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cc_toolchain_config.bzl

Source:cc_toolchain_config.bzl

1# Copyright 2019 The Bazel Authors. All rights reserved.2#3# Licensed under the Apache License, Version 2.0 (the "License");4# you may not use this file except in compliance with the License.5# You may obtain a copy of the License at6#7#    http://www.apache.org/licenses/LICENSE-2.08#9# Unless required by applicable law or agreed to in writing, software10# distributed under the License is distributed on an "AS IS" BASIS,11# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.12# See the License for the specific language governing permissions and13# limitations under the License.14"""A Starlark cc_toolchain configuration rule"""15load(16    "@bazel_tools//tools/cpp:cc_toolchain_config_lib.bzl",17    "action_config",18    "artifact_name_pattern",19    "env_entry",20    "env_set",21    "feature",22    "feature_set",23    "flag_group",24    "flag_set",25    "tool",26    "tool_path",27    "variable_with_value",28    "with_feature_set",29)30load("@bazel_tools//tools/build_defs/cc:action_names.bzl", "ACTION_NAMES")31all_compile_actions = [32    ACTION_NAMES.c_compile,33    ACTION_NAMES.cpp_compile,34    ACTION_NAMES.linkstamp_compile,35    ACTION_NAMES.assemble,36    ACTION_NAMES.preprocess_assemble,37    ACTION_NAMES.cpp_header_parsing,38    ACTION_NAMES.cpp_module_compile,39    ACTION_NAMES.cpp_module_codegen,40    ACTION_NAMES.clif_match,41    ACTION_NAMES.lto_backend,42]43all_cpp_compile_actions = [44    ACTION_NAMES.cpp_compile,45    ACTION_NAMES.linkstamp_compile,46    ACTION_NAMES.cpp_header_parsing,47    ACTION_NAMES.cpp_module_compile,48    ACTION_NAMES.cpp_module_codegen,49    ACTION_NAMES.clif_match,50]51preprocessor_compile_actions = [52    ACTION_NAMES.c_compile,53    ACTION_NAMES.cpp_compile,54    ACTION_NAMES.linkstamp_compile,55    ACTION_NAMES.preprocess_assemble,56    ACTION_NAMES.cpp_header_parsing,57    ACTION_NAMES.cpp_module_compile,58    ACTION_NAMES.clif_match,59]60codegen_compile_actions = [61    ACTION_NAMES.c_compile,62    ACTION_NAMES.cpp_compile,63    ACTION_NAMES.linkstamp_compile,64    ACTION_NAMES.assemble,65    ACTION_NAMES.preprocess_assemble,66    ACTION_NAMES.cpp_module_codegen,67    ACTION_NAMES.lto_backend,68]69all_link_actions = [70    ACTION_NAMES.cpp_link_executable,71    ACTION_NAMES.cpp_link_dynamic_library,72    ACTION_NAMES.cpp_link_nodeps_dynamic_library,73]74def _windows_msvc_impl(ctx):75    toolchain_identifier = "msvc_x64"76    host_system_name = "local"77    target_system_name = "local"78    target_cpu = "x64_windows"79    target_libc = "msvcrt"80    compiler = "msvc-cl"81    abi_version = "local"82    abi_libc_version = "local"83    cc_target_os = None84    builtin_sysroot = None85    cxx_builtin_include_directories = [86        "/usr/local/include",87        "/usr/local/lib/clang/7.0.0/include",88        "/usr/include/x86_64-linux-gnu",89        "/usr/include",90        "/usr/include/c++/4.9",91        "/usr/include/x86_64-linux-gnu/c++/4.9",92        "/usr/include/c++/4.9/backward",93    ]94    cpp_link_nodeps_dynamic_library_action = action_config(95        action_name = ACTION_NAMES.cpp_link_nodeps_dynamic_library,96        implies = [97            "nologo",98            "shared_flag",99            "linkstamps",100            "output_execpath_flags",101            "input_param_flags",102            "user_link_flags",103            "default_link_flags",104            "linker_subsystem_flag",105            "linker_param_file",106            "msvc_env",107            "no_stripping",108            "has_configured_linker_path",109            "def_file",110        ],111        tools = [tool(path = "")],112    )113    cpp_link_static_library_action = action_config(114        action_name = ACTION_NAMES.cpp_link_static_library,115        implies = [116            "nologo",117            "archiver_flags",118            "input_param_flags",119            "linker_param_file",120            "msvc_env",121        ],122        tools = [tool(path = "")],123    )124    assemble_action = action_config(125        action_name = ACTION_NAMES.assemble,126        implies = [127            "compiler_input_flags",128            "compiler_output_flags",129            "nologo",130            "msvc_env",131            "sysroot",132        ],133        tools = [tool(path = "")],134    )135    preprocess_assemble_action = action_config(136        action_name = ACTION_NAMES.preprocess_assemble,137        implies = [138            "compiler_input_flags",139            "compiler_output_flags",140            "nologo",141            "msvc_env",142            "sysroot",143        ],144        tools = [tool(path = "")],145    )146    c_compile_action = action_config(147        action_name = ACTION_NAMES.c_compile,148        implies = [149            "compiler_input_flags",150            "compiler_output_flags",151            "default_compile_flags",152            "nologo",153            "msvc_env",154            "parse_showincludes",155            "user_compile_flags",156            "sysroot",157            "unfiltered_compile_flags",158        ],159        tools = [tool(path = "")],160    )161    cpp_compile_action = action_config(162        action_name = ACTION_NAMES.cpp_compile,163        implies = [164            "compiler_input_flags",165            "compiler_output_flags",166            "default_compile_flags",167            "nologo",168            "msvc_env",169            "parse_showincludes",170            "user_compile_flags",171            "sysroot",172            "unfiltered_compile_flags",173        ],174        tools = [tool(path = "")],175    )176    cpp_link_executable_action = action_config(177        action_name = ACTION_NAMES.cpp_link_executable,178        implies = [179            "nologo",180            "linkstamps",181            "output_execpath_flags",182            "input_param_flags",183            "user_link_flags",184            "default_link_flags",185            "linker_subsystem_flag",186            "linker_param_file",187            "msvc_env",188            "no_stripping",189        ],190        tools = [tool(path = "")],191    )192    cpp_link_dynamic_library_action = action_config(193        action_name = ACTION_NAMES.cpp_link_dynamic_library,194        implies = [195            "nologo",196            "shared_flag",197            "linkstamps",198            "output_execpath_flags",199            "input_param_flags",200            "user_link_flags",201            "default_link_flags",202            "linker_subsystem_flag",203            "linker_param_file",204            "msvc_env",205            "no_stripping",206            "has_configured_linker_path",207            "def_file",208        ],209        tools = [tool(path = "")],210    )211    action_configs = [212        assemble_action,213        preprocess_assemble_action,214        c_compile_action,215        cpp_compile_action,216        cpp_link_executable_action,217        cpp_link_dynamic_library_action,218        cpp_link_nodeps_dynamic_library_action,219        cpp_link_static_library_action,220    ]221    msvc_link_env_feature = feature(222        name = "msvc_link_env",223        env_sets = [224            env_set(225                actions = all_link_actions +226                          [ACTION_NAMES.cpp_link_static_library],227                env_entries = [env_entry(key = "LIB", value = "")],228            ),229        ],230    )231    shared_flag_feature = feature(232        name = "shared_flag",233        flag_sets = [234            flag_set(235                actions = [236                    ACTION_NAMES.cpp_link_dynamic_library,237                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,238                ],239                flag_groups = [flag_group(flags = ["/DLL"])],240            ),241        ],242    )243    determinism_feature = feature(244        name = "determinism",245        enabled = True,246        flag_sets = [247            flag_set(248                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],249                flag_groups = [250                    flag_group(251                        flags = [252                            "/wd4117",253                            "-D__DATE__=\"redacted\"",254                            "-D__TIMESTAMP__=\"redacted\"",255                            "-D__TIME__=\"redacted\"",256                        ],257                    ),258                ],259            ),260        ],261    )262    sysroot_feature = feature(263        name = "sysroot",264        flag_sets = [265            flag_set(266                actions = [267                    ACTION_NAMES.assemble,268                    ACTION_NAMES.preprocess_assemble,269                    ACTION_NAMES.c_compile,270                    ACTION_NAMES.cpp_compile,271                    ACTION_NAMES.cpp_header_parsing,272                    ACTION_NAMES.cpp_module_compile,273                    ACTION_NAMES.cpp_module_codegen,274                    ACTION_NAMES.cpp_link_executable,275                    ACTION_NAMES.cpp_link_dynamic_library,276                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,277                ],278                flag_groups = [279                    flag_group(280                        flags = ["--sysroot=%{sysroot}"],281                        iterate_over = "sysroot",282                        expand_if_available = "sysroot",283                    ),284                ],285            ),286        ],287    )288    unfiltered_compile_flags_feature = feature(289        name = "unfiltered_compile_flags",290        flag_sets = [291            flag_set(292                actions = [293                    ACTION_NAMES.preprocess_assemble,294                    ACTION_NAMES.c_compile,295                    ACTION_NAMES.cpp_compile,296                    ACTION_NAMES.cpp_header_parsing,297                    ACTION_NAMES.cpp_module_compile,298                    ACTION_NAMES.cpp_module_codegen,299                ],300                flag_groups = [301                    flag_group(302                        flags = ["%{unfiltered_compile_flags}"],303                        iterate_over = "unfiltered_compile_flags",304                        expand_if_available = "unfiltered_compile_flags",305                    ),306                ],307            ),308        ],309    )310    copy_dynamic_libraries_to_binary_feature = feature(name = "copy_dynamic_libraries_to_binary")311    input_param_flags_feature = feature(312        name = "input_param_flags",313        flag_sets = [314            flag_set(315                actions = [316                    ACTION_NAMES.cpp_link_dynamic_library,317                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,318                ],319                flag_groups = [320                    flag_group(321                        flags = ["/IMPLIB:%{interface_library_output_path}"],322                        expand_if_available = "interface_library_output_path",323                    ),324                ],325            ),326            flag_set(327                actions = all_link_actions,328                flag_groups = [329                    flag_group(330                        flags = ["%{libopts}"],331                        iterate_over = "libopts",332                        expand_if_available = "libopts",333                    ),334                ],335            ),336            flag_set(337                actions = all_link_actions +338                          [ACTION_NAMES.cpp_link_static_library],339                flag_groups = [340                    flag_group(341                        iterate_over = "libraries_to_link",342                        flag_groups = [343                            flag_group(344                                iterate_over = "libraries_to_link.object_files",345                                flag_groups = [flag_group(flags = ["%{libraries_to_link.object_files}"])],346                                expand_if_equal = variable_with_value(347                                    name = "libraries_to_link.type",348                                    value = "object_file_group",349                                ),350                            ),351                            flag_group(352                                flag_groups = [flag_group(flags = ["%{libraries_to_link.name}"])],353                                expand_if_equal = variable_with_value(354                                    name = "libraries_to_link.type",355                                    value = "object_file",356                                ),357                            ),358                            flag_group(359                                flag_groups = [flag_group(flags = ["%{libraries_to_link.name}"])],360                                expand_if_equal = variable_with_value(361                                    name = "libraries_to_link.type",362                                    value = "interface_library",363                                ),364                            ),365                            flag_group(366                                flag_groups = [367                                    flag_group(368                                        flags = ["%{libraries_to_link.name}"],369                                        expand_if_false = "libraries_to_link.is_whole_archive",370                                    ),371                                    flag_group(372                                        flags = ["/WHOLEARCHIVE:%{libraries_to_link.name}"],373                                        expand_if_true = "libraries_to_link.is_whole_archive",374                                    ),375                                ],376                                expand_if_equal = variable_with_value(377                                    name = "libraries_to_link.type",378                                    value = "static_library",379                                ),380                            ),381                        ],382                        expand_if_available = "libraries_to_link",383                    ),384                ],385            ),386        ],387    )388    fastbuild_feature = feature(389        name = "fastbuild",390        flag_sets = [391            flag_set(392                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],393                flag_groups = [flag_group(flags = ["/Od", "/Z7"])],394            ),395            flag_set(396                actions = all_link_actions,397                flag_groups = [398                    flag_group(399                        flags = ["", "/INCREMENTAL:NO"],400                    ),401                ],402            ),403        ],404        implies = ["generate_pdb_file"],405    )406    user_compile_flags_feature = feature(407        name = "user_compile_flags",408        flag_sets = [409            flag_set(410                actions = [411                    ACTION_NAMES.preprocess_assemble,412                    ACTION_NAMES.c_compile,413                    ACTION_NAMES.cpp_compile,414                    ACTION_NAMES.cpp_header_parsing,415                    ACTION_NAMES.cpp_module_compile,416                    ACTION_NAMES.cpp_module_codegen,417                ],418                flag_groups = [419                    flag_group(420                        flags = ["%{user_compile_flags}"],421                        iterate_over = "user_compile_flags",422                        expand_if_available = "user_compile_flags",423                    ),424                ],425            ),426        ],427    )428    archiver_flags_feature = feature(429        name = "archiver_flags",430        flag_sets = [431            flag_set(432                actions = [ACTION_NAMES.cpp_link_static_library],433                flag_groups = [434                    flag_group(435                        flags = ["/OUT:%{output_execpath}"],436                        expand_if_available = "output_execpath",437                    ),438                ],439            ),440        ],441    )442    default_link_flags_feature = feature(443        name = "default_link_flags",444        enabled = True,445        flag_sets = [446            flag_set(447                actions = all_link_actions,448                flag_groups = [flag_group(flags = ["/MACHINE:X64"])],449            ),450        ],451    )452    static_link_msvcrt_feature = feature(name = "static_link_msvcrt")453    dynamic_link_msvcrt_debug_feature = feature(454        name = "dynamic_link_msvcrt_debug",455        flag_sets = [456            flag_set(457                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],458                flag_groups = [flag_group(flags = ["/MDd"])],459            ),460            flag_set(461                actions = all_link_actions,462                flag_groups = [flag_group(flags = ["/DEFAULTLIB:msvcrtd.lib"])],463            ),464        ],465        requires = [feature_set(features = ["dbg"])],466    )467    dbg_feature = feature(468        name = "dbg",469        flag_sets = [470            flag_set(471                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],472                flag_groups = [flag_group(flags = ["/Od", "/Z7"])],473            ),474            flag_set(475                actions = all_link_actions,476                flag_groups = [477                    flag_group(478                        flags = ["", "/INCREMENTAL:NO"],479                    ),480                ],481            ),482        ],483        implies = ["generate_pdb_file"],484    )485    opt_feature = feature(486        name = "opt",487        flag_sets = [488            flag_set(489                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],490                flag_groups = [flag_group(flags = ["/O2"])],491            ),492        ],493        implies = ["frame_pointer"],494    )495    supports_interface_shared_libraries_feature = feature(496        name = "supports_interface_shared_libraries",497        enabled = True,498    )499    user_link_flags_feature = feature(500        name = "user_link_flags",501        flag_sets = [502            flag_set(503                actions = all_link_actions,504                flag_groups = [505                    flag_group(506                        flags = ["%{user_link_flags}"],507                        iterate_over = "user_link_flags",508                        expand_if_available = "user_link_flags",509                    ),510                ],511            ),512        ],513    )514    default_compile_flags_feature = feature(515        name = "default_compile_flags",516        enabled = True,517        flag_sets = [518            flag_set(519                actions = [520                    ACTION_NAMES.assemble,521                    ACTION_NAMES.preprocess_assemble,522                    ACTION_NAMES.linkstamp_compile,523                    ACTION_NAMES.c_compile,524                    ACTION_NAMES.cpp_compile,525                    ACTION_NAMES.cpp_header_parsing,526                    ACTION_NAMES.cpp_module_compile,527                    ACTION_NAMES.cpp_module_codegen,528                    ACTION_NAMES.lto_backend,529                    ACTION_NAMES.clif_match,530                ],531                flag_groups = [532                    flag_group(533                        flags = [534                            "/DCOMPILER_MSVC",535                            "/DNOMINMAX",536                            "/D_WIN32_WINNT=0x0601",537                            "/D_CRT_SECURE_NO_DEPRECATE",538                            "/D_CRT_SECURE_NO_WARNINGS",539                            "/bigobj",540                            "/Zm500",541                            "/EHsc",542                            "/wd4351",543                            "/wd4291",544                            "/wd4250",545                            "/wd4996",546                        ],547                    ),548                ],549            ),550        ],551    )552    msvc_compile_env_feature = feature(553        name = "msvc_compile_env",554        env_sets = [555            env_set(556                actions = [557                    ACTION_NAMES.c_compile,558                    ACTION_NAMES.cpp_compile,559                    