Mercurial > repos > sybila > ebcsgen_pctl_model_checking
changeset 0:ea5108514910 draft
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
author | sybila |
---|---|
date | Fri, 09 Sep 2022 17:04:25 +0000 |
parents | |
children | 602c6cab487e |
files | ebcsgen_pctl_model_checking.py ebcsgen_pctl_model_checking.xml macros.xml test-data/pctl_model_checking.bcsl.ts |
diffstat | 4 files changed, 167 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_pctl_model_checking.py Fri Sep 09 17:04:25 2022 +0000 @@ -0,0 +1,34 @@ +import argparse + +from eBCSgen.Analysis.PCTL import PCTL +from eBCSgen.Errors.FormulaParsingError import FormulaParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Parsing.ParseBCSL import load_TS_from_json +from eBCSgen.Parsing.ParsePCTLformula import PCTLparser + + +args_parser = argparse.ArgumentParser(description='Model checking') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') +optional = args_parser.add_argument_group('optional arguments') + +required.add_argument('--transition_file', required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--formula', type=str, required=True) + +args = args_parser.parse_args() + +ts = load_TS_from_json(args.transition_file) + +if len(ts.params) != 0: + raise InvalidInputError("Provided transition system is parametrised - model checking cannot be executed.") + +formula = PCTLparser().parse(args.formula) +if formula.success: + result = PCTL.model_checking(ts, formula, storm_local=True) + f = open(args.output, "w") + f.write(result.decode("utf-8")) + f.close() +else: + raise FormulaParsingError(formula.data, args.formula)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_pctl_model_checking.xml Fri Sep 09 17:04:25 2022 +0000 @@ -0,0 +1,41 @@ +<tool id="eBCSgen_PCTL_model_checking" name="eBCSgen - PCTL model checking" version="@TOOL_VERSION@_galaxy0"> + <description>- explicit PCTL model checking of transition system</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <container type="docker">sybila/ebcsgen:v@TOOL_VERSION@</container> + </requirements> + + <options sanitize="False"/> + <command>python3 ${__tool_directory__}/ebcsgen_pctl_model_checking.py + --transition_file '$transition_file' + --output '$output' + --formula '$formula' + </command> + + <inputs> + <param format="bcsl.ts" name="transition_file" type="data" label="Computed Transition system"/> + <param name="formula" type="text" label="PCTL formula"> + <validator type="empty_field"/> + </param> + </inputs> + + <outputs> + <data label="PCTL model checking of ${on_string}" format="storm.check" name="output"/> + </outputs> + + <tests> + <test> + <param name="transition_file" value="pctl_model_checking.bcsl.ts" ftype="bcsl.ts"/> + <param name="formula" value="P <= 0.5[F X()::rep=1]"/> + <output name="output" ftype="storm.check"> + <assert_contents> + <has_text text="Result (for initial states): false"/> + </assert_contents> + </output> + </test> + </tests> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 09 17:04:25 2022 +0000 @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">2.0.3</token> + + <xml name="creator"> + <creator> + <person + givenName="Matej" + familyName="Troják" + url="https://github.com/xtrojak" + identifier="0000-0003-0841-2707" /> + <organization + url="https://sybila.fi.muni.cz/" + email="sybila@fi.muni.cz" + name="SYBILA MUNI" /> + </creator> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pctl_model_checking.bcsl.ts Fri Sep 09 17:04:25 2022 +0000 @@ -0,0 +1,75 @@ +{ + "nodes": { + "1": "(inf, inf, inf)", + "2": "(1, 2, 0)", + "3": "(0, 1, 0)", + "4": "(0, 2, 0)", + "5": "(2, 1, 0)", + "6": "(2, 2, 0)", + "7": "(1, 1, 0)" + }, + "edges": [ + { + "s": 7, + "t": 3, + "p": 0.8 + }, + { + "s": 3, + "t": 4, + "p": 1.0 + }, + { + "s": 5, + "t": 7, + "p": 0.9855072463768116 + }, + { + "s": 1, + "t": 1, + "p": 1 + }, + { + "s": 2, + "t": 1, + "p": 0.2 + }, + { + "s": 5, + "t": 6, + "p": 0.014492753623188406 + }, + { + "s": 6, + "t": 1, + "p": 0.014492753623188406 + }, + { + "s": 6, + "t": 2, + "p": 0.9855072463768116 + }, + { + "s": 4, + "t": 1, + "p": 1.0 + }, + { + "s": 2, + "t": 4, + "p": 0.8 + }, + { + "s": 7, + "t": 2, + "p": 0.2 + } + ], + "ordering": [ + "X()::rep", + "Y()::rep", + "Z()::rep" + ], + "initial": 5, + "bound": 2 +} \ No newline at end of file