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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...

__init__.py

Source:__init__.py

1"""2Package generated from /System/Library/CoreServices/Finder.app3"""4from warnings import warnpy3k5warnpy3k("In 3.x, the Finder package is removed.", stacklevel=2)6import aetools7Error = aetools.Error8import Standard_Suite9import Legacy_suite10import Containers_and_folders11import Files12import Finder_Basics13import Finder_items14import Window_classes15import Type_Definitions16import Enumerations17_code_to_module = {18    'CoRe' : Standard_Suite,19    'fleg' : Legacy_suite,20    'fndr' : Containers_and_folders,21    'fndr' : Files,22    'fndr' : Finder_Basics,23    'fndr' : Finder_items,24    'fndr' : Window_classes,25    'tpdf' : Type_Definitions,26    'tpnm' : Enumerations,27}28_code_to_fullname = {29    'CoRe' : ('Finder.Standard_Suite', 'Standard_Suite'),30    'fleg' : ('Finder.Legacy_suite', 'Legacy_suite'),31    'fndr' : ('Finder.Containers_and_folders', 'Containers_and_folders'),32    'fndr' : ('Finder.Files', 'Files'),33    'fndr' : ('Finder.Finder_Basics', 'Finder_Basics'),34    'fndr' : ('Finder.Finder_items', 'Finder_items'),35    'fndr' : ('Finder.Window_classes', 'Window_classes'),36    'tpdf' : ('Finder.Type_Definitions', 'Type_Definitions'),37    'tpnm' : ('Finder.Enumerations', 'Enumerations'),38}39from Standard_Suite import *40from Legacy_suite import *41from Containers_and_folders import *42from Files import *43from Finder_Basics import *44from Finder_items import *45from Window_classes import *46from Type_Definitions import *47from Enumerations import *48def getbaseclasses(v):49    if not getattr(v, '_propdict', None):50        v._propdict = {}51        v._elemdict = {}52        for superclassname in getattr(v, '_superclassnames', []):53            superclass = eval(superclassname)54            getbaseclasses(superclass)55            v._propdict.update(getattr(superclass, '_propdict', {}))56            v._elemdict.update(getattr(superclass, '_elemdict', {}))57        v._propdict.update(getattr(v, '_privpropdict', {}))58        v._elemdict.update(getattr(v, '_privelemdict', {}))59import StdSuites60#61# Set property and element dictionaries now that all classes have been defined62#63getbaseclasses(StdSuites.Type_Names_Suite.small_integer)64getbaseclasses(StdSuites.Type_Names_Suite.system_dictionary)65getbaseclasses(StdSuites.Type_Names_Suite.color_table)66getbaseclasses(StdSuites.Type_Names_Suite.fixed_point)67getbaseclasses(StdSuites.Type_Names_Suite.string)68getbaseclasses(StdSuites.Type_Names_Suite.type_element_info)69getbaseclasses(StdSuites.Type_Names_Suite.machine_location)70getbaseclasses(StdSuites.Type_Names_Suite.PostScript_picture)71getbaseclasses(StdSuites.Type_Names_Suite.type_property_info)72getbaseclasses(StdSuites.Type_Names_Suite.menu_item)73getbaseclasses(StdSuites.Type_Names_Suite.scrap_styles)74getbaseclasses(StdSuites.Type_Names_Suite.fixed_rectangle)75getbaseclasses(StdSuites.Type_Names_Suite.null)76getbaseclasses(StdSuites.Type_Names_Suite.type_event_info)77getbaseclasses(StdSuites.Type_Names_Suite.rotation)78getbaseclasses(StdSuites.Type_Names_Suite.long_fixed_rectangle)79getbaseclasses(StdSuites.Type_Names_Suite.long_point)80getbaseclasses(StdSuites.Type_Names_Suite.target_id)81getbaseclasses(StdSuites.Type_Names_Suite.type_suite_info)82getbaseclasses(StdSuites.Type_Names_Suite.type_parameter_info)83getbaseclasses(StdSuites.Type_Names_Suite.long_fixed_point)84getbaseclasses(StdSuites.Type_Names_Suite.bounding_rectangle)85getbaseclasses(StdSuites.Type_Names_Suite.TIFF_picture)86getbaseclasses(StdSuites.Type_Names_Suite.long_fixed)87getbaseclasses(StdSuites.Type_Names_Suite.version)88getbaseclasses(StdSuites.Type_Names_Suite.RGB16_color)89getbaseclasses(StdSuites.Type_Names_Suite.double_integer)90getbaseclasses(StdSuites.Type_Names_Suite.location_reference)91getbaseclasses(StdSuites.Type_Names_Suite.point)92getbaseclasses(StdSuites.Type_Names_Suite.application_dictionary)93getbaseclasses(StdSuites.Type_Names_Suite.unsigned_integer)94getbaseclasses(StdSuites.Type_Names_Suite.menu)95getbaseclasses(StdSuites.Type_Names_Suite.small_real)96getbaseclasses(StdSuites.Type_Names_Suite.fixed)97getbaseclasses(StdSuites.Type_Names_Suite.type_class_info)98getbaseclasses(StdSuites.Type_Names_Suite.RGB96_color)99getbaseclasses(StdSuites.Type_Names_Suite.dash_style)100getbaseclasses(StdSuites.Type_Names_Suite.pixel_map_record)101getbaseclasses(StdSuites.Type_Names_Suite.extended_real)102getbaseclasses(StdSuites.Type_Names_Suite