ACTION_NAMES.cpp_module_compile,560                    ACTION_NAMES.cpp_module_codegen,561                    ACTION_NAMES.cpp_header_parsing,562                    ACTION_NAMES.assemble,563                    ACTION_NAMES.preprocess_assemble,564                ],565                env_entries = [env_entry(key = "INCLUDE", value = "")],566            ),567        ],568    )569    preprocessor_defines_feature = feature(570        name = "preprocessor_defines",571        enabled = True,572        flag_sets = [573            flag_set(574                actions = [575                    ACTION_NAMES.assemble,576                    ACTION_NAMES.preprocess_assemble,577                    ACTION_NAMES.c_compile,578                    ACTION_NAMES.cpp_compile,579                    ACTION_NAMES.cpp_header_parsing,580                    ACTION_NAMES.cpp_module_compile,581                ],582                flag_groups = [583                    flag_group(584                        flags = ["/D%{preprocessor_defines}"],585                        iterate_over = "preprocessor_defines",586                    ),587                ],588            ),589        ],590    )591    generate_pdb_file_feature = feature(592        name = "generate_pdb_file",593        requires = [594            feature_set(features = ["dbg"]),595            feature_set(features = ["fastbuild"]),596        ],597    )598    output_execpath_flags_feature = feature(599        name = "output_execpath_flags",600        flag_sets = [601            flag_set(602                actions = all_link_actions,603                flag_groups = [604                    flag_group(605                        flags = ["/OUT:%{output_execpath}"],606                        expand_if_available = "output_execpath",607                    ),608                ],609            ),610        ],611    )612    dynamic_link_msvcrt_no_debug_feature = feature(613        name = "dynamic_link_msvcrt_no_debug",614        flag_sets = [615            flag_set(616                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],617                flag_groups = [flag_group(flags = ["/MD"])],618            ),619            flag_set(620                actions = all_link_actions,621                flag_groups = [flag_group(flags = ["/DEFAULTLIB:msvcrt.lib"])],622            ),623        ],624        requires = [625            feature_set(features = ["fastbuild"]),626            feature_set(features = ["opt"]),627        ],628    )629    disable_assertions_feature = feature(630        name = "disable_assertions",631        enabled = True,632        flag_sets = [633            flag_set(634                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],635                flag_groups = [flag_group(flags = ["/DNDEBUG"])],636                with_features = [with_feature_set(features = ["opt"])],637            ),638        ],639    )640    has_configured_linker_path_feature = feature(name = "has_configured_linker_path")641    supports_dynamic_linker_feature = feature(name = "supports_dynamic_linker", enabled = True)642    no_stripping_feature = feature(name = "no_stripping")643    linker_param_file_feature = feature(644        name = "linker_param_file",645        flag_sets = [646            flag_set(647                actions = all_link_actions +648                          [ACTION_NAMES.cpp_link_static_library],649                flag_groups = [650                    flag_group(651                        flags = ["@%{linker_param_file}"],652                        expand_if_available = "linker_param_file",653                    ),654                ],655            ),656        ],657    )658    ignore_noisy_warnings_feature = feature(659        name = "ignore_noisy_warnings",660        enabled = True,661        flag_sets = [662            flag_set(663                actions = [ACTION_NAMES.cpp_link_static_library],664                flag_groups = [flag_group(flags = ["/ignore:4221"])],665            ),666        ],667    )668    no_legacy_features_feature = feature(name = "no_legacy_features")669    parse_showincludes_feature = feature(670        name = "parse_showincludes",671        flag_sets = [672            flag_set(673                actions = [674                    ACTION_NAMES.preprocess_assemble,675                    ACTION_NAMES.c_compile,676                    ACTION_NAMES.cpp_compile,677                    ACTION_NAMES.cpp_module_compile,678                    ACTION_NAMES.cpp_header_parsing,679                ],680                flag_groups = [flag_group(flags = ["/showIncludes"])],681            ),682        ],683    )684    static_link_msvcrt_no_debug_feature = feature(685        name = "static_link_msvcrt_no_debug",686        flag_sets = [687            flag_set(688                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],689                flag_groups = [flag_group(flags = ["/MT"])],690            ),691            flag_set(692                actions = all_link_actions,693                flag_groups = [flag_group(flags = ["/DEFAULTLIB:libcmt.lib"])],694            ),695        ],696        requires = [697            feature_set(features = ["fastbuild"]),698            feature_set(features = ["opt"]),699        ],700    )701    treat_warnings_as_errors_feature = feature(702        name = "treat_warnings_as_errors",703        flag_sets = [704            flag_set(705                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],706                flag_groups = [flag_group(flags = ["/WX"])],707            ),708        ],709    )710    windows_export_all_symbols_feature = feature(name = "windows_export_all_symbols")711    no_windows_export_all_symbols_feature = feature(name = "no_windows_export_all_symbols")712    include_paths_feature = feature(713        name = "include_paths",714        enabled = True,715        flag_sets = [716            flag_set(717                actions = [718                    ACTION_NAMES.assemble,719                    ACTION_NAMES.preprocess_assemble,720                    ACTION_NAMES.c_compile,721                    ACTION_NAMES.cpp_compile,722                    ACTION_NAMES.cpp_header_parsing,723                    ACTION_NAMES.cpp_module_compile,724                ],725                flag_groups = [726                    flag_group(727                        flags = ["/I%{quote_include_paths}"],728                        iterate_over = "quote_include_paths",729                    ),730                    flag_group(731                        flags = ["/I%{include_paths}"],732                        iterate_over = "include_paths",733                    ),734                    flag_group(735                        flags = ["/I%{system_include_paths}"],736                        iterate_over = "system_include_paths",737                    ),738                ],739            ),740        ],741    )742    linkstamps_feature = feature(743        name = "linkstamps",744        flag_sets = [745            flag_set(746                actions = all_link_actions,747                flag_groups = [748                    flag_group(749                        flags = ["%{linkstamp_paths}"],750                        iterate_over = "linkstamp_paths",751                        expand_if_available = "linkstamp_paths",752                    ),753                ],754            ),755        ],756    )757    targets_windows_feature = feature(758        name = "targets_windows",759        enabled = True,760        implies = ["copy_dynamic_libraries_to_binary"],761    )762    linker_subsystem_flag_feature = feature(763        name = "linker_subsystem_flag",764        flag_sets = [765            flag_set(766                actions = all_link_actions,767                flag_groups = [flag_group(flags = ["/SUBSYSTEM:CONSOLE"])],768            ),769        ],770    )771    static_link_msvcrt_debug_feature = feature(772        name = "static_link_msvcrt_debug",773        flag_sets = [774            flag_set(775                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],776                flag_groups = [flag_group(flags = ["/MTd"])],777            ),778            flag_set(779                actions = all_link_actions,780                flag_groups = [flag_group(flags = ["/DEFAULTLIB:libcmtd.lib"])],781            ),782        ],783        requires = [feature_set(features = ["dbg"])],784    )785    frame_pointer_feature = feature(786        name = "frame_pointer",787        flag_sets = [788            flag_set(789                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],790                flag_groups = [flag_group(flags = ["/Oy-"])],791            ),792        ],793    )794    compiler_output_flags_feature = feature(795        name = "compiler_output_flags",796        flag_sets = [797            flag_set(798                actions = [ACTION_NAMES.assemble],799                flag_groups = [800                    flag_group(801                        flag_groups = [802                            flag_group(803                                flags = ["/Fo%{output_file}", "/Zi"],804                                expand_if_available = "output_file",805                                expand_if_not_available = "output_assembly_file",806                            ),807                        ],808                        expand_if_not_available = "output_preprocess_file",809                    ),810                ],811            ),812            flag_set(813                actions = [814                    ACTION_NAMES.preprocess_assemble,815                    ACTION_NAMES.c_compile,816                    ACTION_NAMES.cpp_compile,817                    ACTION_NAMES.cpp_header_parsing,818                    ACTION_NAMES.cpp_module_compile,819                    ACTION_NAMES.cpp_module_codegen,820                ],821                flag_groups = [822                    flag_group(823                        flag_groups = [824                            flag_group(825                                flags = ["/Fo%{output_file}"],826                                expand_if_not_available = "output_preprocess_file",827                            ),828                        ],829                        expand_if_available = "output_file",830                        expand_if_not_available = "output_assembly_file",831                    ),832                    flag_group(833                        flag_groups = [834                            flag_group(835                                flags = ["/Fa%{output_file}"],836                                expand_if_available = "output_assembly_file",837                            ),838                        ],839                        expand_if_available = "output_file",840                    ),841                    flag_group(842                        flag_groups = [843                            flag_group(844                                flags = ["/P", "/Fi%{output_file}"],845                                expand_if_available = "output_preprocess_file",846                            ),847                        ],848                        expand_if_available = "output_file",849                    ),850                ],851            ),852        ],853    )854    nologo_feature = feature(855        name = "nologo",856        flag_sets = [857            flag_set(858                actions = [859                    ACTION_NAMES.c_compile,860                    ACTION_NAMES.cpp_compile,861                    ACTION_NAMES.cpp_module_compile,862                    ACTION_NAMES.cpp_module_codegen,863                    ACTION_NAMES.cpp_header_parsing,864                    ACTION_NAMES.assemble,865                    ACTION_NAMES.preprocess_assemble,866                    ACTION_NAMES.cpp_link_executable,867                    ACTION_NAMES.cpp_link_dynamic_library,868                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,869                    ACTION_NAMES.cpp_link_static_library,870                ],871                flag_groups = [flag_group(flags = ["/nologo"])],872            ),873        ],874    )875    smaller_binary_feature = feature(876        name = "smaller_binary",877        enabled = True,878        flag_sets = [879            flag_set(880                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],881                flag_groups = [flag_group(flags = ["/Gy", "/Gw"])],882                with_features = [with_feature_set(features = ["opt"])],883            ),884            flag_set(885                actions = all_link_actions,886                flag_groups = [flag_group(flags = ["/OPT:ICF", "/OPT:REF"])],887                with_features = [with_feature_set(features = ["opt"])],888            ),889        ],890    )891    compiler_input_flags_feature = feature(892        name = "compiler_input_flags",893        flag_sets = [894            flag_set(895                actions = [896                    ACTION_NAMES.assemble,897                    ACTION_NAMES.preprocess_assemble,898                    ACTION_NAMES.c_compile,899                    ACTION_NAMES.cpp_compile,900                    ACTION_NAMES.cpp_header_parsing,901                    ACTION_NAMES.cpp_module_compile,902                    ACTION_NAMES.cpp_module_codegen,903                ],904                flag_groups = [905                    flag_group(906                        flags = ["/c", "%{source_file}"],907                        expand_if_available = "source_file",908                    ),909                ],910            ),911        ],912    )913    def_file_feature = feature(914        name = "def_file",915        flag_sets = [916            flag_set(917                actions = all_link_actions,918                flag_groups = [919                    flag_group(920                        flags = ["/DEF:%{def_file_path}", "/ignore:4070"],921                        expand_if_available = "def_file_path",922                    ),923                ],924            ),925        ],926    )927    msvc_env_feature = feature(928        name = "msvc_env",929        env_sets = [930            env_set(931                actions = [932                    ACTION_NAMES.c_compile,933                    ACTION_NAMES.cpp_compile,934                    ACTION_NAMES.cpp_module_compile,935                    ACTION_NAMES.cpp_module_codegen,936                    ACTION_NAMES.cpp_header_parsing,937                    ACTION_NAMES.assemble,938                    ACTION_NAMES.preprocess_assemble,939                    ACTION_NAMES.cpp_link_executable,940                    ACTION_NAMES.cpp_link_dynamic_library,941                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,942                    ACTION_NAMES.cpp_link_static_library,943                ],944                env_entries = [945                    env_entry(key = "PATH", value = ""),946                    env_entry(key = "TMP", value = ""),947                    env_entry(key = "TEMP", value = ""),948                ],949            ),950        ],951        implies = ["msvc_compile_env", "msvc_link_env"],952    )953    features = [954        no_legacy_features_feature,955        nologo_feature,956        has_configured_linker_path_feature,957        no_stripping_feature,958        targets_windows_feature,959        copy_dynamic_libraries_to_binary_feature,960        default_compile_flags_feature,961        msvc_env_feature,962        msvc_compile_env_feature,963        msvc_link_env_feature,964        include_paths_feature,965        preprocessor_defines_feature,966        parse_showincludes_feature,967        generate_pdb_file_feature,968        shared_flag_feature,969        linkstamps_feature,970        output_execpath_flags_feature,971        archiver_flags_feature,972        input_param_flags_feature,973        linker_subsystem_flag_feature,974        user_link_flags_feature,975        default_link_flags_feature,976        linker_param_file_feature,977        static_link_msvcrt_feature,978        static_link_msvcrt_no_debug_feature,979        dynamic_link_msvcrt_no_debug_feature,980        static_link_msvcrt_debug_feature,981        dynamic_link_msvcrt_debug_feature,982        dbg_feature,983        fastbuild_feature,984        opt_feature,985        frame_pointer_feature,986        disable_assertions_feature,987        determinism_feature,988        treat_warnings_as_errors_feature,989        smaller_binary_feature,990        ignore_noisy_warnings_feature,991        user_compile_flags_feature,992        sysroot_feature,993        unfiltered_compile_flags_feature,994        compiler_output_flags_feature,995        compiler_input_flags_feature,996        def_file_feature,997        windows_export_all_symbols_feature,998        no_windows_export_all_symbols_feature,999        supports_dynamic_linker_feature,1000        supports_interface_shared_libraries_feature,1001    ]1002    artifact_name_patterns = [1003        artifact_name_pattern(1004            category_name = "object_file",1005            prefix = "",1006            extension = ".obj",1007        ),1008        artifact_name_pattern(1009            category_name = "static_library",1010            prefix = "",1011            extension = ".lib",1012        ),1013        artifact_name_pattern(1014            category_name = "alwayslink_static_library",1015            prefix = "",1016            extension = ".lo.lib",1017        ),1018        artifact_name_pattern(1019            category_name = "executable",1020            prefix = "",1021            extension = ".exe",1022        ),1023        artifact_name_pattern(1024            category_name = "dynamic_library",1025            prefix = "",1026            extension = ".dll",1027        ),1028        artifact_name_pattern(1029            category_name = "interface_library",1030            prefix = "",1031            extension = ".if.lib",1032        ),1033    ]1034    make_variables = []1035    tool_paths = [1036        tool_path(name = "ar", path = ""),1037        tool_path(name = "ml", path = ""),1038        tool_path(name = "cpp", path = ""),1039        tool_path(name = "gcc", path = ""),1040        tool_path(name = "gcov", path = "wrapper/bin/msvc_nop.bat"),1041        tool_path(name = "ld", path = ""),1042        tool_path(name = "nm", path = "wrapper/bin/msvc_nop.bat"),1043        tool_path(1044            name = "objcopy",1045            path = "wrapper/bin/msvc_nop.bat",1046        ),1047        tool_path(1048            name = "objdump",1049            path = "wrapper/bin/msvc_nop.bat",1050        ),1051        tool_path(1052            name = "strip",1053            path = "wrapper/bin/msvc_nop.bat",1054        ),1055    ]1056    return cc_common.create_cc_toolchain_config_info(1057        ctx = ctx,1058        features = features,1059        action_configs = action_configs,1060        artifact_name_patterns = artifact_name_patterns,1061        cxx_builtin_include_directories = cxx_builtin_include_directories,1062        toolchain_identifier = toolchain_identifier,1063        host_system_name = host_system_name,1064        target_system_name = target_system_name,1065        target_cpu = target_cpu,1066        target_libc = target_libc,1067        compiler = compiler,1068        abi_version = abi_version,1069        abi_libc_version = abi_libc_version,1070        tool_paths = tool_paths,1071        make_variables = make_variables,1072        builtin_sysroot = builtin_sysroot,1073        cc_target_os = None,1074    )1075def _windows_msys_mingw_impl(ctx):1076    toolchain_identifier = "msys_x64_mingw"1077    host_system_name = "local"1078    target_system_name = "local"1079    target_cpu = "x64_windows"1080    target_libc = "mingw"1081    compiler = "mingw-gcc"1082    abi_version = "local"1083    abi_libc_version = "local"1084    cc_target_os = None1085    builtin_sysroot = None1086    action_configs = []1087    targets_windows_feature = feature(1088        name = "targets_windows",1089        implies = ["copy_dynamic_libraries_to_binary"],1090        enabled = True,1091    )1092    copy_dynamic_libraries_to_binary_feature = feature(name = "copy_dynamic_libraries_to_binary")1093    gcc_env_feature = feature(1094        name = "gcc_env",1095        enabled = True,1096        env_sets = [1097            env_set(1098                actions = [1099                    ACTION_NAMES.c_compile,1100                    