Index

A

add_doc() (in module vogue.tools.cli_utils) add_or_update_bioinfo_processed() (vogue.adapter.plugin.VogueAdapter method) add_or_update_bioinfo_raw() (vogue.adapter.plugin.VogueAdapter method)

add_or_update_bioinfo_samples() (vogue.adapter.plugin.VogueAdapter method) add_or_update_document() (vogue.adapter.plugin.VogueAdapter method) app_tag() (vogue.adapter.plugin.VogueAdapter method)

B

bioinfo_processed() (vogue.adapter.plugin.VogueAdapter method) bioinfo_raw() (vogue.adapter.plugin.VogueAdapter method) bioinfo_samples_aggregate() (vogue.adapter.plugin.VogueAdapter method) build_analysis() (in module vogue.build.bioinfo_analysis) build_application_tag() (in module vogue.build.application_tag) build_bioinfo_sample() (in module vogue.build.bioinfo_analysis) build_mip_dna_sample() (vogue.parse.build.sample_analysis.Mip_dna method)

build_mongo_case() (in module vogue.build.bioinfo_analysis) build_processed_case() (in module vogue.build.bioinfo_analysis) build_reagent_label() (in module vogue.build.reagent_label) build_reagent_label_category() (in module vogue.build.reagent_label_category) build_run() (in module vogue.build.flowcell) build_sample() (in module vogue.build.sample) build_unprocessed_case() (in module vogue.build.bioinfo_analysis) build_uSalt_sample() (vogue.parse.build.sample_analysis.uSalt method)

C

check_dates() (in module vogue.adapter.plugin) check_file() (in module vogue.tools.cli_utils)

concat_dict_keys() (in module vogue.tools.cli_utils) convert_defaultdict_to_regular_dict() (in module vogue.tools.cli_utils) convert_dot() (in module vogue.tools.cli_utils)

D

datetime2date() (in module vogue.parse.build.sample)

delete_sample() (vogue.adapter.plugin.VogueAdapter method) dict_replace_dot() (in module vogue.tools.cli_utils)

E

extract_valid_analysis() (in module vogue.build.bioinfo_analysis)

F

filter_none() (in module vogue.parse.build.flowcell) (in module vogue.parse.build.reagent_label) find_genotype_plate() (vogue.adapter.plugin.VogueAdapter method)

find_samples() (vogue.adapter.plugin.VogueAdapter method) flowcell() (vogue.adapter.plugin.VogueAdapter method) flowcells_aggregate() (vogue.adapter.plugin.VogueAdapter method)

G

genotype_analysis_aggregate() (vogue.adapter.plugin.VogueAdapter method) get_all_reagent_label_names_grouped_by_category() (vogue.adapter.plugin.VogueAdapter method) get_category() (vogue.adapter.plugin.VogueAdapter method) get_common_keys() (in module vogue.build.bioinfo_analysis) get_concentration_and_nr_defrosts() (in module vogue.parse.build.sample) get_define_step_data() (in module vogue.parse.build.reagent_label) get_final_conc_and_amount_dna() (in module vogue.parse.build.sample)

get_latest_analysis() (in module vogue.parse.build.sample_analysis) get_latest_input_artifact() (in module vogue.parse.build.sample) get_library_size() (in module vogue.parse.build.sample) get_microbial_library_concentration() (in module vogue.parse.build.sample) get_number_of_days() (in module vogue.parse.build.sample) get_output_artifact() (in module vogue.parse.build.sample) get_reagent_label_categories() (vogue.adapter.plugin.VogueAdapter method) get_reagent_label_category() (vogue.adapter.plugin.VogueAdapter method)

I

InsertError

inspect_analysis_result() (in module vogue.parse.load.bioinfo_analysis)

J

json_read() (in module vogue.tools.cli_utils)

L

load_all() (in module vogue.load.flowcell) (in module vogue.load.reagent_label) (in module vogue.load.reagent_label_category) (in module vogue.load.sample) load_all_dry() (in module vogue.load.sample) load_analysis() (in module vogue.load.bioinfo_analysis) load_aplication_tags() (in module vogue.load.application_tag)

load_one() (in module vogue.load.flowcell) (in module vogue.load.reagent_label) (in module vogue.load.sample) load_one_dry() (in module vogue.load.sample) load_recent() (in module vogue.load.flowcell) (in module vogue.load.reagent_label) (in module vogue.load.sample) load_sample() (in module vogue.load.genotype)