.long_rectangle)103getbaseclasses(process)104getbaseclasses(application_process)105getbaseclasses(desk_accessory_process)106getbaseclasses(application)107getbaseclasses(trash_2d_object)108getbaseclasses(desktop_2d_object)109getbaseclasses(container)110getbaseclasses(folder)111getbaseclasses(disk)112getbaseclasses(application)113getbaseclasses(alias_file)114getbaseclasses(package)115getbaseclasses(file)116getbaseclasses(application_file)117getbaseclasses(internet_location_file)118getbaseclasses(document_file)119getbaseclasses(clipping)120getbaseclasses(preferences_window)121getbaseclasses(Finder_window)122getbaseclasses(window)123getbaseclasses(clipping_window)124getbaseclasses(information_window)125getbaseclasses(item)126getbaseclasses(icon_view_options)127getbaseclasses(preferences)128getbaseclasses(alias_list)129getbaseclasses(icon_family)130getbaseclasses(label)131getbaseclasses(column)132getbaseclasses(list_view_options)133#134# Indices of types declared in this module135#136_classdeclarations = {137    'shor' : StdSuites.Type_Names_Suite.small_integer,138    'aeut' : StdSuites.Type_Names_Suite.system_dictionary,139    'clrt' : StdSuites.Type_Names_Suite.color_table,140    'fpnt' : StdSuites.Type_Names_Suite.fixed_point,141    'TEXT' : StdSuites.Type_Names_Suite.string,142    'elin' : StdSuites.Type_Names_Suite.type_element_info,143    'mLoc' : StdSuites.Type_Names_Suite.machine_location,144    'EPS ' : StdSuites.Type_Names_Suite.PostScript_picture,145    'pinf' : StdSuites.Type_Names_Suite.type_property_info,146    'cmen' : StdSuites.Type_Names_Suite.menu_item,147    'styl' : StdSuites.Type_Names_Suite.scrap_styles,148    'frct' : StdSuites.Type_Names_Suite.fixed_rectangle,149    'null' : StdSuites.Type_Names_Suite.null,150    'evin' : StdSuites.Type_Names_Suite.type_event_info,151    'trot' : StdSuites.Type_Names_Suite.rotation,152    'lfrc' : StdSuites.Type_Names_Suite.long_fixed_rectangle,153    'lpnt' : StdSuites.Type_Names_Suite.long_point,154    'targ' : StdSuites.Type_Names_Suite.target_id,155    'suin' : StdSuites.Type_Names_Suite.type_suite_info,156    'pmin' : StdSuites.Type_Names_Suite.type_parameter_info,157    'lfpt' : StdSuites.Type_Names_Suite.long_fixed_point,158    'qdrt' : StdSuites.Type_Names_Suite.bounding_rectangle,159    'TIFF' : StdSuites.Type_Names_Suite.TIFF_picture,160    'lfxd' : StdSuites.Type_Names_Suite.long_fixed,161    'vers' : StdSuites.Type_Names_Suite.version,162    'tr16' : StdSuites.Type_Names_Suite.RGB16_color,163    'comp' : StdSuites.Type_Names_Suite.double_integer,164    'insl' : StdSuites.Type_Names_Suite.location_reference,165    'QDpt' : StdSuites.Type_Names_Suite.point,166    'aete' : StdSuites.Type_Names_Suite.application_dictionary,167    'magn' : StdSuites.Type_Names_Suite.unsigned_integer,168    'cmnu' : StdSuites.Type_Names_Suite.menu,169    'sing' : StdSuites.Type_Names_Suite.small_real,170    'fixd' : StdSuites.Type_Names_Suite.fixed,171    'gcli' : StdSuites.Type_Names_Suite.type_class_info,172    'tr96' : StdSuites.Type_Names_Suite.RGB96_color,173    'tdas' : StdSuites.Type_Names_Suite.dash_style,174    'tpmm' : StdSuites.Type_Names_Suite.pixel_map_record,175    'exte' : StdSuites.Type_Names_Suite.extended_real,176    'lrct' : StdSuites.Type_Names_Suite.long_rectangle,177    'prcs' : process,178    'pcap' : application_process,179    'pcda' : desk_accessory_process,180    'capp' : application,181    'ctrs' : trash_2d_object,182    'cdsk' : desktop_2d_object,183    'ctnr' : container,184    'cfol' : folder,185    'cdis' : disk,186    'capp' : application,187    'alia' : alias_file,188    'pack' : package,189    'file' : file,190    'appf' : application_file,191    'inlf' : internet_location_file,192    'docf' : document_file,193    'clpf' : clipping,194    'pwnd' : preferences_window,195    'brow' : Finder_window,196    'cwin' : window,197    'lwnd' : clipping_window,198    'iwnd' : information_window,199    'cobj' : item,200    'icop' : icon_view_options,201    'cprf' : preferences,202    'alst' : alias_list,203    'ifam' : icon_family,204    'clbl' : label,205    'lvcl' : column,206    'lvop' : list_view_options,207}208class Finder(Standard_Suite_Events,209        Legacy_suite_Events,210        Containers_and_folders_Events,211        Files_Events,212        Finder_Basics_Events,213        Finder_items_Events,214        Window_classes_Events,215        Type_Definitions_Events,216        Enumerations_Events,217        aetools.TalkTo):218    _signature = 'MACS'219    _moduleName = 'Finder'220    _elemdict = application._elemdict...