ACTION_NAMES.cpp_compile,1101                    ACTION_NAMES.cpp_module_compile,1102                    ACTION_NAMES.cpp_module_codegen,1103                    ACTION_NAMES.cpp_header_parsing,1104                    ACTION_NAMES.assemble,1105                    ACTION_NAMES.preprocess_assemble,1106                    ACTION_NAMES.cpp_link_executable,1107                    ACTION_NAMES.cpp_link_dynamic_library,1108                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,1109                    ACTION_NAMES.cpp_link_static_library,1110                ],1111                env_entries = [1112                    env_entry(key = "PATH", value = "NOT_USED"),1113                ],1114            ),1115        ],1116    )1117    msys_mingw_flags = [1118    ]1119    msys_mingw_link_flags = [1120    ]1121    default_compile_flags_feature = feature(1122        name = "default_compile_flags",1123        enabled = True,1124        flag_sets = [1125            flag_set(1126                actions = [1127                    ACTION_NAMES.assemble,1128                    ACTION_NAMES.preprocess_assemble,1129                    ACTION_NAMES.linkstamp_compile,1130                    ACTION_NAMES.c_compile,1131                    ACTION_NAMES.cpp_compile,1132                    ACTION_NAMES.cpp_header_parsing,1133                    ACTION_NAMES.cpp_module_compile,1134                    ACTION_NAMES.cpp_module_codegen,1135                    ACTION_NAMES.lto_backend,1136                    ACTION_NAMES.clif_match,1137                ],1138            ),1139            flag_set(1140                actions = [1141                    ACTION_NAMES.linkstamp_compile,1142                    ACTION_NAMES.cpp_compile,1143                    ACTION_NAMES.cpp_header_parsing,1144                    ACTION_NAMES.cpp_module_compile,1145                    ACTION_NAMES.cpp_module_codegen,1146                    ACTION_NAMES.lto_backend,1147                    ACTION_NAMES.clif_match,1148                ],1149                flag_groups = ([flag_group(flags = msys_mingw_flags)] if msys_mingw_flags else []),1150            ),1151        ],1152    )1153    default_link_flags_feature = feature(1154        name = "default_link_flags",1155        enabled = True,1156        flag_sets = [1157            flag_set(1158                actions = all_link_actions,1159                flag_groups = ([flag_group(flags = msys_mingw_link_flags)] if msys_mingw_link_flags else []),1160            ),1161        ],1162    )1163    supports_dynamic_linker_feature = feature(name = "supports_dynamic_linker", enabled = True)1164    features = [1165        targets_windows_feature,1166        copy_dynamic_libraries_to_binary_feature,1167        gcc_env_feature,1168        default_compile_flags_feature,1169        default_link_flags_feature,1170        supports_dynamic_linker_feature,1171    ]1172    cxx_builtin_include_directories = [1173    ]1174    artifact_name_patterns = [1175        artifact_name_pattern(1176            category_name = "executable",1177            prefix = "",1178            extension = ".exe",1179        ),1180    ]1181    make_variables = []1182    tool_paths = [1183    ]1184    return cc_common.create_cc_toolchain_config_info(1185        ctx = ctx,1186        features = features,1187        action_configs = action_configs,1188        artifact_name_patterns = artifact_name_patterns,1189        cxx_builtin_include_directories = cxx_builtin_include_directories,1190        toolchain_identifier = toolchain_identifier,1191        host_system_name = host_system_name,1192        target_system_name = target_system_name,1193        target_cpu = target_cpu,1194        target_libc = target_libc,1195        compiler = compiler,1196        abi_version = abi_version,1197        abi_libc_version = abi_libc_version,1198        tool_paths = tool_paths,1199        make_variables = make_variables,1200        builtin_sysroot = builtin_sysroot,1201        cc_target_os = cc_target_os,1202    )1203def _armeabi_impl(ctx):1204    toolchain_identifier = "stub_armeabi-v7a"1205    host_system_name = "armeabi-v7a"1206    target_system_name = "armeabi-v7a"1207    target_cpu = "armeabi-v7a"1208    target_libc = "armeabi-v7a"1209    compiler = "compiler"1210    abi_version = "armeabi-v7a"1211    abi_libc_version = "armeabi-v7a"1212    cc_target_os = None1213    builtin_sysroot = None1214    action_configs = []1215    supports_pic_feature = feature(name = "supports_pic", enabled = True)1216    supports_dynamic_linker_feature = feature(name = "supports_dynamic_linker", enabled = True)1217    features = [supports_dynamic_linker_feature, supports_pic_feature]1218    cxx_builtin_include_directories = []1219    artifact_name_patterns = []1220    make_variables = []1221    tool_paths = [1222        tool_path(name = "ar", path = "/bin/false"),1223        tool_path(name = "compat-ld", path = "/bin/false"),1224        tool_path(name = "cpp", path = "/bin/false"),1225        tool_path(name = "dwp", path = "/bin/false"),1226        tool_path(name = "gcc", path = "/bin/false"),1227        tool_path(name = "gcov", path = "/bin/false"),1228        tool_path(name = "ld", path = "/bin/false"),1229        tool_path(name = "nm", path = "/bin/false"),1230        tool_path(name = "objcopy", path = "/bin/false"),1231        tool_path(name = "objdump", path = "/bin/false"),1232        tool_path(name = "strip", path = "/bin/false"),1233    ]1234    return cc_common.create_cc_toolchain_config_info(1235        ctx = ctx,1236        features = features,1237        action_configs = action_configs,1238        artifact_name_patterns = artifact_name_patterns,1239        cxx_builtin_include_directories = cxx_builtin_include_directories,1240        toolchain_identifier = toolchain_identifier,1241        host_system_name = host_system_name,1242        target_system_name = target_system_name,1243        target_cpu = target_cpu,1244        target_libc = target_libc,1245        compiler = compiler,1246        abi_version = abi_version,1247        abi_libc_version = abi_libc_version,1248        tool_paths = tool_paths,1249        make_variables = make_variables,1250        builtin_sysroot = builtin_sysroot,1251        cc_target_os = cc_target_os,1252    )1253def _impl(ctx):1254    if ctx.attr.cpu == "armeabi-v7a":1255        return _armeabi_impl(ctx)1256    elif ctx.attr.cpu == "x64_windows" and ctx.attr.compiler == "msvc-cl":1257        return _windows_msvc_impl(ctx)1258    elif ctx.attr.cpu == "x64_windows" and ctx.attr.compiler == "mingw-gcc":1259        return _windows_msys_mingw_impl(ctx)1260    tool_paths = [1261        tool_path(name = "ar", path = "/usr/bin/ar"),1262        tool_path(name = "ld", path = "/usr/bin/ld"),1263        tool_path(name = "cpp", path = "/usr/bin/cpp"),1264        tool_path(name = "gcc", path = "/usr/local/bin/clang"),1265        tool_path(name = "dwp", path = "/usr/bin/dwp"),1266        tool_path(name = "gcov", path = "None"),1267        tool_path(name = "nm", path = "/usr/bin/nm"),1268        tool_path(name = "objcopy", path = "/usr/bin/objcopy"),1269        tool_path(name = "objdump", path = "/usr/bin/objdump"),1270        tool_path(name = "strip", path = "/usr/bin/strip"),1271    ]1272    cxx_builtin_include_directories = [1273        "/usr/local/include",1274        "/usr/local/lib/clang/7.0.0/include",1275        "/usr/include/x86_64-linux-gnu",1276        "/usr/include",1277        "/usr/include/c++/4.9",1278        "/usr/include/x86_64-linux-gnu/c++/4.9",1279        "/usr/include/c++/4.9/backward",1280    ]1281    action_configs = []1282    compile_flags = [1283        "-U_FORTIFY_SOURCE",1284        "-fstack-protector",1285        "-Wall",1286        "-Wthread-safety",1287        "-Wself-assign",1288        "-fcolor-diagnostics",1289        "-fno-omit-frame-pointer",1290    ]1291    dbg_compile_flags = [1292        "-g",1293    ]1294    opt_compile_flags = [1295        "-g0",1296        "-O2",1297        "-D_FORTIFY_SOURCE=1",1298        "-DNDEBUG",1299        "-ffunction-sections",1300        "-fdata-sections",1301    ]1302    cxx_flags = [1303        "-std=c++0x",1304    ]1305    link_flags = [1306        "-fuse-ld=gold",1307        "-Wl,-no-as-needed",1308        "-Wl,-z,relro,-z,now",1309        "-B/usr/local/bin",1310        "-lstdc++",1311        "-lm",1312    ]1313    opt_link_flags = [1314        "-Wl,--gc-sections",1315    ]1316    unfiltered_compile_flags = [1317        "-no-canonical-prefixes",1318        "-Wno-builtin-macro-redefined",1319        "-D__DATE__=\"redacted\"",1320        "-D__TIMESTAMP__=\"redacted\"",1321        "-D__TIME__=\"redacted\"",1322    ]1323    targets_windows_feature = feature(1324        name = "targets_windows",1325        implies = ["copy_dynamic_libraries_to_binary"],1326        enabled = True,1327    )1328    copy_dynamic_libraries_to_binary_feature = feature(name = "copy_dynamic_libraries_to_binary")1329    gcc_env_feature = feature(1330        name = "gcc_env",1331        enabled = True,1332        env_sets = [1333            env_set(1334                actions = [1335                    ACTION_NAMES.c_compile,1336                    ACTION_NAMES.cpp_compile,1337                    ACTION_NAMES.cpp_module_compile,1338                    ACTION_NAMES.cpp_module_codegen,1339                    ACTION_NAMES.cpp_header_parsing,1340                    ACTION_NAMES.assemble,1341                    ACTION_NAMES.preprocess_assemble,1342                    ACTION_NAMES.cpp_link_executable,1343                    ACTION_NAMES.cpp_link_dynamic_library,1344                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,1345                    ACTION_NAMES.cpp_link_static_library,1346                ],1347                env_entries = [1348                    env_entry(key = "PATH", value = "NOT_USED"),1349                ],1350            ),1351        ],1352    )1353    windows_features = [1354        targets_windows_feature,1355        copy_dynamic_libraries_to_binary_feature,1356        gcc_env_feature,1357    ]1358    coverage_feature = feature(1359        name = "coverage",1360        provides = ["profile"],1361        flag_sets = [1362            flag_set(1363                actions = [1364                    ACTION_NAMES.preprocess_assemble,1365                    ACTION_NAMES.c_compile,1366                    ACTION_NAMES.cpp_compile,1367                    ACTION_NAMES.cpp_header_parsing,1368                    ACTION_NAMES.cpp_module_compile,1369                ],1370                flag_groups = [1371                    flag_group(flags = ["--coverage"]),1372                ],1373            ),1374            flag_set(1375                actions = [1376                    ACTION_NAMES.cpp_link_dynamic_library,1377                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,1378                    ACTION_NAMES.cpp_link_executable,1379                ],1380                flag_groups = [1381                    flag_group(flags = ["--coverage"]),1382                ],1383            ),1384        ],1385    )1386    supports_pic_feature = feature(1387        name = "supports_pic",1388        enabled = True,1389    )1390    supports_start_end_lib_feature = feature(1391        name = "supports_start_end_lib",1392        enabled = True,1393    )1394    default_compile_flags_feature = feature(1395        name = "default_compile_flags",1396        enabled = True,1397        flag_sets = [1398            flag_set(1399                actions = [1400                    ACTION_NAMES.assemble,1401                    ACTION_NAMES.preprocess_assemble,1402                    ACTION_NAMES.linkstamp_compile,1403                    ACTION_NAMES.c_compile,1404                    ACTION_NAMES.cpp_compile,1405                    ACTION_NAMES.cpp_header_parsing,1406                    ACTION_NAMES.cpp_module_compile,1407                    ACTION_NAMES.cpp_module_codegen,1408                    ACTION_NAMES.lto_backend,1409                    ACTION_NAMES.clif_match,1410                ],1411                flag_groups = ([flag_group(flags = compile_flags)] if compile_flags else []),1412            ),1413            flag_set(1414                actions = [1415                    ACTION_NAMES.assemble,1416                    ACTION_NAMES.preprocess_assemble,1417                    ACTION_NAMES.linkstamp_compile,1418                    ACTION_NAMES.c_compile,1419                    ACTION_NAMES.cpp_compile,1420                    ACTION_NAMES.cpp_header_parsing,1421                    ACTION_NAMES.cpp_module_compile,1422                    ACTION_NAMES.cpp_module_codegen,1423                    ACTION_NAMES.lto_backend,1424                    ACTION_NAMES.clif_match,1425                ],1426                flag_groups = ([flag_group(flags = dbg_compile_flags)] if dbg_compile_flags else []),1427                with_features = [with_feature_set(features = ["dbg"])],1428            ),1429            flag_set(1430                actions = [1431                    ACTION_NAMES.assemble,1432                    ACTION_NAMES.preprocess_assemble,1433                    ACTION_NAMES.linkstamp_compile,1434                    ACTION_NAMES.c_compile,1435                    ACTION_NAMES.cpp_compile,1436                    ACTION_NAMES.cpp_header_parsing,1437                    ACTION_NAMES.cpp_module_compile,1438                    ACTION_NAMES.cpp_module_codegen,1439                    ACTION_NAMES.lto_backend,1440                    ACTION_NAMES.clif_match,1441                ],1442                flag_groups = ([flag_group(flags = opt_compile_flags)] if opt_compile_flags else []),1443                with_features = [with_feature_set(features = ["opt"])],1444            ),1445            flag_set(1446                actions = [1447                    ACTION_NAMES.linkstamp_compile,1448                    ACTION_NAMES.cpp_compile,1449                    ACTION_NAMES.cpp_header_parsing,1450                    ACTION_NAMES.cpp_module_compile,1451                    ACTION_NAMES.cpp_module_codegen,1452                    ACTION_NAMES.lto_backend,1453                    ACTION_NAMES.clif_match,1454                ],1455                flag_groups = ([flag_group(flags = cxx_flags)] if cxx_flags else []),1456            ),1457        ],1458    )1459    default_link_flags_feature = feature(1460        name = "default_link_flags",1461        enabled = True,1462        flag_sets = [1463            flag_set(1464                actions = all_link_actions,1465                flag_groups = ([flag_group(flags = link_flags)] if link_flags else []),1466            ),1467            flag_set(1468                actions = all_link_actions,1469                flag_groups = ([flag_group(flags = opt_link_flags)] if opt_link_flags else []),1470                with_features = [with_feature_set(features = ["opt"])],1471            ),1472        ],1473    )1474    dbg_feature = feature(name = "dbg")1475    opt_feature = feature(name = "opt")1476    sysroot_feature = feature(1477        name = "sysroot",1478        enabled = True,1479        flag_sets = [1480            flag_set(1481                actions = [1482                    ACTION_NAMES.preprocess_assemble,1483                    ACTION_NAMES.linkstamp_compile,1484                    ACTION_NAMES.c_compile,1485                    ACTION_NAMES.cpp_compile,1486                    ACTION_NAMES.cpp_header_parsing,1487                    ACTION_NAMES.cpp_module_compile,1488                    ACTION_NAMES.cpp_module_codegen,1489                    ACTION_NAMES.lto_backend,1490                    ACTION_NAMES.clif_match,1491                    ACTION_NAMES.cpp_link_executable,1492                    ACTION_NAMES.cpp_link_dynamic_library,1493                    ACTION_NAMES.cpp_link_nodeps_dynamic_library,1494                ],1495                flag_groups = [1496                    flag_group(1497                        flags = ["--sysroot=%{sysroot}"],1498                        expand_if_available = "sysroot",1499                    ),1500                ],1501            ),1502        ],1503    )1504    fdo_optimize_feature = feature(1505        name = "fdo_optimize",1506        flag_sets = [1507            flag_set(1508                actions = [ACTION_NAMES.c_compile, ACTION_NAMES.cpp_compile],1509                flag_groups = [1510                    flag_group(1511                        flags = [1512                            "-fprofile-use=%{fdo_profile_path}",1513                            "-fprofile-correction",1514                        ],1515                        expand_if_available = "fdo_profile_path",1516                    ),1517                ],1518            ),1519        ],1520        provides = ["profile"],1521    )1522    supports_dynamic_linker_feature = feature(name = "supports_dynamic_linker", enabled = True)1523    user_compile_flags_feature = feature(1524        name = "user_compile_flags",1525        enabled = True,1526        flag_sets = [1527            flag_set(1528                actions = [1529                    ACTION_NAMES.assemble,1530                    ACTION_NAMES.preprocess_assemble,1531                    ACTION_NAMES.linkstamp_compile,1532                    ACTION_NAMES.c_compile,1533                    ACTION_NAMES.cpp_compile,1534                    ACTION_NAMES.cpp_header_parsing,1535                    ACTION_NAMES.cpp_module_compile,1536                    ACTION_NAMES.cpp_module_codegen,1537                    ACTION_NAMES.lto_backend,1538                    ACTION_NAMES.clif_match,1539                ],1540                flag_groups = [1541                    flag_group(1542                        flags = ["%{user_compile_flags}"],1543                        iterate_over = "user_compile_flags",1544                        expand_if_available = "user_compile_flags",1545                    ),1546                ],1547            ),1548        ],1549    )1550    unfiltered_compile_flags_feature = feature(1551        name = "unfiltered_compile_flags",1552        enabled = True,1553        flag_sets = [1554            flag_set(1555                actions = [1556                    ACTION_NAMES.assemble,1557                    ACTION_NAMES.preprocess_assemble,1558                    ACTION_NAMES.linkstamp_compile,1559                    ACTION_NAMES.c_compile,1560                    ACTION_NAMES.cpp_compile,1561                    ACTION_NAMES.cpp_header_parsing,1562                    ACTION_NAMES.cpp_module_compile,1563                    ACTION_NAMES.cpp_module_codegen,1564                    ACTION_NAMES.lto_backend,1565                    ACTION_NAMES.clif_match,1566                ],1567                flag_groups = ([flag_group(flags = unfiltered_compile_flags)] if unfiltered_compile_flags else []),1568            ),1569        ],1570    )1571    features = [1572        supports_pic_feature,1573        supports_start_end_lib_feature,1574        coverage_feature,1575        default_compile_flags_feature,1576        default_link_flags_feature,1577        fdo_optimize_feature,1578        supports_dynamic_linker_feature,1579        dbg_feature,1580        opt_feature,1581        user_compile_flags_feature,1582        sysroot_feature,1583        unfiltered_compile_flags_feature,1584    ]1585    artifact_name_patterns = [1586    ]1587    make_variables = []1588    return cc_common.create_cc_toolchain_config_info(1589        ctx = ctx,1590        features = features,1591        action_configs = action_configs,1592        artifact_name_patterns = artifact_name_patterns,1593        cxx_builtin_include_directories = cxx_builtin_include_directories,1594        toolchain_identifier = "linux_gnu_x86",1595        host_system_name = "i686-unknown-linux-gnu",1596        target_system_name = "x86_64-unknown-linux-gnu",1597        target_cpu = "k8",1598        target_libc = "glibc_2.19",1599        compiler = "clang",1600        abi_version = "gcc",1601        abi_libc_version = "glibc_2.19",1602        tool_paths = tool_paths,1603        make_variables = make_variables,1604        builtin_sysroot = "",1605        cc_target_os = None,1606    )1607cc_toolchain_config = rule(1608    implementation = _impl,1609    attrs = {1610        "cpu": attr.string(mandatory = True),1611        "compiler": attr.string(),1612    },1613    provides = [CcToolchainConfigInfo],...