M

Mip_dna (class in vogue.parse.build.sample_analysis) MissingApplicationTag module vogue vogue.adapter vogue.adapter.plugin vogue.build vogue.build.application_tag vogue.build.bioinfo_analysis vogue.build.flowcell vogue.build.reagent_label vogue.build.reagent_label_category vogue.build.sample vogue.commands vogue.commands.base vogue.commands.load vogue.commands.load.application_tag vogue.commands.load.base vogue.commands.load.bioinfo vogue.commands.load.bioinfo.base vogue.commands.load.bioinfo.bioinfo_process vogue.commands.load.bioinfo.bioinfo_raw vogue.commands.load.bioinfo.bioinfo_sample vogue.commands.load.flowcell vogue.commands.load.genotype vogue.commands.load.reagent_label vogue.commands.load.reagent_label_category vogue.commands.load.sample vogue.constants vogue.constants.constants vogue.constants.lims_constants vogue.exceptions vogue.load vogue.load.application_tag vogue.load.bioinfo_analysis vogue.load.flowcell vogue.load.genotype vogue.load.reagent_label vogue.load.reagent_label_category vogue.load.sample vogue.models vogue.models.bioinfo_analysis vogue.parse vogue.parse.build vogue.parse.build.flowcell vogue.parse.build.reagent_label vogue.parse.build.sample vogue.parse.build.sample_analysis vogue.parse.load vogue.parse.load.bioinfo_analysis vogue.tools vogue.tools.cli_utils

R

reagent_label_aggregate() (vogue.adapter.plugin.VogueAdapter method) reagent_label_data() (in module vogue.parse.build.reagent_label)

recursive_default_dict() (in module vogue.tools.cli_utils) reduce_keys() (in module vogue.parse.build.sample_analysis) run_data() (in module vogue.parse.build.flowcell)

S

sample() (vogue.adapter.plugin.VogueAdapter method) sample_analysis() (vogue.adapter.plugin.VogueAdapter method) sample_collection_ids() (vogue.adapter.plugin.VogueAdapter method)

samples_aggregate() (vogue.adapter.plugin.VogueAdapter method) setup() (vogue.adapter.plugin.VogueAdapter method) str_to_datetime() (in module vogue.parse.build.sample)

U

update_mongo_doc_case() (in module vogue.build.bioinfo_analysis)

uSalt (class in vogue.parse.build.sample_analysis)

V

vogue module vogue.adapter module vogue.adapter.plugin module vogue.build module vogue.build.application_tag module vogue.build.bioinfo_analysis module vogue.build.flowcell module vogue.build.reagent_label module vogue.build.reagent_label_category module vogue.build.sample module vogue.commands module vogue.commands.base module vogue.commands.load module vogue.commands.load.application_tag module vogue.commands.load.base module vogue.commands.load.bioinfo module vogue.commands.load.bioinfo.base module vogue.commands.load.bioinfo.bioinfo_process module vogue.commands.load.bioinfo.bioinfo_raw module vogue.commands.load.bioinfo.bioinfo_sample module vogue.commands.load.flowcell module vogue.commands.load.genotype module vogue.commands.load.reagent_label module vogue.commands.load.reagent_label_category module vogue.commands.load.sample module

vogue.constants module vogue.constants.constants module vogue.constants.lims_constants module vogue.exceptions module vogue.load module vogue.load.application_tag module vogue.load.bioinfo_analysis module vogue.load.flowcell module vogue.load.genotype module vogue.load.reagent_label module vogue.load.reagent_label_category module vogue.load.sample module vogue.models module vogue.models.bioinfo_analysis module vogue.parse module vogue.parse.build module vogue.parse.build.flowcell module vogue.parse.build.reagent_label module vogue.parse.build.sample module vogue.parse.build.sample_analysis module vogue.parse.load module vogue.parse.load.bioinfo_analysis module vogue.tools module vogue.tools.cli_utils module VogueAdapter (class in vogue.adapter.plugin) VogueError VogueRestError

Y

yaml_read() (in module vogue.tools.cli_utils)