collect_coco_voc_gtgraph.py

Source:collect_coco_voc_gtgraph.py

1import pickle2import numpy as np3#compute attribute graph4NUM_ATTR_REL = 2005def cout_w(prob, num=NUM_ATTR_REL,dim=1):6    prob_weight = prob[:, :num]7    sum_value = np.sum(prob_weight, keepdims=True, axis=dim) + 0.18    prob_weight = prob_weight / np.repeat(sum_value, prob_weight.shape[dim], axis=dim)9    return prob_weight10def cp_kl(a, b):11    # compute kl diverse12    if np.sum(a) == 0 or np.sum(b) == 0:13        return 114    sum_ = a * np.log(a / b)15    all_value = [x for x in sum_ if str(x) != 'nan' and str(x) != 'inf']16    kl = np.sum(all_value)17    return kl18def compute_js(attr_prob):19    cls_num = attr_prob.shape[0]20    similarity = np.zeros((cls_num, cls_num))21    similarity[0, 1:] = 122    similarity[1:, 0] = 123    for i in range(1, cls_num):24        if i % 50 == 0:25            print('had proccessed {} cls...\n'.format(i))26        for j in range(1, cls_num):27            if i == j:28                similarity[i,j] = 029            else:30                similarity[i,j] = 0.5 * (cp_kl(attr_prob[i, :], 0.5*(attr_prob[i, :] + attr_prob[j,:]))31                                         + cp_kl(attr_prob[j, :], 0.5*(attr_prob[i, :] + attr_prob[j, :])))32    return similarity33if __name__ == '__main__':34    # We collect coco/voc gt graph by matching classes names with VG.35    # First, you should download attribute/relationship frequency statistic matrix.36    # Second, you should save your dataset classes names. We provide VG names and COCO names.37    data_path = 'Your Path ...'38    vg_class_names_dict = pickle.load(open(data_path + 'vg_3000_name_to_ind.pkl', 'rb'))39    dataset = 'coco'40    vg_ind_cls = {v: k for k, v in vg_class_names_dict.items()}41    vg_class_names = []42    vg_class_names_list = list(vg_class_names_dict)43    for i in vg_class_names_list:44        if i == '__background__':45            vg_class_names.append(i)46        else:47            vg_class_names.append(i.split('.')[0])48    # replace voc name with corresponding to VG49    VOC_class_names = pickle.load(open(data_path + 'VOC_class_names.pkl', 'rb'))50    VOC_class_names = list(VOC_class_names)51    VOC_class_names[VOC_class_names.index('aeroplane')] = 'airplane'52    VOC_class_names[VOC_class_names.index('diningtable')] = 'table'53    VOC_class_names[VOC_class_names.index('motorbike')] = 'motorcycle'54    VOC_class_names[VOC_class_names.index('pottedplant')] = 'plant'55    VOC_class_names[VOC_class_names.index('tvmonitor')] = 'television'56    # replace COCO name with corresponding to VG57    COCO_class_names = pickle.load(open('/data/detection/coco/coco_name.pkl', 'rb'))58    COCO_class_names = list(COCO_class_names)59    COCO_class_names = [n.strip().replace(' ', '_') for n in COCO_class_names]60    COCO_class_names[COCO_class_names.index('tv')] = 'television'61    