Python Variant.toJSON方法代码示例

# 需要导入模块: from xbrowse import Variant [as 别名]
# 或者: from xbrowse.Variant import toJSON [as 别名]
def add_or_edit_variant_tags(request):

    family = None
    if 'family_id' in request.GET:
        project, family = get_project_and_family_for_user(request.user, request.GET)
    else:
        project = utils.get_project_for_user(request.user, request.GET)

    form = api_forms.VariantTagsForm(project, request.GET)
    if not form.is_valid():
        ret = {
            'is_error': True,
            'error': server_utils.form_error_string(form)
        }
        return JSONResponse(ret)

    variant = get_datastore(project.project_id).get_single_variant(
            project.project_id,
            family.family_id,
            form.cleaned_data['xpos'],
            form.cleaned_data['ref'],
            form.cleaned_data['alt'],
    )

    if not variant:
        variant = Variant(form.cleaned_data['xpos'], form.cleaned_data['ref'], form.cleaned_data['alt'])

    variant_tags_to_delete = {
        variant_tag.id: variant_tag for variant_tag in VariantTag.objects.filter(
            family=family,
            xpos=form.cleaned_data['xpos'],
            ref=form.cleaned_data['ref'],
            alt=form.cleaned_data['alt'])
    }

    project_tag_events = {}
    for project_tag in form.cleaned_data['project_tags']:
        # retrieve tags
        tag, created = VariantTag.objects.get_or_create(
            project_tag=project_tag,
            family=family,
            xpos=form.cleaned_data['xpos'],
            ref=form.cleaned_data['ref'],
            alt=form.cleaned_data['alt'],
        )

        if not created:
            # this tag already exists so just keep it (eg. remove it from the set of tags that will be deleted)
            del variant_tags_to_delete[tag.id]
            continue

        # this a new tag, so update who saved it and when
        project_tag_events[project_tag] = "add_variant_tag"

        tag.user = request.user
        tag.date_saved = timezone.now()
        tag.search_url = form.cleaned_data['search_url']
        tag.save()

    # delete the tags that are no longer checked.
    for variant_tag in variant_tags_to_delete.values():
        project_tag_events[variant_tag.project_tag] = "delete_variant_tag"
        variant_tag.delete()


    # add the extra info after updating the tag info in the database, so that the new tag info is added to the variant JSON
    add_extra_info_to_variants_family(get_reference(), family, [variant,])

    # log tag creation
    for project_tag, event_type in project_tag_events.items():
        try:
            settings.EVENTS_COLLECTION.insert({
                'event_type': event_type,
                'date': timezone.now(),
                'project_id': ''.join(project.project_id),
                'family_id': family.family_id,
                'tag': project_tag.tag,
                'title': project_tag.title,

                'xpos':form.cleaned_data['xpos'],
                'pos':variant.pos,
                'chrom': variant.chr,
                'ref':form.cleaned_data['ref'],
                'alt':form.cleaned_data['alt'],
                'gene_names': ", ".join(variant.extras['gene_names'].values()),
                'username': request.user.username,
                'email': request.user.email,
                'search_url': form.cleaned_data.get('search_url'),
            })
        except Exception as e:
            logging.error("Error while logging add_variant_tag event: %s" % e)

    return JSONResponse({
        'is_error': False,
        'variant': variant.toJSON(),
    })