data_pivot.style_manager.add_select("texts", values.text_style), "max_width": $(''), - "dpe": $('').html(DataPivotExtension.get_options(data_pivot)) + "dpe": $('').html(this.data_pivot.dpe_options) }; // set default values @@ -1416,7 +1416,7 @@ var _DataPivot_settings_pointdata = function(data_pivot, values){ "header_name": $(''), "marker_style": this.data_pivot.style_manager.add_select(style_type, values.marker_style), "conditional_formatting": this.conditional_formatter.data, - "dpe": $('').html(DataPivotExtension.get_options(data_pivot)) + "dpe": $('').html(this.data_pivot.dpe_options) }; // set default values @@ -2641,8 +2641,8 @@ _.extend(DataPivot_visualization.prototype, D3Plot.prototype, { obj.style(property, d._styles['points_' + i][property]); } }) - .style('cursor', function(d){return(datum._dpe_datatype)?'pointer':'auto';}) - .on("click", function(d){if(datum._dpe_datatype){self.dpe.render_plottip(datum, d);}}); + .style('cursor', function(d){return(datum._dpe_key)?'pointer':'auto';}) + .on("click", function(d){if(datum._dpe_key){self.dpe.render_plottip(datum, d);}}); }); this.g_labels = this.vis.append("g"); @@ -2714,9 +2714,9 @@ _.extend(DataPivot_visualization.prototype, D3Plot.prototype, { "col": j, "text": txt.toLocaleString(), "style": v._styles['text_' + j], - "cursor": (desc._dpe_datatype)?'pointer':'auto', + "cursor": (desc._dpe_key)?'pointer':'auto', "onclick": function(){ - if(desc._dpe_datatype)self.dpe.render_plottip(desc, v); + if(desc._dpe_key)self.dpe.render_plottip(desc, v); } }) }); @@ -2880,126 +2880,140 @@ _.extend(DataPivot_visualization.prototype, D3Plot.prototype, { DataPivotExtension = function(){}; _.extend(DataPivotExtension, { + values: [ + { + _dpe_name: "study", + _dpe_key: "study id", + _dpe_cls: Study, + _dpe_option_txt: "Show study", + }, + { + _dpe_name: "experiment", + _dpe_key: "experiment id", + _dpe_cls: Experiment, + _dpe_option_txt: "Show experiment", + }, + { + _dpe_name: "animal_group", + _dpe_key: "animal group id", + _dpe_cls: AnimalGroup, + _dpe_option_txt: "Show animal group", + }, + { + _dpe_name: "endpoint", + _dpe_key: "endpoint id", + _dpe_cls: Endpoint, + _dpe_option_txt: "Show endpoint (basic)", + _dpe_options: { + complete: false + }, + }, + { + _dpe_name: "endpoint_complete", + _dpe_key: "endpoint id", + _dpe_cls: Endpoint, + _dpe_option_txt: "Show endpoint (complete)", + _dpe_options: { + complete: true + }, + }, + { + _dpe_name: "study_population", + _dpe_key: "study population id", + _dpe_cls: StudyPopulation, + _dpe_option_txt: "Show study population", + }, + { + _dpe_name: "comparison_set", + _dpe_key: "comparison set id", + _dpe_cls: ComparisonSet, + _dpe_option_txt: "Show comparison set", + }, + { + _dpe_name: "exposure", + _dpe_key: "exposure id", + _dpe_cls: Exposure, + _dpe_option_txt: "Show exposure", + }, + { + _dpe_name: "outcome", + _dpe_key: "outcome id", + _dpe_cls: Outcome, + _dpe_option_txt: "Show outcome", + }, + { + _dpe_name: "result", + _dpe_key: "result id", + _dpe_cls: Result, + _dpe_option_txt: "Show result", + }, + { + _dpe_name: "meta_protocol", + _dpe_key: "protocol id", + _dpe_cls: MetaProtocol, + _dpe_option_txt: "Show protocol", + }, + { + _dpe_name: "meta_result", + _dpe_key: "meta result id", + _dpe_cls: MetaResult, + _dpe_option_txt: "Show meta result", + }, + { + _dpe_name: "iv_chemical", + _dpe_key: "chemical id", + _dpe_cls: IVChemical, + _dpe_option_txt: "Show chemical", + }, + { + _dpe_name: "iv_experiment", + _dpe_key: "IVExperiment id", + _dpe_cls: IVExperiment, + _dpe_option_txt: "Show experiment", + }, + { + _dpe_name: "iv_endpoint", + _dpe_key: "IVEndpoint id", + _dpe_cls: IVEndpoint, + _dpe_option_txt: "Show endpoint", + } + ], + extByName: function(){ + return _.indexBy(DataPivotExtension.values, '_dpe_name'); + }, + extByColumnKey: function(){ + return _.groupBy(DataPivotExtension.values, '_dpe_key'); + }, update_extensions: function(obj, key){ - var map = d3.map({ - "study": { - _dpe_key: "Study HAWC ID", - _dpe_datatype: "study", - _dpe_cls: Study - }, - "experiment": { - _dpe_key: "Experiment ID", - _dpe_datatype: "experiment", - _dpe_cls: Experiment - }, - "animal_group": { - _dpe_key: "Animal Group ID", - _dpe_datatype: "animal_group", - _dpe_cls: AnimalGroup - }, - "endpoint": { - _dpe_key: "Endpoint Key", - _dpe_datatype: "endpoint", - _dpe_cls: Endpoint, - options: { - complete: false - } - }, - "endpoint_complete": { - _dpe_key: "Endpoint Key", - _dpe_datatype: "endpoint", - _dpe_cls: Endpoint, - options: { - complete: true - } - }, - "study_population": { - _dpe_key: "Study Population Key", - _dpe_datatype: "study_population", - _dpe_cls: StudyPopulation - }, - "comparison_set": { - _dpe_key: "Comparison Set ID", - _dpe_datatype: "comparison_set", - _dpe_cls: ComparisonSet - }, - "exposure": { - _dpe_key: "Exposure Key", - _dpe_datatype: "exposure", - _dpe_cls: Exposure - }, - "assessed_outcome": { - _dpe_key: "Assessed Outcome Key", - _dpe_datatype: "assessed_outcome", - _dpe_cls: Outcome - }, - "result": { - _dpe_key: "Result ID", - _dpe_datatype: "result", - _dpe_cls: Result - }, - "meta_protocol": { - _dpe_key: "Protocol Primary Key", - _dpe_datatype: "meta_protocol", - _dpe_cls: MetaProtocol - }, - "meta_result": { - _dpe_key: "Result Primary Key", - _dpe_datatype: "meta_result", - _dpe_cls: MetaResult - }, - "iv_chemical": { - _dpe_key: "Chemical HAWC ID", - _dpe_datatype: "iv_chemical", - _dpe_cls: IVChemical - }, - "iv_experiment": { - _dpe_key: "IVExperiment HAWC ID", - _dpe_datatype: "iv_experiment", - _dpe_cls: IVExperiment - }, - "iv_endpoint": { - _dpe_key: "IVEndpoint HAWC ID", - _dpe_datatype: "iv_endpoint", - _dpe_cls: IVEndpoint - } - }), - match = map.get(key); - + var dpe_keys = DataPivotExtension.extByName(), + match = dpe_keys[key]; if (match){ - $.extend(obj, match); + _.extend(obj, match); } else { console.log("Unrecognized DPE key: {0}".printf(key)); } }, get_options: function(dp){ // extension options dependent on available data-columns - var opts = [''.printf(DataPivot.NULL_CASE)]; + var build_opt = function(val, txt){ + return ''.printf(val, txt) + }, + opts = [ + build_opt(DataPivot.NULL_CASE, DataPivot.NULL_CASE) + ], + headers; if (dp.data.length>0){ - var headers = d3.set(d3.map(dp.data[0]).keys()), - options = d3.map({ - "Study HAWC ID": [''], - "Study Population Key": [''], - "Exposure Key": [''], - "Comparison Set ID": [''], - "Protocol Primary Key": [''], - "Result Primary Key": [''], - "Experiment ID": [''], - "Animal Group ID": [''], - "Endpoint Key": [ - '', - '' - ], - "Assessed Outcome Key": [''], - "Result ID": [''], - "Chemical HAWC ID": [''], - "IVExperiment HAWC ID": [''], - "IVEndpoint HAWC ID": [''], - }); - - options.entries().forEach(function(v){ - if(headers.has(v.key)) opts.push.apply(opts, v.value); + headers = d3.set(d3.map(dp.data[0]).keys()); + _.each(DataPivotExtension.extByColumnKey(), function(vals, key){ + if(headers.has(key)){ + opts.push.apply( + opts, + vals.map(function(d){ + return build_opt(d._dpe_name, d._dpe_option_txt); + }) + ); + } }); } return opts; @@ -3007,10 +3021,10 @@ _.extend(DataPivotExtension, { }); DataPivotExtension.prototype = { render_plottip: function(settings, datarow){ - var Cls = settings._dpe_cls, - key = settings._dpe_key, - options = settings.options - Cls.displayAsModal(datarow[key], options); + settings._dpe_cls.displayAsModal( + datarow[settings._dpe_key], + settings._dpe_options + ); } }; From 0e0cf47bf598a34a63debafa469ab61970632c4d Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Thu, 8 Oct 2015 16:12:39 -0400 Subject: [PATCH 16/17] fix study filtering by evidence type --- project/summary/forms.py | 21 ++++++++++++++------- project/summary/models.py | 26 ++++++++++++++++++++------ 2 files changed, 34 insertions(+), 13 deletions(-) diff --git a/project/summary/forms.py b/project/summary/forms.py index 0f43bfc3..b11c90c0 100644 --- a/project/summary/forms.py +++ b/project/summary/forms.py @@ -159,8 +159,10 @@ def setInitialValues(self): if k in [ "animal_group__experiment__study__in", - "exposure__study_population__study__in", - "experiment__study__in"]: + "study_population__study__in", + "experiment__study__in", + "protocol__study__in", + ]: self.fields["prefilter_study"].initial = True self.fields["studies"].initial = v @@ -210,12 +212,17 @@ def setPrefilters(self, data): if data.get('prefilter_study') is True: studies = data.get("studies", []) - if data.get('evidence_type') == 1: # Epi - prefilters["exposure__study_population__study__in"] = studies - elif data.get('evidence_type') == 2: # in-vitro - prefilters["experiment__study__in"] = studies - else: # assume bioassay + evidence_type = data.get('evidence_type', None) + if evidence_type == 0: # Bioassay prefilters["animal_group__experiment__study__in"] = studies + if evidence_type == 1: # Epi + prefilters["study_population__study__in"] = studies + elif evidence_type == 2: # in-vitro + prefilters["experiment__study__in"] = studies + elif evidence_type == 4: # meta + prefilters["protocol__study__in"] = studies + else: + raise ValueError("Unknown evidence type") if data.get('prefilter_system') is True: prefilters["system__in"] = data.get("systems", []) diff --git a/project/summary/models.py b/project/summary/models.py index 0593600d..0ec86226 100644 --- a/project/summary/models.py +++ b/project/summary/models.py @@ -560,6 +560,7 @@ class Prefilter(object): """ @classmethod def setFiltersFromForm(cls, filters, d): + evidence_type = d.get('evidence_type') if d.get('prefilter_system'): filters["system__in"] = d.getlist('systems') @@ -574,15 +575,28 @@ def setFiltersFromForm(cls, filters, d): if d.get('prefilter_study'): studies = d.get("studies", []) - if d.get('evidence_type') == 1: # Epi - filters["exposure__study_population__study__in"] = studies - elif d.get('evidence_type') == 2: # in-vitro - filters["experiment__study__in"] = studies - else: # assume bioassay + if evidence_type == 0: # Bioassay filters["animal_group__experiment__study__in"] = studies + if evidence_type == 1: # Epi + filters["study_population__study__in"] = studies + elif evidence_type == 2: # in-vitro + filters["experiment__study__in"] = studies + elif evidence_type == 4: # meta + filters["protocol__study__in"] = studies + else: + raise ValueError("Unknown evidence type") if d.get("published_only"): - filters["animal_group__experiment__study__published"] = True + if evidence_type == 0: # Bioassay + filters["animal_group__experiment__study__published"] = True + if evidence_type == 1: # Epi + filters["study_population__study__published"] = True + elif evidence_type == 2: # in-vitro + filters["experiment__study__published"] = True + elif evidence_type == 4: # meta + filters["protocol__study__published"] = True + else: + raise ValueError("Unknown evidence type") @classmethod def setFiltersFromObj(cls, filters, prefilters): From 5012ca7f546526c43f8c67d5bde40a1c2c06096f Mon Sep 17 00:00:00 2001 From: Andy Shapiro Date: Sat, 10 Oct 2015 22:45:58 -0400 Subject: [PATCH 17/17] fix result group ordering --- project/epi/migrations/0003_auto_20151010_2145.py | 18 ++++++++++++++++++ project/epi/models.py | 2 +- 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 project/epi/migrations/0003_auto_20151010_2145.py diff --git a/project/epi/migrations/0003_auto_20151010_2145.py b/project/epi/migrations/0003_auto_20151010_2145.py new file mode 100644 index 00000000..5618617e --- /dev/null +++ b/project/epi/migrations/0003_auto_20151010_2145.py @@ -0,0 +1,18 @@ +# -*- coding: utf-8 -*- +from __future__ import unicode_literals + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('epi', '0002_load_fixtures'), + ] + + operations = [ + migrations.AlterModelOptions( + name='groupresult', + options={'ordering': ('result', 'group__group_id')}, + ), + ] diff --git a/project/epi/models.py b/project/epi/models.py index 290c357d..16943d22 100644 --- a/project/epi/models.py +++ b/project/epi/models.py @@ -1015,7 +1015,7 @@ class GroupResult(models.Model): auto_now=True) class Meta: - ordering = ('result', 'group__comparison_set_id') + ordering = ('result', 'group__group_id') @property def p_value_text(self):