COCO_class_names[COCO_class_names.index('fire_hydrant')] = 'fireplug'62    COCO_class_names[COCO_class_names.index('stop_sign')] = 'sign'63    COCO_class_names[COCO_class_names.index('handbag')] = 'bag'64    COCO_class_names[COCO_class_names.index('suitcase')] = 'case'65    COCO_class_names[COCO_class_names.index('skis')] = 'ski'66    COCO_class_names[COCO_class_names.index('sports_ball')] = 'ball'67    COCO_class_names[COCO_class_names.index('wine_glass')] = 'goblet'68    COCO_class_names[COCO_class_names.index('orange')] = 'fruit'  # mandarin citrus69    COCO_class_names[COCO_class_names.index('hot_dog')] = 'hotdog'70    COCO_class_names[COCO_class_names.index('donut')] = 'doughnut'71    COCO_class_names[COCO_class_names.index('couch')] = 'sofa'72    COCO_class_names[COCO_class_names.index('remote')] = 'remote_control'73    COCO_class_names[COCO_class_names.index('cell_phone')] = 'mobile'74    COCO_class_names[COCO_class_names.index('dining_table')] = 'table'75    COCO_class_names[COCO_class_names.index('teddy_bear')] = 'teddy'76    COCO_class_names[COCO_class_names.index('hair_drier')] = 'hand_blower'77    index_vg_of_DATASET = []78    if dataset == 'voc':79        for i in COCO_class_names:80            if i == 'potted_plant':81                index_vg_of_DATASET.append(1333)82            else:83                index_vg_of_DATASET.append(vg_class_names.index(i))84    elif dataset == 'coco':85        for i in COCO_class_names:86            index_vg_of_DATASET.append(vg_class_names.index(i))87    # Attribute graph88    graph_a = pickle.load(open(data_path + 'vg_attr_frequency_3000.pkl', 'rb'))89    new_graph = graph_a[index_vg_of_DATASET,]90    new_graph = cout_w(new_graph, num=len(new_graph))91    new_graph = compute_js(new_graph)92    new_graph = 1 - new_graph93    pickle.dump(new_graph, open(data_path + dataset + '_graph_a.pkl', 'wb'))94    # Relation graph95    graph_r = pickle.load(open(data_path + 'vg_pair_frequency_3000.pkl', 'rb'))96    index_vg_of_DATASET_ = [x for x in index_vg_of_DATASET[1:]]97    # graph_r_COCO = graph_r[[x for x in index_vg_of_COCO_big],]98    new_graph = graph_r[index_vg_of_DATASET_, :]99    new_graph = new_graph[:, index_vg_of_DATASET_]100    relation_matrix = new_graph + new_graph.transpose()101    relation_matrix_row_sum = relation_matrix.sum(1)102    num_classes = len(index_vg_of_DATASET) - 1103    for i in range(num_classes):104        relation_matrix[i, i] = relation_matrix_row_sum[i] + 1105    prob_relation_matrix = np.zeros((num_classes, num_classes))106    for i in range(num_classes):107        for j in range(num_classes):108            prob_relation_matrix[i, j] = relation_matrix[i, j] / (109                    np.sqrt(relation_matrix[i, i]) * np.sqrt(relation_matrix[j, j]))110    graph_r_ = np.zeros((num_classes + 1, num_classes + 1))111    graph_r_[1:, 1:] = prob_relation_matrix...