save_plan_step_data.py

Source:save_plan_step_data.py

1# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved2from django.utils.translation import ugettext as _3from django.core.urlresolvers import reverse4from iondb.rundb.plan.page_plan.kits_step_data import KitsFieldNames5from iondb.rundb.plan.page_plan.abstract_step_data import AbstractStepData6from iondb.rundb.models import (7    dnaBarcode,8    SampleAnnotation_CV,9    KitInfo,10    QCType,11    PlannedExperiment,12    Sample,13)14from iondb.rundb.labels import (15    Sample as _Sample,16    ModelsQcTypeToLabelsQcTypeAsDict,17    ModelsQcTypeToLabelsQcType,18)19from iondb.utils import validation20from iondb.rundb.plan.page_plan.step_helper_types import StepHelperType21from iondb.rundb.plan.page_plan.step_names import StepNames22from iondb.rundb.plan.page_plan.application_step_data import ApplicationFieldNames23from iondb.rundb.plan.page_plan.reference_step_data import ReferenceFieldNames24from iondb.rundb.plan.page_plan.ionreporter_step_data import IonReporterFieldNames25from iondb.rundb.plan.plan_validator import (26    validate_plan_name,27    validate_notes,28    validate_sample_name,29    validate_sample_tube_label,30    validate_barcode_sample_association,31    validate_QC,32    validate_targetRegionBedFile_for_runType,33    validate_chipBarcode,34)35from iondb.utils.utils import convert36from collections import OrderedDict37# from iondb.utils import toBoolean38import json39import logging40logger = logging.getLogger(__name__)41MAX_LENGTH_SAMPLE_DESCRIPTION = 102442MAX_LENGTH_SAMPLE_NAME = 12743class SavePlanFieldNames:44    UPLOADERS = "uploaders"45    SET_ID = "setid"46    SETID_SUFFIX = "setid_suffix"47    EXTERNAL_ID = "externalId"48    WORKFLOW = "Workflow"49    GENDER = "Gender"50    POPULATION = "Population"51    MOUSE_STRAINS = "mouseStrains"52    CANCER_TYPE = "cancerType"53    CELLULARITY_PCT = "cellularityPct"54    BIOPSY_DAYS = "biopsyDays"55    CELL_NUM = "cellNum"56    COUPLE_ID = "coupleID"57    EMBRYO_ID = "embryoID"58    BACTERIAL_MARKER_TYPE = "BacterialMarkerType"59    WITNESS = "Witness"60    NUCLEOTIDE_TYPE = "NucleotideType"61    RELATIONSHIP_TYPE = "Relation"62    RELATION_ROLE = "RelationRole"63    PLAN_NAME = "planName"64    SAMPLE = "sample"65    NOTE = "note"66    SAMPLE_COLLECTION_DATE = "SampleCollectionDate"67    SAMPLE_RECEIPT_DATE = "SampleReceiptDate"68    SELECTED_IR = "selectedIr"69    IR_CONFIG_JSON = "irConfigJson"70    BARCODE_SET = "barcodeSet"71    BARCODE_SAMPLE_TUBE_LABEL = "barcodeSampleTubeLabel"72    BARCODE_TO_SAMPLE = "barcodeToSample"73    BARCODE_SETS = "barcodeSets"74    BARCODE_SETS_BARCODES = "barcodeSets_barcodes"75    BARCODE_SETS_STATIC = "barcodeSets_static"76    END_BARCODE_SET = "endBarcodeSet"77    END_BARCODE_SETS = "endBarcodeSets"78    END_BARCODES_SUBSET = "endBarcodes_subset"79    END_BARCODE_SETS_BARCODES = "endBarcodeSets_barcodes"80    # note: barcodeKitName was named barcodeId in the plannedexperiment API for backward compatibility. It could be confusing81    # since UI uses barcodeId and endBarcodeId to represent selected barcode for a sample82    END_BARCODE_ID = "endBarcodeId"83    BARCODE_SAMPLE_BARCODE_ID_UI_KEY = "barcodeId"84    BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY = "endBarcodeId"85    DUAL_BARCODES_DB_KEY = "dualBarcodes"86    SAMPLE_TO_BARCODE = "sampleToBarcode"87    SAMPLE_EXTERNAL_ID = "sampleExternalId"88    SAMPLE_NAME = "sampleName"89    SAMPLE_DESCRIPTION = "sampleDescription"90    TUBE_LABEL = "tubeLabel"91    CHIP_BARCODE_LABEL = "chipBarcodeLabel"92    CHIP_BARCODE = "chipBarcode"93    IR_SAMPLE_COLLECTION_DATE = "irSampleCollectionDate"94    IR_SAMPLE_RECEIPT_DATE = "irSampleReceiptDate"95    IR_PLUGIN_ENTRIES = "irPluginEntries"96    IR_GENDER = "irGender"97    IR_POPULATION = "irPopulation"98    IR_MOUSE_STRAINS = "irmouseStrains"99    IR_CANCER_TYPE = "ircancerType"100    IR_CELLULARITY_PCT = "ircellularityPct"101    IR_BIOPSY_DAYS = "irbiopsyDays"102    IR_CELL_NUM = "ircellNum"103    IR_COUPLE_ID = "ircoupleID"104    IR_EMBRYO_ID = "irembryoID"105    IR_BACTERIAL_MARKER_TYPE = "irBacterialMarkerType"106    IR_WITNESS = "irWitness"107    IR_WORKFLOW = "irWorkflow"108    IR_MULTIPLE_WORKFLOW_SINGLE_SAMPLE = "irMultipleWorkflowSelected"109    IR_ISFACTORY = "tag_isFactoryProvidedWorkflow"110    IR_DOWN = "irDown"111    IR_RELATION_ROLE = "irRelationRole"112    IR_RELATIONSHIP_TYPE = "irRelationshipType"113    IR_APPLICATION_TYPE = "ApplicationType"114    IR_SET_ID = "irSetID"115    BAD_SAMPLE_NAME = "bad_sample_name"116    BAD_SAMPLE_EXTERNAL_ID = "bad_sample_external_id"117    BAD_SAMPLE_DESCRIPTION = "bad_sample_description"118    BAD_TUBE_LABEL = "bad_tube_label"119    BAD_CHIP_BARCODE = "bad_chip_barcode"120    BARCODE_SAMPLE_NUCLEOTIDE_TYPE = "nucleotideType"121    BARCODE_SAMPLE_REFERENCE = "reference"122    BARCODE_SAMPLE_TARGET_REGION_BED_FILE = "targetRegionBedFile"123    BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE = "hotSpotRegionBedFile"124    BARCODE_SAMPLE_SSE_BED_FILE = "sseBedFile"125    BARCODE_SAMPLE_CONTROL_SEQ_TYPE = "controlSequenceType"126    BARCODE_SAMPLE_CONTROL_TYPE = "controlType"127    BARCODE_SAMPLE_END_BARCODE_DB_KEY = "endBarcode"128    BARCODE_SAMPLE_INFO = "barcodeSampleInfo"129    NO_SAMPLES = "no_samples"130    DESCRIPTION = "description"131    BAD_IR_SET_ID = "badIrSetId"132    SAMPLE_ANNOTATIONS = "sampleAnnotations"133    CONTROL_SEQ_TYPES = "controlSeqTypes"134    BARCODE_KIT_SELECTABLE_TYPE = "barcodeKitSelectableType"135    PLAN_REFERENCE = "plan_reference"136    PLAN_TARGET_REGION_BED_FILE = "plan_targetRegionBedFile"137    PLAN_HOTSPOT_REGION_BED_FILE = "plan_hotSpotRegionBedFile"138    SAMPLES_TABLE_LIST = "samplesTableList"139    SAMPLES_TABLE = "samplesTable"140    NUM_SAMPLES = "numberOfSamples"141    APPL_PRODUCT = "applProduct"142    RUN_TYPE = "runType"143    ONCO_SAME_SAMPLE = "isOncoSameSample"144    REFERENCE_STEP_HELPER = "referenceStepHelper"145    NO_BARCODE = "no_barcode"146    BAD_BARCODES = "bad_barcodes"147    APPLICATION_TYPE = "applicationType"148    FIRE_VALIDATION = "fireValidation"149    LIMS_META = "LIMS_meta"150    META = "meta"151    APPLICATION_GROUP_NAME = "applicationGroupName"152    HAS_PGS_DATA = "hasPgsData"153    HAS_ONCO_DATA = "hasOncoData"154class MonitoringFieldNames:155    QC_TYPES = "qcTypes"156def get_ir_userinput_dict(row, irWorkflow):157    sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()158    ir_userinput_dict = {159        SavePlanFieldNames.SAMPLE: sample_name,160        SavePlanFieldNames.SAMPLE_NAME: sample_name.replace(" ", "_"),161        SavePlanFieldNames.SAMPLE_EXTERNAL_ID: row.get(162            SavePlanFieldNames.SAMPLE_EXTERNAL_ID, ""163        ),164        SavePlanFieldNames.SAMPLE_DESCRIPTION: row.get(165            SavePlanFieldNames.SAMPLE_DESCRIPTION, ""166        ),167        SavePlanFieldNames.SAMPLE_COLLECTION_DATE: row.get(168            SavePlanFieldNames.IR_SAMPLE_COLLECTION_DATE, ""169        ),170        SavePlanFieldNames.SAMPLE_RECEIPT_DATE: row.get(171            SavePlanFieldNames.IR_SAMPLE_RECEIPT_DATE, ""172        ),173        SavePlanFieldNames.WORKFLOW: irWorkflow,174        SavePlanFieldNames.IR_ISFACTORY: row.get(175            SavePlanFieldNames.IR_ISFACTORY176        ),177        SavePlanFieldNames.RELATION_ROLE: row.get(178            SavePlanFieldNames.IR_RELATION_ROLE, ""179        ),180        SavePlanFieldNames.RELATIONSHIP_TYPE: row.get(181            SavePlanFieldNames.IR_RELATIONSHIP_TYPE, ""182        ),183        SavePlanFieldNames.SET_ID: row.get(SavePlanFieldNames.IR_SET_ID, ""),184        SavePlanFieldNames.GENDER: row.get(SavePlanFieldNames.IR_GENDER, ""),185        SavePlanFieldNames.POPULATION: row.get(186            SavePlanFieldNames.IR_POPULATION, ""187        ),188        SavePlanFieldNames.MOUSE_STRAINS: row.get(189            SavePlanFieldNames.IR_MOUSE_STRAINS, ""190        ),191        SavePlanFieldNames.NUCLEOTIDE_TYPE: row.get(192            SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, ""193        ),194        SavePlanFieldNames.CANCER_TYPE: row.get(195            SavePlanFieldNames.IR_CANCER_TYPE, ""196        ),197        SavePlanFieldNames.CELLULARITY_PCT: row.get(198            SavePlanFieldNames.IR_CELLULARITY_PCT, ""199        ),200        SavePlanFieldNames.BIOPSY_DAYS: row.get(201            SavePlanFieldNames.IR_BIOPSY_DAYS, ""202        ),203        SavePlanFieldNames.CELL_NUM: row.get(204            SavePlanFieldNames.IR_CELL_NUM, ""205        ),206        SavePlanFieldNames.COUPLE_ID: row.get(207            SavePlanFieldNames.IR_COUPLE_ID, ""208        ),209        SavePlanFieldNames.EMBRYO_ID: row.get(210            SavePlanFieldNames.IR_EMBRYO_ID, ""211        ),212        SavePlanFieldNames.BACTERIAL_MARKER_TYPE: row.get(SavePlanFieldNames.IR_BACTERIAL_MARKER_TYPE, ""),213        SavePlanFieldNames.WITNESS: row.get(SavePlanFieldNames.IR_WITNESS, ""),214        SavePlanFieldNames.IR_APPLICATION_TYPE: row.get(215            SavePlanFieldNames.IR_APPLICATION_TYPE, ""216        ),217    }218    barcode_id = row.get(SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY)219    if barcode_id:220        ir_userinput_dict[KitsFieldNames.BARCODE_ID] = barcode_id221        endBarcode_id = row.get(222            SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY223        )224        if endBarcode_id:225            ir_userinput_dict[SavePlanFieldNames.END_BARCODE_ID] = endBarcode_id226    return ir_userinput_dict227def update_ir_plugin_from_samples_table(samplesTable):228    # save IR fields for non-barcoded and barcoded plans229    userInputInfo = []230    for row in samplesTable:231        sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()232        if sample_name:233            multiWorkflowSelectedObj = row.get(SavePlanFieldNames.IR_MULTIPLE_WORKFLOW_SINGLE_SAMPLE) or []234            if multiWorkflowSelectedObj and isinstance(multiWorkflowSelectedObj[0], dict):235                multiWorkflowSelectedList = [obj.get('workflow') for obj in multiWorkflowSelectedObj]236                if "Upload Only" not in multiWorkflowSelectedList:237                    for obj in multiWorkflowSelectedObj:238                        row[SavePlanFieldNames.IR_ISFACTORY] = obj["tag"]239                        ir_userinput_dict = get_ir_userinput_dict(row, obj["workflow"])240                        userInputInfo.append(ir_userinput_dict)241            else:242                irWorflowSelected = row.get(SavePlanFieldNames.IR_WORKFLOW, "")243                ir_userinput_dict = get_ir_userinput_dict(row, irWorflowSelected)244                userInputInfo.append(ir_userinput_dict)245    return userInputInfo246class SavePlanStepData(AbstractStepData):247    def __init__(self, sh_type):248        super(SavePlanStepData, self).__init__(sh_type)249        self.resourcePath = "rundb/plan/page_plan/page_plan_save_plan.html"250        self.prev_step_url = reverse("page_plan_output")251        self.next_step_url = reverse("page_plan_save")252        self.savedFields = OrderedDict()253        self.savedFields[SavePlanFieldNames.PLAN_NAME] = None254        self.savedFields[SavePlanFieldNames.NOTE] = None255        self.savedFields[SavePlanFieldNames.APPLICATION_TYPE] = ""256        self.savedFields[SavePlanFieldNames.IR_DOWN] = "0"257        self.savedFields[SavePlanFieldNames.BARCODE_SET] = ""258        self.savedFields[SavePlanFieldNames.END_BARCODE_SET] = ""259        self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE] = ""260        self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE] = ""261        self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE] = ""262        self.prepopulatedFields[SavePlanFieldNames.SELECTED_IR] = None263        self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW] = None264        self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY] = False265        self.prepopulatedFields[SavePlanFieldNames.IR_CONFIG_JSON] = None266        self.prepopulatedFields[SavePlanFieldNames.SAMPLE_ANNOTATIONS] = list(267            SampleAnnotation_CV.objects.filter(isActive=True).order_by(268                "annotationType", "value"269            )270        )271        self.savedFields[SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL] = None272        self.savedFields[SavePlanFieldNames.CHIP_BARCODE_LABEL] = None273        self.savedObjects[SavePlanFieldNames.BARCODE_TO_SAMPLE] = OrderedDict()274        barcodeObjs_list = list(275            dnaBarcode.objects.filter(active=True)276            .values_list("name", flat=True)277            .distinct()278            .order_by("name")279        )280        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS] = barcodeObjs_list281        all_barcodes = {}282        for bc in (283            dnaBarcode.objects.filter(active=True)284            .order_by("name", "index")285            .values("name", "id_str", "sequence")286        ):287            all_barcodes.setdefault(bc["name"], []).append(bc)288        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS_BARCODES] = json.dumps(289            all_barcodes290        )291        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS_STATIC] = (292            dnaBarcode.objects.filter(active=True)293            .exclude(end_sequence="")294            .values_list("name", flat=True)295            .distinct()296        )297        self.prepopulatedFields[SavePlanFieldNames.END_BARCODE_SETS] = barcodeObjs_list298        self.prepopulatedFields[299            SavePlanFieldNames.END_BARCODE_SETS_BARCODES300        ] = json.dumps(all_barcodes)301        self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE] = OrderedDict()302        self.savedObjects[SavePlanFieldNames.IR_PLUGIN_ENTRIES] = []303        self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "1"304        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = [305            {"row": "1", "sampleName": u"Sample 1"}306        ]307        self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(308            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]309        )310        self.prepopulatedFields[SavePlanFieldNames.NUM_SAMPLES] = 1311        self.savedFields[SavePlanFieldNames.ONCO_SAME_SAMPLE] = False312        # logger.debug("save_plan_step_data samplesTable=%s" %(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]))313        self.prepopulatedFields[314            SavePlanFieldNames.CONTROL_SEQ_TYPES315        ] = KitInfo.objects.filter(316            kitType="ControlSequenceKitType", isActive=True317        ).order_by(318            "name"319        )320        self.savedObjects[SavePlanFieldNames.REFERENCE_STEP_HELPER] = None321        self.savedObjects[SavePlanFieldNames.APPL_PRODUCT] = None322        self.savedFields[SavePlanFieldNames.LIMS_META] = None323        self.savedObjects[SavePlanFieldNames.META] = {}324        self.prepopulatedFields[SavePlanFieldNames.APPLICATION_GROUP_NAME] = ""325        self.prepopulatedFields[SavePlanFieldNames.HAS_ONCO_DATA] = False326        self.prepopulatedFields[SavePlanFieldNames.HAS_PGS_DATA] = False327        self._dependsOn.append(StepNames.IONREPORTER)328        self._dependsOn.append(StepNames.APPLICATION)329        self._dependsOn.append(StepNames.KITS)330        # self._dependsOn.append(StepNames.REFERENCE)331        self.sh_type = sh_type332        # Monitoring333        self.qcNames = []334        self.ModelsQcTypeToLabelsQcTypeAsDict = ModelsQcTypeToLabelsQcTypeAsDict335        all_qc_types = list(QCType.objects.all().order_by("qcName"))336        self.prepopulatedFields[MonitoringFieldNames.QC_TYPES] = all_qc_types337        for qc_type in all_qc_types:338            self.savedFields[qc_type.qcName] = qc_type.defaultThreshold339            self.qcNames.append(qc_type.qcName)340    def getStepName(self):341        return StepNames.SAVE_PLAN342    def validateField(self, field_name, new_field_value):343        self.validationErrors.pop(field_name, None)344        # if the plan has been sequenced, do not enforce the target bed file to be selected345        planStatus = self.getDefaultSectionPrepopulatedFieldDict().get("planStatus", "")346        if field_name == SavePlanFieldNames.PLAN_NAME:347            errors = validate_plan_name(348                new_field_value,349                field_label=_("workflow.step.saveplan.fields.planName.label"),350            )  # 'Plan Name'351            if errors:352                self.validationErrors[field_name] = "\n".join(errors)353        elif field_name == SavePlanFieldNames.NOTE:354            errors = validate_notes(355                new_field_value,356                field_label=_("workflow.step.saveplan.fields.note.label"),357            )358            if errors:359                self.validationErrors[field_name] = "\n".join(errors)360        elif field_name == SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL:361            errors = validate_sample_tube_label(362                new_field_value,363                field_label=_(364                    "workflow.step.sample.fields.barcodeSampleTubeLabel.label"365                ),366            )367            if errors:368                self.validationErrors[field_name] = "\n".join(errors)369        elif field_name == SavePlanFieldNames.CHIP_BARCODE_LABEL:370            errors = validate_chipBarcode(371                new_field_value,372                field_label=_("workflow.step.saveplan.fields.chipBarcodeLabel.label"),373            )374            if errors:375                self.validationErrors[field_name] = "\n".join(errors)376        elif field_name in self.qcNames:377            """378            All