def _retrieve_analysis_groups(project):
group_models = AnalysisGroup.objects.filter(project=project)
groups = get_json_for_analysis_groups(group_models, project_guid=project.guid)
return {group['analysisGroupGuid']: group for group in groups}
def _get_projects_details(projects, user, project_category_guid=None):
for project in projects:
check_project_permissions(project, user)
prefetch_related_objects(projects, 'can_view_group')
project_models_by_guid = {project.guid: project for project in projects}
projects_json = get_json_for_projects(projects, user)
locus_lists = LocusList.objects.filter(
projects__in=projects).prefetch_related('projects')
project_guid = projects[0].guid if len(projects) == 1 else None
functional_data_tag_types = get_json_for_variant_functional_data_tag_types(
)
variant_tag_types_by_guid = {
vtt.guid: vtt
for vtt in VariantTagType.objects.filter(
Q(project__in=projects)
| Q(project__isnull=True)).prefetch_related('project')
}
variant_tag_types = _get_json_for_models(
list(variant_tag_types_by_guid.values()))
for project_json in projects_json:
project = project_models_by_guid[project_json['projectGuid']]
project_json.update({
'locusListGuids': [
locus_list.guid for locus_list in locus_lists
if project in locus_list.projects.all()
],
'variantTagTypes': [
vtt for vtt in variant_tag_types
if variant_tag_types_by_guid[vtt['variantTagTypeGuid']].project
is None or variant_tag_types_by_guid[vtt['variantTagTypeGuid']]
.project.guid == project_json['projectGuid']
],
'variantFunctionalTagTypes':
functional_data_tag_types,
})
family_models = Family.objects.filter(project__in=projects)
families = _get_json_for_families(family_models,
user,
project_guid=project_guid,
skip_nested=True)
individual_models = Individual.objects.filter(family__in=family_models)
individuals = _get_json_for_individuals(individual_models,
user=user,
project_guid=project_guid,
add_hpo_details=True,
skip_nested=True)
sample_models = Sample.objects.filter(individual__in=individual_models)
samples = get_json_for_samples(sample_models,
project_guid=project_guid,
skip_nested=True)
igv_sample_models = IgvSample.objects.filter(
individual__in=individual_models)
igv_samples = get_json_for_samples(igv_sample_models,
project_guid=project_guid,
skip_nested=True)
analysis_group_models = AnalysisGroup.objects.filter(project__in=projects)
analysis_groups = get_json_for_analysis_groups(analysis_group_models,
project_guid=project_guid,
skip_nested=True)
if not project_guid:
project_id_to_guid = {project.id: project.guid for project in projects}
family_id_to_guid = {
family.id: family.guid
for family in family_models
}
individual_id_to_guid = {
individual.id: individual.guid
for individual in individual_models
}
family_guid_to_project_guid = {}
individual_guid_to_project_guid = {}
for family in families:
project_guid = project_id_to_guid[family.pop('projectId')]
family['projectGuid'] = project_guid
family_guid_to_project_guid[family['familyGuid']] = project_guid
for individual in individuals:
family_guid = family_id_to_guid[individual.pop('familyId')]
project_guid = family_guid_to_project_guid[family_guid]
individual['familyGuid'] = family_guid
individual['projectGuid'] = project_guid
individual_guid_to_project_guid[
individual['individualGuid']] = project_guid
for sample in samples:
individual_guid = individual_id_to_guid[sample.pop('individualId')]
sample['individualGuid'] = individual_guid
sample['projectGuid'] = individual_guid_to_project_guid[
individual_guid]
for sample in igv_samples:
individual_guid = individual_id_to_guid[sample.pop('individualId')]
sample['individualGuid'] = individual_guid
sample['projectGuid'] = individual_guid_to_project_guid[
individual_guid]
for group in analysis_groups:
group['projectGuid'] = project_id_to_guid[group.pop('projectId')]
individual_guids_by_family = defaultdict(list)
for individual in individuals:
individual_guids_by_family[individual['familyGuid']].append(
individual['individualGuid'])
for family in families:
family['individualGuids'] = individual_guids_by_family[
family['familyGuid']]
sample_guids_by_individual = defaultdict(list)
for sample in samples:
sample_guids_by_individual[sample['individualGuid']].append(
sample['sampleGuid'])
igv_sample_guids_by_individual = defaultdict(list)
for sample in igv_samples:
igv_sample_guids_by_individual[sample['individualGuid']].append(
sample['sampleGuid'])
for individual in individuals:
individual['sampleGuids'] = sample_guids_by_individual[
individual['individualGuid']]
individual['igvSampleGuids'] = igv_sample_guids_by_individual[
individual['individualGuid']]
response = {
'projectsByGuid': {p['projectGuid']: p
for p in projects_json},
'familiesByGuid': {f['familyGuid']: f
for f in families},
'individualsByGuid': {i['individualGuid']: i
for i in individuals},
'samplesByGuid': {s['sampleGuid']: s
for s in samples},
'igvSamplesByGuid': {s['sampleGuid']: s
for s in igv_samples},
'locusListsByGuid': {
ll['locusListGuid']: ll