test_names.py

Source:test_names.py

2Tests for `api.names`.3"""4from textwrap import dedent5import pytest6def _assert_definition_names(definitions, names):7    assert [d.name for d in definitions] == names8def _check_names(get_names, source, names):9    definitions = get_names(dedent(source))10    _assert_definition_names(definitions, names)11    return definitions12def test_get_definitions_flat(get_names):13    _check_names(get_names, """14        import module15        class Class:16            pass17        def func():18            pass19        data = None20        """, ['module', 'Class', 'func', 'data'])21def test_dotted_assignment(get_names):22    _check_names(get_names, """23    x = Class()24    x.y.z = None25    """, ['x', 'z'])  # TODO is this behavior what we want?26def test_multiple_assignment(get_names):27    _check_names(get_names, "x = y = None", ['x', 'y'])28def test_multiple_imports(get_names):29    _check_names(get_names, """30    from module import a, b31    from another_module import *32    """, ['a', 'b'])33def test_nested_definitions(get_names):34    definitions = _check_names(get_names, """35    class Class:36        def f():37            pass38        def g():39            pass40    """, ['Class'])41    subdefinitions = definitions[0].defined_names()42    _assert_definition_names(subdefinitions, ['f', 'g'])43    assert [d.full_name for d in subdefinitions] == ['__main__.Class.f', '__main__.Class.g']44def test_nested_class(get_names):45    definitions = _check_names(get_names, """46    class L1:47        class L2:48            class L3:49                def f(): pass50            def f(): pass51        def f(): pass52    def f(): pass53    """, ['L1', 'f'])54    subdefs = definitions[0].defined_names()55    subsubdefs = subdefs[0].defined_names()56    _assert_definition_names(subdefs, ['L2', 'f'])57    _assert_definition_names(subsubdefs, ['L3', 'f'])58    _assert_definition_names(subsubdefs[0].defined_names(), ['f'])59def test_class_fields_with_all_scopes_false(get_names):60    definitions = _check_names(get_names, """61    from module import f62    g = f(f)63    class C:64        h = g65    def foo(x=a):66       bar = x67       return bar68    """, ['f', 'g', 'C', 'foo'])69    C_subdefs = definitions[-2].defined_names()70    foo_subdefs = definitions[-1].defined_names()71    _assert_definition_names(C_subdefs, ['h'])72    _assert_definition_names(foo_subdefs, ['x', 'bar'])73def test_async_stmt_with_all_scopes_false(get_names):74    definitions = _check_names(get_names, """75    from module import f76    import asyncio77    g = f(f)78    class C:79        h = g80        def __init__(self):81            pass82        async def __aenter__(self):83            pass84    def foo(x=a):85       bar = x86       return bar87    async def async_foo(duration):88        async def wait():89            await asyncio.sleep(100)90        for i in range(duration//100):91            await wait()92        return duration//100*10093    async with C() as cinst:94        d = cinst95    """, ['f', 'asyncio', 'g', 'C', 'foo', 'async_foo', 'cinst', 'd'])96    C_subdefs = definitions[3].defined_names()97    foo_subdefs = definitions[4].defined_names()98    async_foo_subdefs = definitions[5].defined_names()99    cinst_subdefs = definitions[6].defined_names()100    _assert_definition_names(C_subdefs, ['h', '__init__', '__aenter__'])101    _assert_definition_names(foo_subdefs, ['x', 'bar'])102    _assert_definition_names(async_foo_subdefs, ['duration', 'wait', 'i'])103    # We treat d as a name outside `async with` block104    _assert_definition_names(cinst_subdefs, [])105def test_follow_imports(get_names):106    # github issue #344107    imp = get_names('import datetime')[0]108    assert imp.name == 'datetime'109    datetime_names = [str(d.name) for d in imp.defined_names()]110    assert 'timedelta' in datetime_names111def test_names_twice(get_names):112    code = dedent('''113    def lol():114        pass115    ''')116    defs = get_names(code)117    assert defs[0].defined_names() == []118def test_simple_name(get_names):119    defs = get_names('foo', references=True)120    assert not defs[0]._name.infer()121def test_no_error(get_names):122    code = dedent("""123        def foo(a, b):124            if a == 10:125                if b is None:126                    print("foo")127                a = 20128        """)129    func_name, = get_names(code)130    a, b, a20 = func_name.defined_names()131    assert a.name == 'a'132    assert b.name == 'b'133    assert a20.name == 'a'134    assert a20.goto() == [a20]135@pytest.mark.parametrize(136    'code, index, is_side_effect', [137        ('x', 0, False),138        ('x.x', 0, False),139        ('x.x', 1, False),140        ('x.x = 3', 0, False),141        ('x.x = 3', 1, True),142        ('def x(x): x.x = 3', 1, False),143        ('def x(x): x.x = 3', 3, True),144        ('import sys; sys.path', 0, False),145        ('import sys; sys.path', 1, False),146        ('import sys; sys.path', 2, False),147        ('import sys; sys.path = []', 2, True),148    ]149)150def test_is_side_effect(get_names, code, index, is_side_effect):151    names = get_names(code, references=True, all_scopes=True)...