qc thresholds must be positive integers379            """380            errors = validate_QC(381                new_field_value, ModelsQcTypeToLabelsQcType(field_name)382            )383            if errors:384                self.validationErrors[field_name] = errors[0]385            else:386                self.validationErrors.pop(field_name, None)387        elif field_name == SavePlanFieldNames.SAMPLES_TABLE:388            sample_table_list = json.loads(new_field_value)389            samples_errors = []390            applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]391            # applProduct object is not saved yet392            if applProduct:393                isTargetRegionSelectionRequired = (394                    applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection395                )396            else:397                isTargetRegionSelectionRequired = False398            applicationGroupName = self.prepopulatedFields[399                SavePlanFieldNames.APPLICATION_GROUP_NAME400            ]401            for row in sample_table_list:402                sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()403                if sample_name:404                    sample_nucleotideType = row.get(405                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, ""406                    )407                    sampleReference = row.get(408                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, ""409                    )410                    sampleTargetRegionBedFile = row.get(411                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, ""412                    )413                    runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]414                    errors = []415                    # if the plan has been sequenced, do not enforce the target bed file to be selected416                    isMainBEDFileValidated = (417                        "default_targetBedFile" in self.validationErrors418                    )419                    if (420                        not isMainBEDFileValidated421                        and planStatus != "run"422                        and (self.sh_type not in StepHelperType.TEMPLATE_TYPES)423                    ):424                        sampleTargetRegionBedFile_label = _(425                            "workflow.step.saveplan.bysample.fields.targetRegionBedFile.label"426                        ) % {"sampleName": sample_name}427                        errors = validate_targetRegionBedFile_for_runType(428                            sampleTargetRegionBedFile,429                            field_label=sampleTargetRegionBedFile_label,430                            runType=runType,431                            reference=sampleReference,432                            nucleotideType=sample_nucleotideType,433                            applicationGroupName=applicationGroupName,434                        )  # "Target Regions BED File for %(sampleName)s"435                    if errors:436                        samples_errors.append("\n".join(errors))437                if samples_errors:438                    self.validationErrors[field_name] = "\n".join(samples_errors)439    def validateStep(self):440        any_samples = False441        self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME] = []442        self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID] = []443        self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION] = []444        self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL] = []445        self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE] = []446        self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID] = []447        self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)448        self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)449        barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]450        selectedBarcodes = []451        endBarcodeSet = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]452        selectedEndBarcodes = []453        samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])454        # logger.debug("save_plan_step_data - anySamples? samplesTable=%s" %(samplesTable))455        for row in samplesTable:456            sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()457            # logger.debug("save_plan_step_data - anySamples? sampleName=%s" %(sample_name))458            if sample_name:459                any_samples = True460                if validate_sample_name(461                    sample_name, field_label=_Sample.displayedName.verbose_name462                ):463                    self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME].append(464                        sample_name465                    )466                external_id = row.get(SavePlanFieldNames.SAMPLE_EXTERNAL_ID, "")467                if external_id:468                    self.validate_field(469                        external_id,470                        self.validationErrors[471                            SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID472                        ],473                    )474                description = row.get(SavePlanFieldNames.SAMPLE_DESCRIPTION, "")475                if description:476                    self.validate_field(477                        description,478                        self.validationErrors[479                            SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION480                        ],481                        False,482                        MAX_LENGTH_SAMPLE_DESCRIPTION,483                    )484                ir_set_id = row.get("irSetId", "")485                if ir_set_id and not (str(ir_set_id).isdigit()):486                    self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID].append(487                        ir_set_id488                    )489                tube_label = row.get("tubeLabel", "")490                if validate_sample_tube_label(491                    tube_label,492                    field_label=_(493                        "workflow.step.saveplan.fields.barcodeSampleTubeLabel.label"494                    ),495                ):496                    self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL].append(497                        tube_label498                    )499                chip_barcode = row.get("chipBarcode", "")500                if validate_chipBarcode(501                    chip_barcode,502                    field_label=_(503                        "workflow.step.saveplan.fields.chipBarcodeLabel.label"504                    ),505                ):506                    self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE].append(507                        chip_barcode508                    )509                if barcodeSet:510                    selectedBarcodes.append(511                        row.get(SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY)512                    )513                    if endBarcodeSet:514                        endBarcode_id_value = row.get(515                            SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY516                        )517                        if endBarcode_id_value:518                            selectedEndBarcodes.append(endBarcode_id_value)519        if any_samples:520            self.validationErrors.pop(SavePlanFieldNames.NO_SAMPLES, None)521        else:522            self.validationErrors[523                SavePlanFieldNames.NO_SAMPLES524            ] = validation.invalid_required_at_least_one(_Sample.verbose_name)525        if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME]:526            self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_NAME, None)527        if not self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL]:528            self.validationErrors.pop(SavePlanFieldNames.BAD_TUBE_LABEL, None)529        if not self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE]:530            self.validationErrors.pop(SavePlanFieldNames.BAD_CHIP_BARCODE, None)531        if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID]:532            self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID, None)533        if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION]:534            self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION, None)535        if not self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID]:536            self.validationErrors.pop(SavePlanFieldNames.BAD_IR_SET_ID, None)537        # 20170928-TODO-WIP538        if barcodeSet:539            errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)540            myErrors = convert(errors)541            if myErrors.get("MISSING_BARCODE", ""):542                self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get(543                    "MISSING_BARCODE", ""544                )545            if myErrors.get("DUPLICATE_BARCODE", ""):546                self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get(547                    "DUPLICATE_BARCODE", ""548                )549        if selectedEndBarcodes:550            applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]551            if applProduct and applProduct.dualBarcodingRule == "no_reuse":552                errors = validate_barcode_sample_association(553                    selectedEndBarcodes, endBarcodeSet, isEndBarcodeExists=True554                )555                myErrors = convert(errors)556                if myErrors.get("DUPLICATE_BARCODE", ""):557                    self.validationErrors[558                        SavePlanFieldNames.BAD_BARCODES559                    ] = myErrors.get("DUPLICATE_BARCODE", "")560    def validate_field(561        self,562        value,563        bad_samples,564        validate_leading_chars=True,565        max_length=MAX_LENGTH_SAMPLE_NAME,566    ):567        exists = False568        if value:569            exists = True570            if not validation.is_valid_chars(value):571                bad_samples.append(value)572            if (573                validate_leading_chars574                and value not in bad_samples575                and not validation.is_valid_leading_chars(value)576            ):577                bad_samples.append(value)578            if value not in bad_samples and not validation.is_valid_length(579                value, max_length580            ):581                bad_samples.append(value)582        return exists583    def updateSavedObjectsFromSavedFields(self):584        self.prepopulatedFields["fireValidation"] = "0"585        for section, sectionObj in list(self.step_sections.items()):586            sectionObj.updateSavedObjectsFromSavedFields()587            if section == StepNames.REFERENCE:588                self.prepopulatedFields[589                    SavePlanFieldNames.PLAN_REFERENCE590                ] = sectionObj.savedFields.get(ReferenceFieldNames.REFERENCE, "")591                self.prepopulatedFields[592                    SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE593                ] = sectionObj.savedFields.get(ReferenceFieldNames.TARGET_BED_FILE, "")594                self.prepopulatedFields[595                    SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE596                ] = sectionObj.savedFields.get(597                    ReferenceFieldNames.HOT_SPOT_BED_FILE, ""598                )599                # logger.debug("save_plan_step_data.updateSavedObjectsFromSavedFields() REFERENCE reference.savedFields=%s" %(sectionObj.savedFields))600        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = json.loads(601            self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]602        )603        self.prepopulatedFields[SavePlanFieldNames.NUM_SAMPLES] = len(604            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]605        )606        self.savedObjects[607            SavePlanFieldNames.IR_PLUGIN_ENTRIES608        ] = update_ir_plugin_from_samples_table(609            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]610        )611        if self.savedFields[SavePlanFieldNames.BARCODE_SET]:612            planReference = self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]613            planHotSptRegionBedFile = self.prepopulatedFields[614                SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE615            ]616            planTargetRegionBedFile = self.prepopulatedFields[617                SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE618            ]619            logger.debug(620                "save_plan_step_data.updateSavedObjectsFromSavedFields() BARCODE_SET PLAN_REFERENCE=%s; TARGET_REGION=%s; HOTSPOT_REGION=%s;"621                % (planReference, planTargetRegionBedFile, planHotSptRegionBedFile)622            )623            reference_step_helper = self.savedObjects[624                SavePlanFieldNames.REFERENCE_STEP_HELPER625            ]626            endBarcodeKit = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]627            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE] = {}628            for row in self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]:629                logger.debug(630                    "save_plan_step_data.updateSavedObjectsFromSavedFields() BARCODE_SET LOOP row=%s"631                    % (row)632                )633                sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()634                if sample_name:635                    id_str = row[SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY]636                    end_id_str = row[637                        SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY638                    ]639                    # update barcodedSamples dict640                    if (641                        sample_name642                        not in self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE]643                    ):644                        self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][645                            sample_name646                        ] = {647                            KitsFieldNames.BARCODES: [],648                            SavePlanFieldNames.BARCODE_SAMPLE_INFO: {},649                            SavePlanFieldNames.DUAL_BARCODES_DB_KEY: [],650                        }651                    sample_nucleotideType = row.get(652                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, ""653                    )654                    sampleReference = row.get(655                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, ""656                    )657                    sampleHotSpotRegionBedFile = row.get(658                        SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, ""659                    )660                    sampleTargetRegionBedFile = row.get(661                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, ""662                    )663                    runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]664                    # logger.debug("save_plan_step_data.updateSavedObjectsFromSavedFields() SETTING reference step helper runType=%s; sample_nucleotideType=%s; sampleReference=%s" %(runType, sample_nucleotideType, sampleReference))665                    sseBedFile = ""666                    if reference_step_helper:667                        sseBedFile = reference_step_helper.get_sseBedFile(668                            sampleTargetRegionBedFile669                        )670                    self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][671                        sample_name672                    ][KitsFieldNames.BARCODES].append(id_str)673                    self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][674                        sample_name675                    ][SavePlanFieldNames.BARCODE_SAMPLE_INFO][id_str] = {676                        SavePlanFieldNames.EXTERNAL_ID: row.get(677                            SavePlanFieldNames.SAMPLE_EXTERNAL_ID, ""678                        ),679                        SavePlanFieldNames.DESCRIPTION: row.get(680                            SavePlanFieldNames.SAMPLE_DESCRIPTION, ""681                        ),682                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE: sample_nucleotideType,683                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE: sampleReference,684                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE: sampleTargetRegionBedFile,685                        SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE: sampleHotSpotRegionBedFile,686                        SavePlanFieldNames.BARCODE_SAMPLE_SSE_BED_FILE: sseBedFile,687                        SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_DB_KEY: row.get(688                            SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY, ""689                        ),690                        SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_SEQ_TYPE: row.get(691                            SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_SEQ_TYPE, ""692                        ),693                        SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_TYPE: row.get(694                            SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_TYPE, ""695                        ),696                    }697                    if endBarcodeKit and id_str:698                        if end_id_str:699                            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][700                                