5i܃ dZddlmZmZmZmZddlZddlZddlm Z ddl m Z ddl m Z ddlmZdd lmZdd lmZmZdd lmZGd d eZej0dZej5dde dddej0dZej5de ddgddej0dZej5ddde ddd d!"ej0dZej5d#d$dej0dZej5d%d&d'ee d(d)ej0dZ e jCZ"e"j5d*e d+dde"j5d,d-dej0dZ#e#jId.Z%e%j5d/d0d1gd0d1d23e%j5d4d5d6e d7dd8ze d9dd:d:d;zd<=e%j5d>d?d@e dAdd8ze dBddd:d:CzddZ?dd„Z@dÄZAdĄZBdńZCdƄZDdDŽZEy)z This file contains parsers with no added help that can be inherited by other parsers, as well as utility functions for parsing the input to those parsers. )print_functionunicode_literalsdivisionabsolute_importN)config)fill) format_table)split_unescaped)InstanceTypesCompleter)DXError DXCLIError) basestringceZdZdZdZy) DXParserErrorc||_yNmsg)selfrs r/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/cli/parsers.py__init__zDXParserError.__init__#s c|jSrr)rs r__str__zDXParserError.__str__&s xxrN)__name__ __module__ __qualname__rrrrrr"s rrF)add_helpz-az--allz9Apply to all results with the same name without promptingwidth_adjustment store_truehelpactionz--colorz@Set when color is used (color=auto is used when stdout is a TTY))offonautor*)r&choicesdefaultz --delimiterz--delim delimiterzAlways use exactly one of DELIMITER to separate fields to be printed; if no delimiter is provided with this flag, TAB will be used? )destr&nargsconstz--jsonzDisplay return value in JSONz--tryTjob_tryzWhen modifying a job that was restarted, apply the change to try T of the restarted job. 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Default is the last job try.)metavarr0typer&z--briefz]Display a brief version of the return value; for most commands, prints a DNAnexus ID per linez --verbosez+If available, displays extra verbose outputzmetadata argumentsz --visibilityhiddenvisiblez#Whether the object is hidden or not)r+r0r,r&z --property propertiesz KEY=VALUEz9Key-value pair to add as a property; repeat as necessary, z0e.g. "--property key1=val1 --property key2=val2" )r#initial_indentsubsequent_indentbreak_on_hyphensappend)r0r5r&r'z--typeTYPEtypesz-Type of the data object; repeat as necessary,z e.g. "--type type1 --type type2")r#r>r<r=)r5r0r&r'z--tagTAGtagsz,Tag of the data object; repeat as necessary,ze.g. "--tag tag1 --tag tag2"z --detailszJSON to store as details)r&z-pz --parentsz#Create any parent folders necessaryz-oz--outputpathz_DNAnexus path for the new data object (default uses current project and folder if not provided))r&r1z KEY[=VALUE]zKey-value pair of a property or simply a property key; if only a key is provided, matches a result that has the key with any value; repeat as necessary, e.g. "--property key1=val1 --property key2"zVTag to match; repeat as necessary, e.g. "--tag tag1 --tag tag2" will require both tagsz--idz4Show only the job tree or job containing this job IDz--namez?Restrict the search by job name (accepts wildcards "*" and "?")z--userzCUsername who launched the job (use "self" to ask for your own jobs)z --projectzCProject context (output project), default is current project if setz--all-projectsz --allprojectszExtend search to all projectsz--appz--appletz --executable executablez$Applet or App ID that job is running)r0r&z--statez'State of the job, e.g. "done", "failed"z--originzJob ID of the top-level jobz--parentz,Job ID of the parent job; implies --all-jobsz--created-afteraDate (e.g. --created-after="2021-12-01" or --created-after="2021-12-01 19:01:33") or integer Unix epoch timestamp in milliseconds (e.g. --created-after=1642196636000) after which the job was last created. You can also specify negative numbers to indicate a time period in the past suffixed by s, m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g. --created-after=-2d for executions created in the last 2 days)z--created-beforeaDate (e.g. --created-before="2021-12-01" or --created-before="2021-12-01 19:01:33") or integer Unix epoch timestamp in milliseconds (e.g. --created-before=1642196636000) before which the job was last created. You can also specify negative numbers to indicate a time period in the past suffixed by s, m, h, d, w, M or y to indicate