format_ids.py

Source:format_ids.py

1from struct import pack, unpack2def parseIP(string):3    bunch = map(int, string.split('.'))4    # pack to bytes5    p = pack('4B', *bunch)6    # unpack as u167    return unpack('>I', p)[0]8def writeIP(raw):9    # pack to bytes10    p = pack('>I', raw)11    # unpack12    return '.'.join(map(str, unpack('4B', p)))13def writeFloat(raw):14    # this is just how floats get printed...15    return '{0:.6f}'.format(raw)16xml_formats = {17    1  : { 'names' : ['void']},18    2  : { 'type' : 'b',  'count' : 1,  'names' : ['s8']},19    3  : { 'type' : 'B',  'count' : 1,  'names' : ['u8']},20    4  : { 'type' : 'h',  'count' : 1,  'names' : ['s16']},21    5  : { 'type' : 'H',  'count' : 1,  'names' : ['u16']},22    6  : { 'type' : 'i',  'count' : 1,  'names' : ['s32']},23    7  : { 'type' : 'I',  'count' : 1,  'names' : ['u32']},24    8  : { 'type' : 'q',  'count' : 1,  'names' : ['s64']},25    9  : { 'type' : 'Q',  'count' : 1,  'names' : ['u64']},26    10 : { 'type' : 'B',  'count' : -1, 'names' : ['bin', 'binary'], 'fromStr' : None},27    11 : { 'type' : 'B',  'count' : -1, 'names' : ['str', 'string'], 'fromStr' : None},28    12 : { 'type' : 'I',  'count' : 1,  'names' : ['ip4'], 'fromStr' : parseIP, 'toStr' : writeIP},29    13 : { 'type' : 'I',  'count' : 1,  'names' : ['time']}, # unix timestamp30    14 : { 'type' : 'f',  'count' : 1,  'names' : ['float', 'f'], 'fromStr' : float, 'toStr' : writeFloat},31    15 : { 'type' : 'd',  'count' : 1,  'names' : ['double', 'd'], 'fromStr' : float, 'toStr' : writeFloat},32    16 : { 'type' : 'b',  'count' : 2,  'names' : ['2s8']},33    17 : { 'type' : 'B',  'count' : 2,  'names' : ['2u8']},34    18 : { 'type' : 'h',  'count' : 2,  'names' : ['2s16']},35    19 : { 'type' : 'H',  'count' : 2,  'names' : ['2u16']},36    20 : { 'type' : 'i',  'count' : 2,  'names' : ['2s32']},37    21 : { 'type' : 'I',  'count' : 2,  'names' : ['2u32']},38    22 : { 'type' : 'q',  'count' : 2,  'names' : ['2s64', 'vs64']},39    23 : { 'type' : 'Q',  'count' : 2,  'names' : ['2u64', 'vu64']},40    24 : { 'type' : 'f',  'count' : 2,  'names' : ['2f'], 'fromStr' : float, 'toStr' : writeFloat},41    25 : { 'type' : 'd',  'count' : 2,  'names' : ['2d', 'vd'], 'fromStr' : float, 'toStr' : writeFloat},42    26 : { 'type' : 'b',  'count' : 3,  'names' : ['3s8']},43    27 : { 'type' : 'B',  'count' : 3,  'names' : ['3u8']},44    28 : { 'type' : 'h',  'count' : 3,  'names' : ['3s16']},45    29 : { 'type' : 'H',  'count' : 3,  'names' : ['3u16']},46    30 : { 'type' : 'i',  'count' : 3,  'names' : ['3s32']},47    31 : { 'type' : 'I',  'count' : 3,  'names' : ['3u32']},48    32 : { 'type' : 'q',  'count' : 3,  'names' : ['3s64']},49    33 : { 'type' : 'Q',  'count' : 3,  'names' : ['3u64']},50    34 : { 'type' : 'f',  'count' : 3,  'names' : ['3f'], 'fromStr' : float, 'toStr' : writeFloat},51    35 : { 'type' : 'd',  'count' : 3,  'names' : ['3d'], 'fromStr' : float, 'toStr' : writeFloat},52    36 : { 'type' : 'b',  'count' : 4,  'names' : ['4s8']},53    37 : { 'type' : 'B',  'count' : 4,  'names' : ['4u8']},54    38 : { 'type' : 'h',  'count' : 4,  'names' : ['4s16']},55    39 : { 'type' : 'H',  'count' : 4,  'names' : ['4u16']},56    40 : { 'type' : 'i',  'count' : 4,  'names' : ['4s32', 'vs32']},57    41 : { 'type' : 'I',  'count' : 4,  'names' : ['4u32', 'vu32']},58    42 : { 'type' : 'q',  'count' : 4,  'names' : ['4s64']},59    43 : { 'type' : 'Q',  'count' : 4,  'names' : ['4u64']},60    44 : { 'type' : 'f',  'count' : 4,  'names' : ['4f', 'vf'], 'fromStr' : float, 'toStr' : writeFloat},61    45 : { 'type' : 'd',  'count' : 4,  'names' : ['4d'], 'fromStr' : float, 'toStr' : writeFloat},62    46 : { 'names' : ['attr']},63    #47 : { 'names' : ['array']}, # TODO: how does this work?64    48 : { 'type' : 'b',  'count' : 16, 'names' : ['vs8']},65    49 : { 'type' : 'B',  'count' : 16, 'names' : ['vu8']},66    50 : { 'type' : 'h',  'count' : 8,  'names' : ['vs16']},67    51 : { 'type' : 'H',  'count' : 8,  'names' : ['vu16']},68    52 : { 'type' : 'b',  'count' : 1,  'names' : ['bool', 'b']},69    53 : { 'type' : 'b',  'count' : 2,  'names' : ['2b']},70    54 : { 'type' : 'b',  'count' : 3,  'names' : ['3b']},71    55 : { 'type' : 'b',  'count' : 4,  'names' : ['4b']},72    56 : { 'type' : 'b',  'count' : 16, 'names' : ['vb']}73}74# little less boilerplate for writing75for key, val in xml_formats.items():76    xml_formats[key]['name'] = xml_formats[key]['names'][0]77xml_types = {}78for key, val in xml_formats.items():79    for n in val['names']:80        xml_types[n] = key81xml_types['nodeStart'] = 182xml_types['nodeEnd'] = 190...