sample_name701                            ][SavePlanFieldNames.DUAL_BARCODES_DB_KEY].append(702                                id_str703                                + PlannedExperiment.get_dualBarcodes_delimiter()704                                + end_id_str705                            )706                        else:707                            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][708                                sample_name709                            ][SavePlanFieldNames.DUAL_BARCODES_DB_KEY].append(id_str)710    def alternateUpdateFromStep(self, updated_step):711        """712        also runs if editing a plan post-sequencing and Application is updated713        """714        if updated_step.getStepName() == StepNames.APPLICATION:715            if updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE]:716                runTypeObj = updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE]717                # make sure hidden nucleotide type field is updated for new Application718                if (719                    self.prepopulatedFields.get(SavePlanFieldNames.RUN_TYPE)720                    and self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]721                    != runTypeObj.runType722                ):723                    nucleotideType = runTypeObj.nucleotideType.upper()724                    if nucleotideType in ["DNA", "RNA"]:725                        for row in self.savedObjects[726                            SavePlanFieldNames.SAMPLES_TABLE_LIST727                        ]:728                            row[729                                SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE730                            ] = nucleotideType731                        self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(732                            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]733                        )734                self.prepopulatedFields[735                    SavePlanFieldNames.RUN_TYPE736                ] = runTypeObj.runType737            else:738                self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE] = ""739    def updateFromStep(self, updated_step):740        if updated_step.getStepName() not in self._dependsOn:741            for sectionKey, sectionObj in list(self.step_sections.items()):742                if sectionObj:743                    # logger.debug("save_plan_step_data.updateFromStep() sectionKey=%s" %(sectionKey))744                    for key in list(sectionObj.getCurrentSavedFieldDict().keys()):745                        sectionObj.updateFromStep(updated_step)746            return747        self.alternateUpdateFromStep(updated_step)748        if updated_step.getStepName() == StepNames.APPLICATION:749            if not updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]:750                logger.debug(751                    "save_plan_step_data.updateFromStep() --- NO-OP --- APPLICATION APPL_PRODUCT IS NOT YET SET!!! "752                )753                return754        if (755            updated_step.getStepName() == StepNames.APPLICATION756            and updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]757        ):758            self.savedObjects[759                SavePlanFieldNames.APPL_PRODUCT760            ] = updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]761        if updated_step.getStepName() == StepNames.KITS:762            barcode_set = updated_step.savedFields[KitsFieldNames.BARCODE_ID]763            if str(barcode_set) != str(764                self.savedFields[SavePlanFieldNames.BARCODE_SET]765            ):766                self.savedFields[SavePlanFieldNames.BARCODE_SET] = barcode_set767                if barcode_set:768                    barcodes = list(769                        dnaBarcode.objects.filter(name=barcode_set).order_by("index")770                    )771                    bc_count = min(772                        len(barcodes),773                        len(self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]),774                    )775                    self.savedObjects[776                        SavePlanFieldNames.SAMPLES_TABLE_LIST777                    ] = self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST][778                        :bc_count779                    ]780                    for i in range(bc_count):781                        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST][i][782                            SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY783                        ] = barcodes[i].id_str784                    self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(785                        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]786                    )787                # if barcode kit selection changes, re-validate788                self.validateStep()789        if updated_step.getStepName() == StepNames.IONREPORTER:790            ir_account_id = updated_step.savedFields[791                IonReporterFieldNames.IR_ACCOUNT_ID792            ]793            ir_workflow = updated_step.savedFields[IonReporterFieldNames.IR_WORKFLOW]794            ir_isfactory = updated_step.savedFields[IonReporterFieldNames.IR_ISFACTORY]795            if ir_account_id and ir_account_id != "0":796                if (797                    self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW]798                    != ir_workflow799                    or self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY]800                    != ir_isfactory801                ):802                    for row in self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]:803                        row[SavePlanFieldNames.IR_WORKFLOW] = ir_workflow804                        row[SavePlanFieldNames.IR_ISFACTORY] = ir_isfactory805                    self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(806                        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]807                    )808            self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW] = ir_workflow809            self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY] = ir_isfactory810            self.prepopulatedFields[SavePlanFieldNames.SELECTED_IR] = ir_account_id811        for sectionKey, sectionObj in list(self.step_sections.items()):812            if sectionObj:813                sectionObj.updateFromStep(updated_step)814        logger.debug(815            "EXIT save_plan_step_data.updateFromStep() self.savedFields=%s"816            % (self.savedFields)817        )818    def getDefaultSection(self):819        """820        Sections are optional for a step.  Return the default section821        """822        if not self.step_sections:823            return None824        return self.step_sections.get(StepNames.REFERENCE, None)825    def getDefaultSectionSavedFieldDict(self):826        """827        Sections are optional for a step.  Return the savedFields dictionary of the default section if it exists.828        Otherwise, return an empty dictionary829        """830        default_value = {}831        if not self.step_sections:832            return default_value833        sectionObj = self.step_sections.get(StepNames.REFERENCE, None)834        if sectionObj:835            # logger.debug("save_plan_step_data.getDefaultSectionSavedFieldDict() sectionObj.savedFields=%s" %(sectionObj.savedFields))836            return sectionObj.savedFields837        else:838            return default_value839    def getDefaultSectionPrepopulatedFieldDict(self):840        """841        Sections are optional for a step.  Return the prepopuldatedFields dictionary of the default section if it exists.842        Otherwise, return an empty dictionary843        """844        default_value = {}845        if not self.step_sections:846            return default_value847        sectionObj = self.step_sections.get(StepNames.REFERENCE, None)848        if sectionObj:849            # logger.debug("save_plan_step_data.getDefaultSectionPrepopulatedFieldsFieldDict() sectionObj.prepopulatedFields=%s" %(sectionObj.prepopulatedFields))850            return sectionObj.prepopulatedFields851        else:...

barcode_by_sample_step_data.py

Source:barcode_by_sample_step_data.py

1# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved2from collections import OrderedDict3from iondb.rundb.plan.page_plan.abstract_step_data import AbstractStepData4from iondb.rundb.models import (5    dnaBarcode,6    SampleAnnotation_CV,7    RunType,8    PlannedExperiment,9)10from iondb.rundb.plan.page_plan.step_names import StepNames11from iondb.rundb.plan.page_plan.application_step_data import ApplicationFieldNames12from iondb.rundb.plan.page_plan.kits_step_data import KitsFieldNames13from iondb.rundb.plan.page_plan.reference_step_data import ReferenceFieldNames14from iondb.rundb.plan.page_plan.save_plan_step_data import (15    SavePlanFieldNames,16    update_ir_plugin_from_samples_table,17)18from iondb.rundb.plan.plan_validator import (19    validate_sample_tube_label,20    validate_barcode_sample_association,21    validate_targetRegionBedFile_for_runType,22    validate_chipBarcode,23)24from iondb.rundb.plan.page_plan.ionreporter_step_data import IonReporterFieldNames25from iondb.utils.utils import convert26from django.core.serializers.json import DjangoJSONEncoder27from django.core.urlresolvers import reverse28from django.utils.translation import ugettext as _29import json30import logging31logger = logging.getLogger(__name__)32class BarcodeBySampleFieldNames:33    # NOTE: this step uses field names from save_plan_step_data for consistency34    SAMPLESET_ITEMS = "samplesetitems"35    ONCO_SAME_SAMPLE = "isOncoSameSample"36    HAS_PGS_DATA = "hasPgsData"37    HAS_ONCO_DATA = "hasOncoData"38    SHOW_SAMPLESET_INFO = "showSampleSetInfo"39class BarcodeBySampleStepData(AbstractStepData):40    def __init__(self, sh_type):41        super(BarcodeBySampleStepData, self).__init__(sh_type)42        self.resourcePath = "rundb/plan/page_plan/page_plan_by_sample_barcode.html"43        self.prev_step_url = reverse("page_plan_plugins")44        self.next_step_url = reverse("page_plan_output")45        self.savedFields = OrderedDict()46        self.savedFields[SavePlanFieldNames.BARCODE_SET] = ""47        self.savedFields[SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL] = ""48        self.savedFields[SavePlanFieldNames.CHIP_BARCODE_LABEL] = ""49        # for non-barcoded planBySampleSet50        self.savedFields[SavePlanFieldNames.TUBE_LABEL] = ""51        self.savedFields[SavePlanFieldNames.APPLICATION_TYPE] = ""52        self.savedFields[SavePlanFieldNames.IR_DOWN] = "0"53        self.prepopulatedFields[SavePlanFieldNames.SELECTED_IR] = None54        self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW] = None55        self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY] = False56        self.prepopulatedFields[BarcodeBySampleFieldNames.SAMPLESET_ITEMS] = []57        self.prepopulatedFields[BarcodeBySampleFieldNames.SHOW_SAMPLESET_INFO] = False58        self.prepopulatedFields[SavePlanFieldNames.SAMPLE_ANNOTATIONS] = list(59            SampleAnnotation_CV.objects.filter(isActive=True).order_by(60                "annotationType", "value"61            )62        )63        self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "1"64        self.savedObjects[SavePlanFieldNames.IR_PLUGIN_ENTRIES] = []65        self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE] = OrderedDict()66        barcodeObjs_list = list(67            dnaBarcode.objects.filter(active=True)68            .values_list("name", flat=True)69            .distinct()70            .order_by("name")71        )72        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS] = barcodeObjs_list73        all_barcodes = {}74        for bc in (75            dnaBarcode.objects.filter(active=True)76            .order_by("name", "index")77            .values("name", "id_str", "sequence")78        ):79            all_barcodes.setdefault(bc["name"], []).append(bc)80        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS_BARCODES] = json.dumps(81            all_barcodes82        )83        self.prepopulatedFields[SavePlanFieldNames.BARCODE_SETS_STATIC] = (84            dnaBarcode.objects.filter(active=True)85            .exclude(end_sequence="")86            .values_list("name", flat=True)87            .distinct()88        )89        self.prepopulatedFields[SavePlanFieldNames.END_BARCODE_SETS] = barcodeObjs_list90        self.prepopulatedFields[91            SavePlanFieldNames.END_BARCODE_SETS_BARCODES92        ] = json.dumps(all_barcodes)93        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = [{"row": "1"}]94        self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(95            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]96        )97        self.prepopulatedFields[SavePlanFieldNames.NUM_SAMPLES] = 198        self.savedFields[SavePlanFieldNames.ONCO_SAME_SAMPLE] = False99        self.savedObjects[SavePlanFieldNames.REFERENCE_STEP_HELPER] = None100        self.savedObjects[SavePlanFieldNames.APPL_PRODUCT] = None101        self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE] = ""102        self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE] = ""103        self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE] = ""104        self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE] = ""105        self.prepopulatedFields[SavePlanFieldNames.APPLICATION_GROUP_NAME] = ""106        self.prepopulatedFields[BarcodeBySampleFieldNames.HAS_ONCO_DATA] = False107        self.prepopulatedFields[BarcodeBySampleFieldNames.HAS_PGS_DATA] = False108        self._dependsOn.append(StepNames.IONREPORTER)109        self._dependsOn.append(StepNames.APPLICATION)110        # self._dependsOn.append(StepNames.REFERENCE)111        self.sh_type = sh_type112    def getStepName(self):113        return StepNames.BARCODE_BY_SAMPLE114    def alternateUpdateFromStep(self, updated_step):115        """116        also runs if editing a plan post-sequencing and Application is updated117        """118        if updated_step.getStepName() == StepNames.APPLICATION:119            if updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE]:120                runTypeObj = updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE]121                # make sure hidden nucleotide type field is updated for new Application122                if (123                    self.prepopulatedFields.get(SavePlanFieldNames.RUN_TYPE)124                    and self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]125                    != runTypeObj.runType126                ):127                    nucleotideType = runTypeObj.nucleotideType.upper()128                    if nucleotideType in ["DNA", "RNA"]:129                        for row in self.savedObjects[130                            SavePlanFieldNames.SAMPLES_TABLE_LIST131                        ]:132                            row["nucleotideType"] = nucleotideType133                        self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(134                            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]135                        )136                self.prepopulatedFields[137                    SavePlanFieldNames.RUN_TYPE138                ] = runTypeObj.runType139            else:140                self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE] = ""141    def updateFromStep(self, updated_step):142        if updated_step.getStepName() not in self._dependsOn:143            return144        self.alternateUpdateFromStep(updated_step)145        if updated_step.getStepName() == StepNames.APPLICATION:146            if not updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]:147                logger.debug(148                    "barcode_by_sample_step_data.updateFromStep() --- NO-OP --- APPLICATION APPL_PRODUCT IS NOT YET SET!!! "149                )150                return151        if updated_step.getStepName() == StepNames.IONREPORTER:152            ir_account_id = updated_step.savedFields[153                IonReporterFieldNames.IR_ACCOUNT_ID154            ]155            ir_workflow = updated_step.savedFields[IonReporterFieldNames.IR_WORKFLOW]156            ir_isfactory = updated_step.savedFields[IonReporterFieldNames.IR_ISFACTORY]157            # update samples table with saved sampleset items fields for IR158            if ir_account_id and ir_account_id != "0":159                if (160                    self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW]161                    != ir_workflow162                    or self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY]163                    != ir_isfactory164                ):165                    sorted_sampleSetItems = self.prepopulatedFields[166                        BarcodeBySampleFieldNames.SAMPLESET_ITEMS167                    ]168                    for row in self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]:169                        row[SavePlanFieldNames.IR_WORKFLOW] = ir_workflow170                        row[SavePlanFieldNames.IR_ISFACTORY] = ir_isfactory171                        sampleset_item = [172                            item173                            for item in sorted_sampleSetItems174                            if item.sample.displayedName == row["sampleName"]175                        ]176                        if len(sampleset_item) > 0:177                            row[178                                