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How to use call_safe method in localstack

Best Python code snippet using localstack_python

variant.py

Source:variant.py

...110    parsed_variant["genetic_models"] = parse_genetic_models(111        variant.INFO.get("GeneticModels"), genmod_key112    )113    ################# Add autozygosity calls if present #################114    parsed_variant["azlength"] = call_safe(int, variant.INFO.get("AZLENGTH"))115    parsed_variant["azqual"] = call_safe(float, variant.INFO.get("AZQUAL"))116    ################ Add STR info if present ################117    # repeat id generally corresponds to gene symbol118    parsed_variant["str_repid"] = call_safe(str, variant.INFO.get("REPID"))119    # repeat unit - used e g in PanelApp naming of STRs120    parsed_variant["str_ru"] = call_safe(str, variant.INFO.get("RU"))121    # repeat unit - used e g in PanelApp naming of STRs122    parsed_variant["str_display_ru"] = call_safe(str, variant.INFO.get("DisplayRU"))123    # repeat ref - reference copy number124    parsed_variant["str_ref"] = call_safe(int, variant.INFO.get("REF"))125    # repeat len - number of repeats found in case126    parsed_variant["str_len"] = call_safe(int, variant.INFO.get("RL"))127    # str status - this indicates the severity of the expansion level128    parsed_variant["str_status"] = call_safe(str, variant.INFO.get("STR_STATUS"))129    # str normal max - max number of repeats to call an STR variant normal130    parsed_variant["str_normal_max"] = call_safe(int, variant.INFO.get("STR_NORMAL_MAX"))131    # str pathological min - min number of repeats to call an STR variant pathologic132    parsed_variant["str_pathologic_min"] = call_safe(int, variant.INFO.get("STR_PATHOLOGIC_MIN"))133    # str disease - disease name annotation134    parsed_variant["str_disease"] = call_safe(str, variant.INFO.get("Disease"))135    # str disease inheritance mode string annotation136    parsed_variant["str_inheritance_mode"] = call_safe(str, variant.INFO.get("InheritanceMode"))137    # str source dict with display string, source type and entry id138    set_source(parsed_variant, variant)139    parsed_variant["str_swegen_mean"] = call_safe(float, variant.INFO.get("SweGenMean"))140    parsed_variant["str_swegen_std"] = call_safe(float, variant.INFO.get("SweGenStd"))141    ################# Add somatic info ##################142    parsed_variant["somatic_score"] = call_safe(int, variant.INFO.get("SOMATICSCORE"))143    ################# Add mitomap info, from HmtNote #################144    set_mitomap_associated_diseases(parsed_variant, variant)145    ################# Add HmtVar variant id, from HmtNote #################146    add_hmtvar(parsed_variant, variant)147    ### Add custom info148    parsed_variant["custom"] = parse_custom_data(variant.INFO.get("SCOUT_CUSTOM"))149    ### Add gene and transcript information150    parsed_transcripts = add_gene_and_transcript_info(parsed_variant, variant, vep_header)151    ################# Add clinsig prediction #################152    set_clnsig(parsed_variant, variant, parsed_transcripts)153    ################# Add the frequencies #################154    frequencies = parse_frequencies(variant, parsed_transcripts)155    parsed_variant["frequencies"] = frequencies156    # SNVs contain INFO field Obs, SVs contain clinical_genomics_loqusObs157    local_obs_old = variant.INFO.get("Obs") or variant.INFO.get("clinical_genomics_loqusObs")158    if local_obs_old:159        parsed_variant["local_obs_old"] = int(local_obs_old)160    # SNVs only161    parsed_variant["local_obs_hom_old"] = call_safe(int, variant.INFO.get("Hom"))162    # SVs only163    parsed_variant["local_obs_old_freq"] = call_safe(164        float, variant.INFO.get("clinical_genomics_loqusFrq")165    )166    set_local_archive_info(parsed_variant, local_archive_info)167    if local_archive_info and "Date" in local_archive_info:168        parsed_variant["local_obs_old_date"] = local_archive_info.get("Date")169    if local_archive_info and "NrCases" in local_archive_info:170        parsed_variant["local_obs_old_nr_cases"] = local_archive_info.get("NrCases")171    if local_archive_info and "Description" in local_archive_info:172        parsed_variant["local_obs_old_desc"] = local_archive_info.get("Description")173    ###################### Add severity predictions ######################174    parsed_variant["cadd_score"] = parse_cadd(variant, parsed_transcripts)175    parsed_variant["spidex"] = call_safe(float, variant.INFO.get("SPIDEX"))176    if len(parsed_transcripts) > 0:177        parsed_variant["revel_score"] = parsed_transcripts[0].get(178            "revel"179        )  # This is actually the value of REVEL_rankscore180        parsed_variant["revel"] = parsed_transcripts[0].get(181            "revel_score"182        )  # This is actually the value of REVEL_score183    ###################### Add conservation ######################184    parsed_variant["conservation"] = parse_conservations(variant, parsed_transcripts)185    parsed_variant["callers"] = parse_callers(variant, category=category)186    set_rank_result(parsed_variant, variant, rank_results_header)187    ###################### Add SV specific annotations ######################188    sv_frequencies = parse_sv_frequencies(variant)189    for key in sv_frequencies:...

internal.py

Source:internal.py

...115    def on_get(self, request):116        from localstack.utils import diagnose117        return {118            "version": {119                "image-version": call_safe(diagnose.get_docker_image_details),120                "localstack-version": call_safe(diagnose.get_localstack_version),121                "host": {122                    "kernel": call_safe(diagnose.get_host_kernel_version),123                },124            },125            "services": call_safe(diagnose.get_service_stats),126            "config": call_safe(diagnose.get_localstack_config),127            "docker-inspect": call_safe(diagnose.inspect_main_container),128            "docker-dependent-image-hashes": call_safe(diagnose.get_important_image_hashes),129            "file-tree": call_safe(diagnose.get_file_tree),130            "important-endpoints": call_safe(diagnose.resolve_endpoints),131            "logs": call_safe(diagnose.get_localstack_logs),132        }133class LocalstackResources(Router):134    """135    Router for localstack-internal HTTP resources.136    """137    def __init__(self):138        super().__init__(dispatcher=resource_dispatcher(pass_response=False))139        self.add_default_routes()140        # TODO: load routes as plugins141    def add_default_routes(self):142        from localstack.services.plugins import SERVICE_PLUGINS143        health_resource = HealthResource(SERVICE_PLUGINS)144        graph_resource = ResourceGraph()145        # two special routes for legacy support (before `/_localstack` was introduced)...

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