Using AI Code Generation

1var wpt = require('webpagetest');2var wpt = new WebPageTest('www.webpagetest.org');3wpt.getLocations(function(err, data) {4    if (err) return console.error(err);5    console.log(data);6});7var wpt = require('webpagetest');8var wpt = new WebPageTest('www.webpagetest.org');9var options = {10};11wpt.runTest(url, options, function(err, data) {12    if (err) return console.error(err);13    console.log(data);14});15var wpt = require('webpagetest');16var wpt = new WebPageTest('www.webpagetest.org');17var testId = '150404_0R_1';18wpt.getTestStatus(testId, function(err, data) {19    if (err) return console.error(err);20    console.log(data);21});22var wpt = require('webpagetest');23var wpt = new WebPageTest('www.webpagetest.org');24var testId = '150404_0R_1';25wpt.getTestResults(testId, function(err, data) {26    if (err) return console.error(err);27    console.log(data);28});29var wpt = require('webpagetest');30var wpt = new WebPageTest('www.webpagetest.org');31var testId = '150404_0R_1';32wpt.getTestVideo(testId, function(err, data) {33    if (err) return console.error(err);34    console.log(data);35});36var wpt = require('webpagetest');

Using AI Code Generation

1var wpt = require('webpagetest');2var wpt = new WebPageTest('www.webpagetest.org');3var options = {4};5wpt.runTest('www.google.com', options, function(err, data) {6    if (err) return console.error(err);7    wpt.getTestResults(data.data.testId, function(err, data) {8        if (err) return console.error(err);9        console.log(data.data.median.firstView.SpeedIndex);10    });11});