for ll in get_json_for_locus_lists(locus_lists, user)
},
'analysisGroupsByGuid':
{ag['analysisGroupGuid']: ag
for ag in analysis_groups},
}
if project_category_guid:
response['projectCategoriesByGuid'] = {
project_category_guid:
ProjectCategory.objects.get(guid=project_category_guid).json()
}
return response
def _get_projects_details(projects, user, project_category_guid=None):
for project in projects:
check_permissions(project, user)
prefetch_related_objects(projects, 'can_view_group')
project_models_by_guid = {project.guid: project for project in projects}
projects_json = get_json_for_projects(projects, user)
locus_lists = set()
functional_data_tag_types = get_json_for_variant_functional_data_tag_types(
)
variant_tag_types_by_guid = {
vtt.guid: vtt
for vtt in VariantTagType.objects.filter(
Q(project__in=projects)
| Q(project__isnull=True)).prefetch_related('project')
}
variant_tag_types = _get_json_for_models(
variant_tag_types_by_guid.values())
for project_json in projects_json:
project = project_models_by_guid[project_json['projectGuid']]
project_locus_lists = get_project_locus_list_models(project)
locus_lists.update(project_locus_lists)
project_json.update({
'locusListGuids':
[locus_list.guid for locus_list in project_locus_lists],
'variantTagTypes': [
vtt for vtt in variant_tag_types
if variant_tag_types_by_guid[vtt['variantTagTypeGuid']].project
is None or variant_tag_types_by_guid[vtt['variantTagTypeGuid']]
.project.guid == project_json['projectGuid']
],
'variantFunctionalTagTypes':
functional_data_tag_types,
})
families = _get_json_for_families(
Family.objects.filter(project__in=projects), user)
individuals = _get_json_for_individuals(
Individual.objects.filter(family__project__in=projects), user=user)
samples = get_json_for_samples(
Sample.objects.filter(individual__family__project__in=projects))
analysis_groups = get_json_for_analysis_groups(
AnalysisGroup.objects.filter(project__in=projects))
individual_guids_by_family = defaultdict(list)
for individual in individuals:
individual_guids_by_family[individual['familyGuid']].append(
individual['individualGuid'])
for family in families:
family['individualGuids'] = individual_guids_by_family[
family['familyGuid']]
sample_guids_by_individual = defaultdict(list)
for sample in samples:
sample_guids_by_individual[sample['individualGuid']].append(
sample['sampleGuid'])
for individual in individuals:
individual['sampleGuids'] = sample_guids_by_individual[
individual['individualGuid']]
response = {
'projectsByGuid': {p['projectGuid']: p
for p in projects_json},
'familiesByGuid': {f['familyGuid']: f
for f in families},
'individualsByGuid': {i['individualGuid']: i
for i in individuals},
'samplesByGuid': {s['sampleGuid']: s
for s in samples},
'locusListsByGuid': {
ll['locusListGuid']: ll
for ll in get_json_for_locus_lists(list(locus_lists), user)
},
'analysisGroupsByGuid':
{ag['analysisGroupGuid']: ag
for ag in analysis_groups},
}
if project_category_guid:
response['projectCategoriesByGuid'] = {
project_category_guid:
ProjectCategory.objects.get(guid=project_category_guid).json()
}
return response
def _get_projects_details(projects, user, project_category_guid=None):
for project in projects:
check_permissions(project, user)
prefetch_related_objects(projects, 'can_view_group')
project_models_by_guid = {project.guid: project for project in projects}
projects_json = get_json_for_projects(projects, user)
locus_lists = set()
functional_data_tag_types = get_json_for_variant_functional_data_tag_types(
)
for project_json in projects_json:
project = project_models_by_guid[project_json['projectGuid']]
project_locus_lists = get_project_locus_list_models(project)
locus_lists.update(project_locus_lists)
project_json.update({
'locusListGuids':
[locus_list.guid for locus_list in project_locus_lists],
'variantTagTypes':
get_project_variant_tag_types(project),
'variantFunctionalTagTypes':
functional_data_tag_types,
})
families = _get_json_for_families(
Family.objects.filter(project__in=projects),
user,
add_individual_guids_field=True)
individuals = _get_json_for_individuals(
Individual.objects.filter(family__project__in=projects),
user=user,
add_sample_guids_field=True)
samples = get_json_for_samples(
Sample.objects.filter(individual__family__project__in=projects))
analysis_groups = get_json_for_analysis_groups(
AnalysisGroup.objects.filter(project__in=projects))
response = {
'projectsByGuid': {p['projectGuid']: p
for p in projects_json},
'familiesByGuid': {f['familyGuid']: f
for f in families},
'individualsByGuid': {i['individualGuid']: i
for i in individuals},
'samplesByGuid': {s['sampleGuid']: s
for s in samples},
'locusListsByGuid': {
ll['locusListGuid']: ll
for ll in get_json_for_locus_lists(list(locus_lists), user)
},
'analysisGroupsByGuid':
{ag['analysisGroupGuid']: ag
for ag in analysis_groups},
}
if project_category_guid:
response['projectCategoriesByGuid'] = {
project_category_guid:
ProjectCategory.objects.get(guid=project_category_guid).json()
}
return response