SavePlanFieldNames.IR_SAMPLE_COLLECTION_DATE179                            ] = sampleset_item[0].sampleCollectionDate180                            row[181                                SavePlanFieldNames.IR_SAMPLE_RECEIPT_DATE182                            ] = sampleset_item[0].sampleReceiptDate183                            row[SavePlanFieldNames.IR_GENDER] = sampleset_item[0].gender184                            row[SavePlanFieldNames.IR_POPULATION] = sampleset_item[185                                0186                            ].population187                            row[SavePlanFieldNames.IR_MOUSE_STRAINS] = sampleset_item[188                                0189                            ].mouseStrains190                            row[SavePlanFieldNames.IR_RELATION_ROLE] = sampleset_item[191                                0192                            ].relationshipRole193                            row[SavePlanFieldNames.IR_SET_ID] = sampleset_item[194                                0195                            ].relationshipGroup196                            row[SavePlanFieldNames.IR_CANCER_TYPE] = sampleset_item[197                                0198                            ].cancerType199                            row[SavePlanFieldNames.IR_CELLULARITY_PCT] = sampleset_item[200                                0201                            ].cellularityPct202                            row[SavePlanFieldNames.IR_BIOPSY_DAYS] = sampleset_item[203                                0204                            ].biopsyDays205                            row[SavePlanFieldNames.IR_CELL_NUM] = sampleset_item[206                                0207                            ].cellNum208                            row[SavePlanFieldNames.IR_COUPLE_ID] = sampleset_item[209                                0210                            ].coupleId211                            row[SavePlanFieldNames.IR_EMBRYO_ID] = sampleset_item[212                                0213                            ].embryoId214                self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = json.dumps(215                    self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST],216                    cls=DjangoJSONEncoder,217                )218            self.prepopulatedFields[SavePlanFieldNames.IR_WORKFLOW] = ir_workflow219            self.prepopulatedFields[SavePlanFieldNames.IR_ISFACTORY] = ir_isfactory220            self.prepopulatedFields[SavePlanFieldNames.SELECTED_IR] = ir_account_id221        if (222            updated_step.getStepName() == StepNames.APPLICATION223            and updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]224        ):225            self.savedObjects[226                SavePlanFieldNames.APPL_PRODUCT227            ] = updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]228    def validateField(self, field_name, new_field_value):229        self.validationErrors.pop(field_name, None)230        errors = None231        if field_name == SavePlanFieldNames.CHIP_BARCODE_LABEL:232            errors = validate_chipBarcode(233                new_field_value,234                field_label=_("workflow.step.sample.fields.chipBarcodeLabel.label"),235            )236        if errors:237            self.validationErrors[field_name] = "\n".join(errors)238        if field_name == SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL:239            errors = validate_sample_tube_label(240                new_field_value,241                field_label=_(242                    "workflow.step.sample.fields.barcodeSampleTubeLabel.label"243                ),244            )245        if errors:246            self.validationErrors[field_name] = "\n".join(errors)247        # if the plan has been sequenced, do not enforce the target bed file to be selected248        planStatus = self.getDefaultSectionPrepopulatedFieldDict().get("planStatus", "")249        if field_name == SavePlanFieldNames.SAMPLES_TABLE:250            sample_table_list = json.loads(new_field_value)251            samples_errors = []252            applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]253            # applProduct object is not saved yet254            if applProduct:255                isTargetRegionSelectionRequired = (256                    applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection257                )258            else:259                isTargetRegionSelectionRequired = False260            applicationGroupName = self.prepopulatedFields[261                SavePlanFieldNames.APPLICATION_GROUP_NAME262            ]263            for row in sample_table_list:264                sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()265                if sample_name:266                    sample_nucleotideType = row.get(267                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, ""268                    )269                    sampleReference = row.get(270                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, ""271                    )272                    sampleTargetRegionBedFile = row.get(273                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, ""274                    )275                    runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]276                    logger.debug(277                        "barcode_by_sample_step_data.validateField() sampleName=%s runType=%s; sample_nucleotideType=%s; sampleReference=%s; sampleTargetRegionBedFile=%s"278                        % (279                            sample_name,280                            runType,281                            sample_nucleotideType,282                            sampleReference,283                            sampleTargetRegionBedFile,284                        )285                    )286                    errors = []287                    # if the plan has been sequenced, do not enforce the target bed file to be selected288                    if planStatus != "run":289                        sampleTargetRegionBedFile_label = _(290                            "workflow.step.saveplan.bysample.fields.targetRegionBedFile.label"291                        ) % {"sampleName": sample_name}292                        errors = validate_targetRegionBedFile_for_runType(293                            sampleTargetRegionBedFile,294                            field_label=sampleTargetRegionBedFile_label,295                            runType=runType,296                            reference=sampleReference,297                            nucleotideType=sample_nucleotideType,298                            applicationGroupName=applicationGroupName,299                        )  # "Target Regions BED File for %(sampleName)s"300                    if errors:301                        samples_errors.append("\n".join(errors))302                if samples_errors:303                    logger.debug(304                        "barcode_by_sample_step_data.validateField() samples_errors=%s"305                        % (samples_errors)306                    )307                    self.validationErrors[field_name] = "\n".join(samples_errors)308    def validateStep(self):309        self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)310        self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)311        samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])312        barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]313        selectedBarcodes = []314        endBarcodeSet = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]315        selectedEndBarcodes = []316        for row in samplesTable:317            sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()318            if sample_name:319                if barcodeSet:320                    selectedBarcodes.append(321                        row.get(SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY)322                    )323                    if endBarcodeSet:324                        endBarcode_id_value = row.get(325                            SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY326                        )327                        if endBarcode_id_value:328                            selectedEndBarcodes.append(endBarcode_id_value)329        if barcodeSet:330            errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)331            myErrors = convert(errors)332            if myErrors.get("MISSING_BARCODE", ""):333                self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get(334                    "MISSING_BARCODE", ""335                )336            if myErrors.get("DUPLICATE_BARCODE", ""):337                self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get(338                    "DUPLICATE_BARCODE", ""339                )340        if selectedEndBarcodes:341            applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]342            if applProduct and applProduct.dualBarcodingRule == "no_reuse":343                errors = validate_barcode_sample_association(344                    selectedEndBarcodes, endBarcodeSet, isEndBarcodeExists=True345                )346                myErrors = convert(errors)347                if myErrors.get("DUPLICATE_BARCODE", ""):348                    self.validationErrors[349                        SavePlanFieldNames.BAD_BARCODES350                    ] = myErrors.get("DUPLICATE_BARCODE", "")351        self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "0"352    def updateSavedObjectsFromSavedFields(self):353        # logger.debug("ENTER barcode_by_sample_step_data.updateSavedObjectsFromSavedFields() self.savedFields[SavePlanFieldNames.BARCODE_SET]=%s" %(self.savedFields[SavePlanFieldNames.BARCODE_SET]))354        self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = json.loads(355            self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]356        )357        self.prepopulatedFields[SavePlanFieldNames.NUM_SAMPLES] = len(358            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]359        )360        self.savedObjects[361            SavePlanFieldNames.IR_PLUGIN_ENTRIES362        ] = update_ir_plugin_from_samples_table(363            self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]364        )365        self.prepopulatedFields[366            SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL367        ] = self.savedFields[SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL]368        self.prepopulatedFields[369            SavePlanFieldNames.CHIP_BARCODE_LABEL370        ] = self.savedFields[SavePlanFieldNames.CHIP_BARCODE_LABEL]371        if self.savedFields[SavePlanFieldNames.BARCODE_SET]:372            # logger.debug("barcode_by_sample_step_data.updateSavedObjectsFromSavedFields() BARCODE_SET self.savedFields=%s" %(self.savedFields))373            # logger.debug("barcode_by_sample_step_data.updateSavedObjectsFromSavedFields() BARCODE_SET self=%s" %(self))374            planReference = self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]375            planHotSpotRegionBedFile = self.prepopulatedFields[376                SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE377            ]378            planTargetRegionBedFile = self.prepopulatedFields[379                SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE380            ]381            logger.debug(382                "barcode_by_sample_step_data.updateSavedObjectsFromSavedFields() BARCODE_SET PLAN_REFERENCE=%s; TARGET_REGION=%s; HOTSPOT_REGION=%s;"383                % (planReference, planTargetRegionBedFile, planHotSpotRegionBedFile)384            )385            reference_step_helper = self.savedObjects[386                SavePlanFieldNames.REFERENCE_STEP_HELPER387            ]388            endBarcodeKit = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]389            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE] = {}390            for row in self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]:391                sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()392                if sample_name:393                    id_str = row[SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY]394                    end_id_str = row[395                        SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY396                    ]397                    # update barcodedSamples dict398                    if (399                        sample_name400                        not in self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE]401                    ):402                        self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][403                            sample_name404                        ] = {405                            KitsFieldNames.BARCODES: [],406                            SavePlanFieldNames.BARCODE_SAMPLE_INFO: {},407                            SavePlanFieldNames.DUAL_BARCODES_DB_KEY: [],408                        }409                    sample_nucleotideType = row.get(410                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, ""411                    )412                    sampleReference = row.get(413                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, ""414                    )415                    sampleHotSpotRegionBedFile = row.get(416                        SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, ""417                    )418                    sampleTargetRegionBedFile = row.get(419                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, ""420                    )421                    runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]422                    # logger.debug("barcode_by_sample_step_data SETTING reference step helper runType=%s; sample_nucleotideType=%s; sampleReference=%s" %(runType, sample_nucleotideType, sampleReference))423                    if not sample_nucleotideType:424                        applicationGroupName = self.prepopulatedFields[425                            SavePlanFieldNames.APPLICATION_GROUP_NAME426                        ]427                        planNucleotideType = self._get_nucleotideType_barcodedSamples(428                            appGroup=applicationGroupName, runType=runType429                        )430                        if planNucleotideType:431                            sample_nucleotideType = planNucleotideType432                    sseBedFile = ""433                    if reference_step_helper:434                        sseBedFile = reference_step_helper.get_sseBedFile(435                            sampleTargetRegionBedFile436                        )437                    self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][438                        sample_name439                    ][KitsFieldNames.BARCODES].append(id_str)440                    self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][441                        sample_name442                    ][SavePlanFieldNames.BARCODE_SAMPLE_INFO][id_str] = {443                        SavePlanFieldNames.EXTERNAL_ID: row.get(444                            SavePlanFieldNames.SAMPLE_EXTERNAL_ID, ""445                        ),446                        SavePlanFieldNames.DESCRIPTION: row.get(447                            SavePlanFieldNames.SAMPLE_DESCRIPTION, ""448                        ),449                        SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE: sample_nucleotideType,450                        SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE: sampleReference,451                        SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE: sampleTargetRegionBedFile,452                        SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE: sampleHotSpotRegionBedFile,453                        SavePlanFieldNames.BARCODE_SAMPLE_SSE_BED_FILE: sseBedFile,454                        SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_DB_KEY: row.get(455                            SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY, ""456                        ),457                        SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_SEQ_TYPE: row.get(458                            SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_SEQ_TYPE, ""459                        ),460                        SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_TYPE: row.get(461                            SavePlanFieldNames.BARCODE_SAMPLE_CONTROL_TYPE, ""462                        ),463                    }464                    if endBarcodeKit and id_str:465                        if end_id_str:466                            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][467                                sample_name468                            ][SavePlanFieldNames.DUAL_BARCODES_DB_KEY].append(469                                id_str470                                + PlannedExperiment.get_dualBarcodes_delimiter()471                                + end_id_str472                            )473                        else:474                            self.savedObjects[SavePlanFieldNames.SAMPLE_TO_BARCODE][475                                sample_name476                            ][SavePlanFieldNames.DUAL_BARCODES_DB_KEY].append(id_str)477    def _get_nucleotideType_barcodedSamples(self, appGroup=None, runType=None):478        value = ""479        runTypeObjs = RunType.objects.filter(runType=runType)480        if runTypeObjs:481            value = runTypeObjs[0].nucleotideType.upper()482        if value not in ["DNA", "RNA"] and appGroup:483            value = appGroup...