Using AI Code Generation

1var wpt = require('webpagetest');2var test = wpt('www.webpagetest.org');3    if (err) return console.error(err);4    console.log('Test status: ' + data.statusText);5    test.getTestStatus(data.data.testId, function(err, data) {6        if (err) return console.error(err);7        console.log('Test status: ' + data.statusText);8        test.getTestResults(data.data.testId, function(err, data) {9            if (err) return console.error(err);10            console.log('Test results: ' + data.statusText);11            console.log('First View: ' + data.data.average.firstView.loadTime);12            console.log('Repeat View: ' + data.data.average.repeatView.loadTime);13        });14    });15});16test.getLocations(function(err, data) {17    if (err) return console.error(err);18    console.log('Locations: ' + data.statusText);19    console.log('Locations: ' + data.data);20});21test.getTesters(function(err, data) {22    if (err) return console.error(err);23    console.log('Testers: ' + data.statusText);24    console.log('Testers: ' + data.data);25});26test.getTesters(function(err, data) {27    if (err) return console.error(err);28    console.log('Testers: ' + data.statusText);29    console.log('Testers: ' + data.data);30});31test.getTesters(function(err, data) {32    if (err) return console.error(err);33    console.log('Testers: ' + data.statusText);34    console.log('Testers: ' + data.data);35});36test.getTesters(function(err, data) {37    if (err) return console.error(err);38    console.log('Testers: ' + data.statusText);39    console.log('Testers: ' + data.data);40});41test.getTesters(function(err, data) {42    if (err) return console.error(err);43    console.log('Testers: ' + data.statusText);44    console.log('Testers: ' + data.data);45});46test.getTesters(function(err, data) {47    if (err) return console.error(err);48    console.log('Testers: ' + data.statusText);49    console.log('Testers: ' + data.data);50});

Using AI Code Generation

1var wptools = require('wptools');2var fs = require('fs');3wptools.page('Barack Obama').then(function(page) {4  return page.names();5}).then(function(names) {6  console.log(names);7  fs.writeFile('names.json', JSON.stringify(names, null, 4), function(err) {8    console.log('File successfully written! - Check your project directory for the names.json file');9  });10}).catch(function(err) {11  console.log(err);12});13var wptools = require('wptools');14var fs = require('fs');15wptools.page('Barack Obama').then(function(page) {16  return page.coordinates();17}).then(function(coordinates) {18  console.log(coordinates);19  fs.writeFile('coordinates.json', JSON.stringify(coordinates, null, 4), function(err) {20    console.log('File successfully written! - Check your project directory for the coordinates.json file');21  });22}).catch(function(err) {23  console.log(err);24});25var wptools = require('wptools');26var fs = require('fs');27wptools.page('Barack Obama').then(function(page) {28  return page.categories();29}).then(function(categories) {30  console.log(categories);31  fs.writeFile('categories.json', JSON.stringify(categories, null, 4), function(err) {32    console.log('File successfully written! - Check your project directory for the categories.json file');33  });34}).catch(function(err) {35  console.log(err);36});37var wptools = require('wptools');38var fs = require('fs');39wptools.page('Barack Obama').then(function(page) {40  return page.infobox();41}).then(function(infobox) {42  console.log(infobox);43  fs.writeFile('infobox.json', JSON.stringify(infobox, null, 4), function(err) {44    console.log('File successfully written! - Check your project directory for the infobox.json file');45  });46}).catch(function(err) {47  console.log(err);48});49var wptools = require('wptools');

Using AI Code Generation

1var wptools = require('wptools');2wptools.page('Barack Obama').get(function(err, page) {3    console.log(page.infobox('name'));4});5var wptools = require('wptools');6wptools.page('Barack Obama').get(function(err, page) {7    console.log(page.infobox('name'));8});9var wptools = require('wptools');10wptools.page('Barack Obama').get(function(err, page) {11    console.log(page.infobox('name'));12});13var wptools = require('wptools');14wptools.page('Barack Obama').get(function(err, page) {15    console.log(page.infobox('name'));16});17var wptools = require('wptools');18wptools.page('Barack Obama').get(function(err, page) {19    console.log(page.infobox('name'));20});21var wptools = require('wptools');22wptools.page('Barack Obama').get(function(err, page) {23    console.log(page.infobox('name'));24});25var wptools = require('wptools');26wptools.page('Barack Obama').get(function(err, page) {27    console.log(page.infobox('name'));28});29var wptools = require('wptools');30wptools.page('Barack Obama').get(function(err, page) {31    console.log(page.infobox('name'));32});

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.