seconds, minutes, hours, days, weeks, months or years (e.g. --created-before=-2d for executions created earlier than 2 days ago)z --no-subjobszDo not show any subjobsz--root-executionz--rootz>Execution ID of the top-level (user-initiated) job or analysisz-nz --num-resultsNz]Max number of results (trees or jobs, as according to the search mode) to return (default 10) )r5r6r&r,z--show-outputszShow job outputs in resultsz--include-restartedzXif specified, results will include restarted jobs and job trees rooted in restarted jobsc|jd}|j}|jdtddd|jdtd dd|jd td ddy) Nz Search modez--treesz8Show entire job trees for all matching results (default)r!r"r$r%z --origin-jobsz-Search and display only top-level origin jobsz --all-jobszJSearch for jobs at all depths matching the query (no tree structure shown))add_argument_groupadd_mutually_exclusive_group add_argumentr )parserfind_executions_search_gpfind_executions_searchs radd_find_executions_search_gprOms & 9 9- H6SSU'' =wKN9OXd'e''dCrFI?JS_'`'' 4AM`c.check_system_requirementssQ(D))1)9%K!$-2HD2P+V*rsystemRequirementsByExecutablezsystemRequirementsByExecutable.regionalOptionszregionalOptions.z.systemRequirementsz .systemRequirementsByExecutable.)r) extra_argsrbrcrrrr)rZrsys_reqs_by_exec executable_id entrypoints regional_optsregion region_specs rprocess_extra_argsrs " \"jj9DO   4?? 2 %doo6J&K L ,t >#/OP *D12B2H2H2Jr.M;!+t41+A`an`o?pqr  / OO,=>M-.+8+>+>+@ L'FK!+t4/;>5kBV6W7GxOb5ce<{J/:;[/\,)*:DABRBXBXBZ!L$>M;'1+t'D(A+BRSYRZZz|I{JAK)L!L L/ 09# \ Z[ [s $E== F z-iz--inputa3An input to be added using "[:]=" (provide "class" if there is no input spec; it can be any job IO class, e.g. "string", "array:string", or "array"; if "class" is "array" or not specified, the value will be attempted to be parsed as JSON and is otherwise treated as a string)z-jz --input-jsonzGThe full input JSON (keys=input field names, values=input field values)z-fz--input-json-filefilenamez0Load input JSON from FILENAME ("-" to use stdin)ceZdZddZy)PrintInstanceTypeHelpNc td|jztttdtttdtttdttdttd|jdk(rtttdttd tttd td tttd ttd tttdttdttdttdtttdttdtttdttdtttdttdtttdttdttttj j ttj j djttdttttjj ttjj djttdttttjj ttjj dj|jdy)Nz$Help: Specifying instance types for aInstance types can be requested with --instance-type-by-executable and --instance-type arguments, with --instance-type-by-executable specification taking priority over --instance-type, workflow's stageSystemRequirements, and specifications provided during app and applet creation.z--instance-type specifications do not propagate to subjobs and sub-analyses launched from a job with a /executable-xxxx/run call, but --instance-type-by-executable do (where executable refers to an app, applet or workflow).ztWhen running an app or an applet, --instance-type lets you specify the instance type to be used by each entry point.aA single instance type can be requested to be used by all entry points by providing the instance type name. Different instance types can also be requested for different entry points of an app or applet by providing a JSON string mapping from function names to instance types, e.g.zD {"main": "mem2_ssd2_v3_x4", "other_function": "mem1_ssd2_v3_x2"}zdx runaWhen running a workflow, --instance-type lets you specify instance types for each entry point of each workflow stage by prepending the request with "=" (where a stage identifier is an ID, a numeric index, or a unique stage name) and repeating the argument for as many stages as desired. If no stage identifier is provided, the value is applied as a default for all stages.Exampleszl1. Run the main entry point of applet-xxxx on mem1_ssd1_v2_x2, and all other entry points on mem1_ssd1_v2_x4z dx run applet-xxxx --instance-type '{"main": "mem1_ssd1_v2_x2", "*": "mem1_ssd1_v2_x4"}'z2. Runs all entry points of the first stage with mem2_ssd2_v3_x2, the main entry point of the second stage with mem1_ssd1_v2_x4, the stage named "BWA" with mem1_ssd1_v2_x2, and all other stages with mem2_ssd2_v3_x4z dx run workflow-xxxx \ --instance-type 0=mem2_ssd2_v3_x2 \ --instance-type 1='{"main": "mem1_ssd1_v2_x4"}' \ --instance-type BWA=mem1_ssd1_v2_x2 \ --instance-type mem2_ssd2_v3_x4aA--instance-type-by-executable argument is a JSON string with a double mapping that specifies instance types by app or applet id, then by entry point within the executable.This specification applies across the entire nested execution tree and is propagated across /executable-xxxx/run calls issued with the execution tree.z More examplesz?3. Force every job in the execution tree to use mem2_ssd1_v2_x2zX dx run workflow-xxxx --instance-type-by-executable '{"*": {"*": "mem2_ssd1_v2_x2"}}'zU4. Force every job in the execution tree executing applet-xyz1 to use mem3_ssd2_v3_x2za dx run workflow-xxxx --instance-type-by-executable '{"applet-xyz1":{"*": "mem3_ssd2_v3_x2"}}'aR5. Force every job executing applet-xyz1 to use mem1_ssd2_v3_x4 for the main entry point and mem1_ssd2_v3_x2 for all other entry points.Also force the collect entry point of all executables other than applet-xyz1 to use mem2_ssd2_v3_x8.Other entry points of executable other than applet-xyz1 may be overridden by lower-priority mechanismsz dx run workflow-xxxx --instance-type-by-executable \ '{"applet-xyz1": {"main": "mem1_ssd2_v3_x4", "*": "mem1_ssd2_v3_x2"}, "*": {"collect": "mem2_ssd2_v3_x8"}}'a86. Force every job executing applet-xxxx to use mem1_ssd2_v3_x2 for all entry points in the entire execution tree. Also force stage 0 executable to run on mem1_ssd2_v3_x4, unless stage 0 invokes applet-xxxx, in which case applet-xxxx's jobs will use mem1_ssd2_v3_x2 as specified by --instance-type-by-executable.z dx run workflow-xxxx \ --instance-type-by-executable '{"applet-xxxx": {"*": "mem1_ssd2_v3_x2"}}' \ --instance-type 0=mem1_ssd2_v3_x4zKSee "Requesting Instance Types" in DNAnexus documentation for more details.zAvailable instance types:r) column_nameszGPU instance types:zFPGA instance types:) printrir r r standard_instance_typesrrlist_fieldsgpu_instance_typesfpga_instance_typesrorps rrtzPrintInstanceTypeHelp.__call__s( 4v{{BC  dQR S  dNO P  dDE F dop q  TU ;;( " G $cd e G *  G $DE F Z [ G $56 7 G 9 : G $[\ ] G / " $XY Z G l n G $gi j G u w G $34 5 G S T G $89 : G ; < G $]_ `  )*  l1IIPPR(,-C-[-[-b-b-d(efg(h(p(pr s  #$  l1DDKKM(,-C-V-V-]-]-_(`ab(c(k(km n  $%  l1EELLN(,-C-W-W-^-^-`(abc(d(l(ln o Arrrurrrrr sarr--instance-typeINSTANCE_TYPE_OR_MAPPINGa@When running an app or applet, the mapping lists executable's entry points or "*" as keys, and instance types to use for these entry points as values. When running a workflow, the specified instance types can be prefixed by a stage name or stage index followed by "=" to apply to a specific stage, or apply to all workflow stages without such prefix. The instance type corresponding to the "*" key is applied to all entry points not explicitly mentioned in the --instance-type mapping. Specifying a single instance type is equivalent to using it for all entry points, so "--instance-type mem1_ssd2_v3_x2" is same as "--instance-type '{"*":"mem1_ssd2_v3_x2"}'. Note that "dx run" calls within the execution subtree may override the values specified at the root of the execution tree. See dx run --instance-type-help for details. )r#replace_whitespace)r5r&r'z--instance-type-by-executableDOUBLE_MAPPINGaSpecifies instance types by app or applet id, then by entry point within the executable. The order of priority for this specification is: * --instance-type, systemRequirements and stageSystemRequirements specified at runtime * stage's systemRequirements, systemRequirements supplied to /app/new and /applet/new at workflow/app/applet build time * systemRequirementsByExecutable specified in downstream executions (if any) See dx run --instance-type-help for details. )r5r&z--instance-type-helpz(Print help for specifying instance types)r1r&r'z5Tag for the resulting execution; repeat as necessary,z--phi containsPHItruefalsezIf set to true, only projects that contain PHI data will be retrieved. 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