analysis_params_step_data.py

Source:analysis_params_step_data.py

1# Copyright (C) 2015 Ion Torrent Systems, Inc. All Rights Reserved2from django.utils.translation import ugettext as _3from iondb.rundb.plan.page_plan.abstract_step_data import AbstractStepData4from django.conf import settings5from iondb.utils import validation6from iondb.rundb.models import AnalysisArgs7from iondb.rundb.plan.page_plan.step_names import StepNames8from iondb.rundb.plan.page_plan.application_step_data import ApplicationFieldNames9from iondb.rundb.plan.page_plan.kits_step_data import KitsFieldNames10from iondb.rundb.plan.page_plan.step_helper_types import StepHelperType11import logging12logger = logging.getLogger(__name__)13class AnalysisParamsFieldNames:14    # AP_DICT = "analysisParamsDict"15    AP_ENTRIES = "analysisParamsEntries"16    AP_DISPLAYED_NAMES = "analysisParamsNames"17    AP_ENTRY_SELECTED = "analysisParamsEntrySelected"18    AP_CUSTOM = "analysisParamsCustom"19    AP_ENTRY_PREVIOUSLY_SELECTED = "analysisParamsEntryPreviouslySelected"20    AP_ENTRY_SYSTEM_SELECTED = "analysisParamsEntrySystemSelected"21    AP_ENTRY_SELECTED_VALUE = _(22        "workflow.step.analysisparams.fields.analysis_params.choice.AP_ENTRY_SELECTED_VALUE"23    )  # "<Previous custom selection>"24    AP_ENTRY_PREVIOUSLY_SELECTED_VALUE = _(25        "workflow.step.analysisparams.fields.analysis_params.choice.AP_ENTRY_PREVIOUSLY_SELECTED_VALUE"26    )  # "<Selection before chip/kits selection change>"27    AP_ENTRY_BEST_MATCH_PLAN_VALUE = _(28        "workflow.step.analysisparams.fields.analysis_params.choice.AP_ENTRY_BEST_MATCH_PLAN_VALUE"29    )  # "System default for this plan"30    AP_ENTRY_BEST_MATCH_TEMPLATE_VALUE = _(31        "workflow.step.analysisparams.fields.analysis_params.choice.AP_ENTRY_BEST_MATCH_TEMPLATE_VALUE"32    )  # "System default for this template"33    AP_BEADFIND_SELECTED = "beadFindSelected"34    AP_ANALYSISARGS_SELECTED = "analysisArgsSelected"35    AP_PREBASECALLER_SELECTED = "preBaseCallerSelected"36    AP_CALIBRATE_SELECTED = "calibrateSelected"37    AP_BASECALLER_SELECTED = "baseCallerSelected"38    AP_ALIGNMENT_SELECTED = "alignmentSelected"39    AP_IONSTATS_SELECTED = "ionStatsSelected"40    AP_THUMBNAIL_BEADFIND_SELECTED = "thumbnailBeadFindSelected"41    AP_THUMBNAIL_ANALYSISARGS_SELECTED = "thumbnailAnalysisArgsSelected"42    AP_THUMBNAIL_PREBASECALLER_SELECTED = "thumbnailPreBaseCallerSelected"43    AP_THUMBNAIL_CALIBRATE_SELECTED = "thumbnailCalibrateSelected"44    AP_THUMBNAIL_BASECALLER_SELECTED = "thumbnailBaseCallerSelected"45    AP_THUMBNAIL_ALIGNMENT_SELECTED = "thumbnailAlignmentSelected"46    AP_THUMBNAIL_IONSTATS_SELECTED = "thumbnailIonStatsSelected"47    APPL_PRODUCT = "applProduct"48    RUN_TYPE = "runType"49    APPLICATION_GROUP_NAME = "applicationGroupName"50    CHIP_TYPE = "chipType"51    SAMPLE_PREPARATION_KIT = "samplePreparationKit"52    LIBRARY_KIT_NAME = "librarykitname"53    TEMPLATE_KIT_NAME = "templatekitname"54    SEQUENCE_KIT_NAME = "sequencekitname"55    CATEGORIES = "categories"56class AnalysisParamsStepData(AbstractStepData):57    def __init__(self, sh_type):58        super(AnalysisParamsStepData, self).__init__(sh_type)59        self.resourcePath = "rundb/plan/page_plan/page_plan_analysis_params.html"60        self._dependsOn.append(StepNames.APPLICATION)61        self._dependsOn.append(StepNames.KITS)62        analysisParamsEntries = list(AnalysisArgs.objects.all().filter(active=True))63        self.prepopulatedFields[64            AnalysisParamsFieldNames.AP_ENTRIES65        ] = analysisParamsEntries66        self.prepopulatedFields[AnalysisParamsFieldNames.AP_DISPLAYED_NAMES] = [67            ap.description for ap in analysisParamsEntries68        ]69        # self.prepopulatedFields[AnalysisParamsFieldNames.AP_ENTRY_BEST_MATCH] = None70        self.savedObjects[AnalysisParamsFieldNames.AP_ENTRY_SELECTED] = ""71        self.savedObjects[AnalysisParamsFieldNames.AP_ENTRY_PREVIOUSLY_SELECTED] = ""72        self.savedFields[AnalysisParamsFieldNames.AP_BEADFIND_SELECTED] = ""73        self.savedFields[AnalysisParamsFieldNames.AP_ANALYSISARGS_SELECTED] = ""74        self.savedFields[AnalysisParamsFieldNames.AP_PREBASECALLER_SELECTED] = ""75        self.savedFields[AnalysisParamsFieldNames.AP_CALIBRATE_SELECTED] = ""76        self.savedFields[AnalysisParamsFieldNames.AP_BASECALLER_SELECTED] = ""77        self.savedFields[AnalysisParamsFieldNames.AP_ALIGNMENT_SELECTED] = ""78        self.savedFields[AnalysisParamsFieldNames.AP_IONSTATS_SELECTED] = ""79        self.savedFields[AnalysisParamsFieldNames.AP_THUMBNAIL_BEADFIND_SELECTED] = ""80        self.savedFields[81            AnalysisParamsFieldNames.AP_THUMBNAIL_ANALYSISARGS_SELECTED82        ] = ""83        self.savedFields[84            AnalysisParamsFieldNames.AP_THUMBNAIL_PREBASECALLER_SELECTED85        ] = ""86        self.savedFields[AnalysisParamsFieldNames.AP_THUMBNAIL_CALIBRATE_SELECTED] = ""87        self.savedFields[AnalysisParamsFieldNames.AP_THUMBNAIL_BASECALLER_SELECTED] = ""88        self.savedFields[AnalysisParamsFieldNames.AP_THUMBNAIL_ALIGNMENT_SELECTED] = ""89        self.savedFields[AnalysisParamsFieldNames.AP_THUMBNAIL_IONSTATS_SELECTED] = ""90        self.savedFields[AnalysisParamsFieldNames.AP_CUSTOM] = "False"91        self.prepopulatedFields[AnalysisParamsFieldNames.APPL_PRODUCT] = ""92        self.prepopulatedFields[AnalysisParamsFieldNames.RUN_TYPE] = ""93        self.prepopulatedFields[AnalysisParamsFieldNames.APPLICATION_GROUP_NAME] = ""94        self.prepopulatedFields[AnalysisParamsFieldNames.CATEGORIES] = ""95        self.prepopulatedFields[AnalysisParamsFieldNames.CHIP_TYPE] = ""96        self.prepopulatedFields[AnalysisParamsFieldNames.SAMPLE_PREPARATION_KIT] = ""97        self.prepopulatedFields[AnalysisParamsFieldNames.LIBRARY_KIT_NAME] = ""98        self.prepopulatedFields[AnalysisParamsFieldNames.TEMPLATE_KIT_NAME] = ""99        self.prepopulatedFields[AnalysisParamsFieldNames.SEQUENCE_KIT_NAME] = ""100        self.sh_type = sh_type101    def getStepName(self):102        return StepNames.ANALYSIS_PARAMS103    def updateSavedObjectsFromSavedFields(self):104        pass105    def validate(self):106        pass107    def hasErrors(self):108        """109        This step is a section of another step. It is crucial not to advertise having errors or110        user will be re-directed to analysis args' resourcePath for error correction.111        Let the parent step take care of the error broadcasting.112        """113        return False114    def validateField(self, field_name, new_field_value):115        pass116    def validateField_in_section(self, field_name, new_field_value):117        """118        field validation for a step that acts as a section to another step119        """120        logger.debug(121            "at analysis_params_step_data.validateField_in_section field_name=%s; new_field_value=%s"122            % (field_name, new_field_value)123        )124        pass125    def updateFromStep(self, updated_step):126        if updated_step.getStepName() not in self._dependsOn:127            return128        # reset best match if key attributes on other chevrons have changed129        needToRefreshSelectionList = False130        if (131            updated_step.getStepName() == StepNames.APPLICATION132            and updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]133        ):134            applProduct = updated_step.savedObjects[ApplicationFieldNames.APPL_PRODUCT]135            logger.debug(136                "analysis_params_step_data - APPL CHEVRON...  applProduct %s; runType=%s; applicationGroupName=%s"137                % (138                    applProduct.productCode,139                    updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE].runType,140                    updated_step.savedFields[141                        ApplicationFieldNames.APPLICATION_GROUP_NAME142                    ],143                )144            )145            if (146                self.prepopulatedFields[AnalysisParamsFieldNames.RUN_TYPE]147                != updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE].runType148                or self.prepopulatedFields[149                    AnalysisParamsFieldNames.APPLICATION_GROUP_NAME150                ]151                != updated_step.savedFields[152                    ApplicationFieldNames.APPLICATION_GROUP_NAME153                ]154            ):155                needToRefreshSelectionList = True156            self.prepopulatedFields[AnalysisParamsFieldNames.APPL_PRODUCT] = ""157            self.prepopulatedFields[158                AnalysisParamsFieldNames.RUN_TYPE159            ] = updated_step.savedObjects[ApplicationFieldNames.RUN_TYPE].runType160            self.prepopulatedFields[161                AnalysisParamsFieldNames.APPLICATION_GROUP_NAME162            ] = updated_step.savedFields[ApplicationFieldNames.APPLICATION_GROUP_NAME]163        elif updated_step.getStepName() == StepNames.KITS:164            if (165                self.prepopulatedFields[AnalysisParamsFieldNames.CHIP_TYPE]166                != updated_step.savedFields[KitsFieldNames.CHIP_TYPE]167                or self.prepopulatedFields[168                    AnalysisParamsFieldNames.SAMPLE_PREPARATION_KIT169                ]170                != updated_step.savedFields[KitsFieldNames.SAMPLE_PREPARATION_KIT]171                or self.prepopulatedFields[AnalysisParamsFieldNames.LIBRARY_KIT_NAME]172                != updated_step.savedFields[KitsFieldNames.LIBRARY_KIT_NAME]173                or self.prepopulatedFields[AnalysisParamsFieldNames.TEMPLATE_KIT_NAME]174                != updated_step.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME]175                or self.prepopulatedFields[AnalysisParamsFieldNames.SEQUENCE_KIT_NAME]176                != updated_step.savedFields[KitsFieldNames.SEQUENCE_KIT_NAME]177            ):178                needToRefreshSelectionList = True179            self.prepopulatedFields[AnalysisParamsFieldNames.CHIP_TYPE] = (180                updated_step.savedFields[KitsFieldNames.CHIP_TYPE]181                if updated_step.savedFields[KitsFieldNames.CHIP_TYPE]182                else ""183            )184            self.prepopulatedFields[185                AnalysisParamsFieldNames.SAMPLE_PREPARATION_KIT186            ] = updated_step.savedFields[KitsFieldNames.SAMPLE_PREPARATION_KIT]187            self.prepopulatedFields[188                AnalysisParamsFieldNames.LIBRARY_KIT_NAME189            ] = updated_step.savedFields[KitsFieldNames.LIBRARY_KIT_NAME]190            self.prepopulatedFields[191                AnalysisParamsFieldNames.TEMPLATE_KIT_NAME192            ] = updated_step.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME]193            self.prepopulatedFields[194                AnalysisParamsFieldNames.SEQUENCE_KIT_NAME195            ] = updated_step.savedFields[KitsFieldNames.SEQUENCE_KIT_NAME]196        if needToRefreshSelectionList:197            self._update_analysisParamsData_selection_list(198                self.prepopulatedFields[AnalysisParamsFieldNames.CHIP_TYPE],199                self.prepopulatedFields[AnalysisParamsFieldNames.SEQUENCE_KIT_NAME],200                self.prepopulatedFields[AnalysisParamsFieldNames.TEMPLATE_KIT_NAME],201                self.prepopulatedFields[AnalysisParamsFieldNames.LIBRARY_KIT_NAME],202                self.prepopulatedFields[203                    AnalysisParamsFieldNames.SAMPLE_PREPARATION_KIT204                ],205                self.prepopulatedFields[AnalysisParamsFieldNames.RUN_TYPE],206                self.prepopulatedFields[207                    AnalysisParamsFieldNames.APPLICATION_GROUP_NAME208                ],209                self.prepopulatedFields[AnalysisParamsFieldNames.CATEGORIES],210            )211    def _update_analysisParamsData_selection_list(212        self,213        chipType,214        sequenceKitName,215        templatingKitName,216        libraryKitName,217        samplePrepKitName,218        applicationType,219        applicationGroupName,220        applicationCategories,221    ):222        possible_match_entries = AnalysisArgs.possible_matches(223            chipType,224            sequenceKitName,225            templatingKitName,226            libraryKitName,227            samplePrepKitName,228            None,229            applicationType,230            applicationGroupName,231            applicationCategories,232        )233        logger.debug(234            "_update_analysisParamsData_selection_list() applicationType=%s; applicationGroupName=%s; applicationCategories=%s"235            % (applicationType, applicationGroupName, applicationCategories)236        )237        best_match_entry = AnalysisArgs.best_match(238            chipType,239            sequenceKitName,240            templatingKitName,241            libraryKitName,242            samplePrepKitName,243            None,244            applicationType,245            applicationGroupName,246            applicationCategories,247        )248        if best_match_entry:249            isTemplate = self.sh_type in StepHelperType.TEMPLATE_TYPES250            for ap in possible_match_entries:251                if ap.name == best_match_entry.name:252                    ap.name = (253                        AnalysisParamsFieldNames.AP_ENTRY_BEST_MATCH_TEMPLATE_VALUE254                        if isTemplate255                        else AnalysisParamsFieldNames.AP_ENTRY_BEST_MATCH_PLAN_VALUE256                    )257                    ap.best_match = True258            if self.savedFields[AnalysisParamsFieldNames.AP_CUSTOM] == "False":259                previously_selected_analysisArgs = {260                    "description": AnalysisParamsFieldNames.AP_ENTRY_PREVIOUSLY_SELECTED_VALUE,261                    "name": "",262                    "beadfindargs": self.savedFields[263                        AnalysisParamsFieldNames.AP_BEADFIND_SELECTED264                    ],265                    "analysisargs": self.savedFields[266                        AnalysisParamsFieldNames.AP_ANALYSISARGS_SELECTED267                    ],268                    "prebasecallerargs": self.savedFields[269                        AnalysisParamsFieldNames.AP_PREBASECALLER_SELECTED270                    ],271                    "calibrateargs": self.savedFields[272                        AnalysisParamsFieldNames.AP_CALIBRATE_SELECTED273                    ],274                    "basecallerargs": self.savedFields[275                        AnalysisParamsFieldNames.AP_BASECALLER_SELECTED276                    ],277                    "alignmentargs": self.savedFields[278                        AnalysisParamsFieldNames.AP_ALIGNMENT_SELECTED279                    ],280                    "ionstatsargs": self.savedFields[281                        AnalysisParamsFieldNames.AP_IONSTATS_SELECTED282                    ],283                    "thumbnailbeadfindargs": self.savedFields[284                        AnalysisParamsFieldNames.AP_THUMBNAIL_BEADFIND_SELECTED285                    ],286                    "thumbnailanalysisargs": self.savedFields[287                        AnalysisParamsFieldNames.AP_THUMBNAIL_ANALYSISARGS_SELECTED288                    ],289                    "prethumbnailbasecallerargs": self.savedFields[290                        AnalysisParamsFieldNames.AP_THUMBNAIL_PREBASECALLER_SELECTED291                    ],292                    "thumbnailcalibrateargs": self.savedFields[293                        AnalysisParamsFieldNames.AP_THUMBNAIL_CALIBRATE_SELECTED294                    ],295                    "thumbnailbasecallerargs": self.savedFields[296                        AnalysisParamsFieldNames.AP_THUMBNAIL_BASECALLER_SELECTED297                    ],298                    "thumbnailalignmentargs": self.savedFields[299                        AnalysisParamsFieldNames.AP_THUMBNAIL_ALIGNMENT_SELECTED300                    ],301                    "thumbnailionstatsargs": self.savedFields[302                        AnalysisParamsFieldNames.AP_THUMBNAIL_IONSTATS_SELECTED303                    ],304                }305                self.savedObjects[306                    AnalysisParamsFieldNames.AP_ENTRY_PREVIOUSLY_SELECTED307                ] = previously_selected_analysisArgs308                best_match_entry.description = (309                    AnalysisParamsFieldNames.AP_ENTRY_SELECTED_VALUE310                )311                self.savedObjects[312                    AnalysisParamsFieldNames.AP_ENTRY_SELECTED313                ] = best_match_entry314                self.savedFields[315                    AnalysisParamsFieldNames.AP_BEADFIND_SELECTED316                ] = best_match_entry.beadfindargs317                self.savedFields[318                    AnalysisParamsFieldNames.AP_ANALYSISARGS_SELECTED319                ] = best_match_entry.analysisargs320                self.savedFields[321                    AnalysisParamsFieldNames.AP_PREBASECALLER_SELECTED322                ] = best_match_entry.prebasecallerargs323                self.savedFields[324                    AnalysisParamsFieldNames.AP_CALIBRATE_SELECTED325                ] = best_match_entry.calibrateargs326                self.savedFields[327                    AnalysisParamsFieldNames.AP_BASECALLER_SELECTED328                ] = best_match_entry.basecallerargs329                self.savedFields[330                    AnalysisParamsFieldNames.AP_ALIGNMENT_SELECTED331                ] = best_match_entry.alignmentargs332                self.savedFields[333                    AnalysisParamsFieldNames.AP_IONSTATS_SELECTED334                ] = best_match_entry.ionstatsargs335                self.savedFields[336                    AnalysisParamsFieldNames.AP_THUMBNAIL_BEADFIND_SELECTED337                ] = best_match_entry.thumbnailbeadfindargs338                self.savedFields[339                    AnalysisParamsFieldNames.AP_THUMBNAIL_ANALYSISARGS_SELECTED340                ] = best_match_entry.thumbnailanalysisargs341                self.savedFields[342                    AnalysisParamsFieldNames.AP_THUMBNAIL_PREBASECALLER_SELECTED343                ] = best_match_entry.prethumbnailbasecallerargs344                self.savedFields[345                    AnalysisParamsFieldNames.AP_THUMBNAIL_CALIBRATE_SELECTED346                ] = best_match_entry.thumbnailcalibrateargs347                self.savedFields[348                    AnalysisParamsFieldNames.AP_THUMBNAIL_BASECALLER_SELECTED349                ] = best_match_entry.thumbnailbasecallerargs350                self.savedFields[351                    AnalysisParamsFieldNames.AP_THUMBNAIL_ALIGNMENT_SELECTED352                ] = best_match_entry.thumbnailalignmentargs353                self.savedFields[354                    AnalysisParamsFieldNames.AP_THUMBNAIL_IONSTATS_SELECTED355                ] = best_match_entry.thumbnailionstatsargs356        else:357            logger.debug(358                "analysis_params_step_data._update_analysisParamsData_selection_list() BEST MATCH NOT FOUND!!! chipType=%s;"359                % (chipType)360            )361        self.prepopulatedFields[362            AnalysisParamsFieldNames.AP_ENTRIES363        ] = possible_match_entries364        self.prepopulatedFields[AnalysisParamsFieldNames.AP_DISPLAYED_NAMES] = [365            ap.description for ap in possible_match_entries...

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