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