Mercurial > repos > sybila > ebcsgen_ctl_model_checking
changeset 0:213df1fd884f draft
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit ab45353a4e518f67057a1789aa527fb3bf1e74d5
author | sybila |
---|---|
date | Thu, 06 Oct 2022 14:39:48 +0000 |
parents | |
children | f5ebb9f9741d |
files | ebcsgen_ctl_model_checking.py ebcsgen_ctl_model_checking.xml macros.xml test-data/simple.bcsl.ts |
diffstat | 4 files changed, 190 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_ctl_model_checking.py Thu Oct 06 14:39:48 2022 +0000 @@ -0,0 +1,33 @@ +import argparse + +from eBCSgen.Analysis.CTL import CTL +from eBCSgen.Errors.FormulaParsingError import FormulaParsingError +from eBCSgen.Errors.InvalidInputError import InvalidInputError +from eBCSgen.Parsing.ParseBCSL import load_TS_from_json +from eBCSgen.Parsing.ParseCTLformula import CTLparser + +args_parser = argparse.ArgumentParser(description='Model checking') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required 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 = CTLparser().parse(args.formula) +if formula.success: + result, states = CTL.model_checking(ts, formula) + output = 'Result: {}\nNumber of satisfying states: {}'.format(result, len(states)) + f = open(args.output, "w") + f.write(output) + f.close() +else: + raise FormulaParsingError(formula.data, args.formula)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_ctl_model_checking.xml Thu Oct 06 14:39:48 2022 +0000 @@ -0,0 +1,42 @@ +<tool id="eBCSgen_CTL_model_checking" name="eBCSgen CTL model checking" version="@TOOL_VERSION@_galaxy0"> + <description>- explicit CTL 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 ${__tool_directory__}/ebcsgen_ctl_model_checking.py + --transition_file '$transition_file' + --formula '$formula' + --output '$output' + </command> + + <inputs> + <param format="bcsl.ts" name="transition_file" type="data" label="Computed Transition system"/> + <param name="formula" type="text" label="CTL formula"> + <validator type="empty_field"/> + </param> + </inputs> + + <outputs> + <data label="CTL model checking of ${on_string}" format="ctl.result" name="output"/> + </outputs> + + <tests> + <test> + <param name="transition_file" value="simple.bcsl.ts" ftype="bcsl.ts"/> + <param name="formula" value="E(F([P(S{a},T{a})::cell > 0]))"/> + <output name="output" ftype="ctl.result"> + <assert_contents> + <has_text text="Result: True"/> + <has_text text="Number of satisfying states: 4"/> + </assert_contents> + </output> + </test> + </tests> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 06 14:39:48 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/simple.bcsl.ts Thu Oct 06 14:39:48 2022 +0000 @@ -0,0 +1,98 @@ +{ + "nodes": { + "1": "(0, 0, 0, 0, 0, 1, 0, 0)", + "2": "(0, 0, 1, 0, 0, 0, 0, 0)", + "3": "(1, 0, 0, 0, 0, 0, 0, 0)", + "4": "(0, 0, 0, 1, 0, 0, 0, 0)", + "5": "(0, 0, 0, 0, 0, 0, 1, 0)", + "6": "(0, 0, 0, 0, 0, 0, 0, 1)", + "7": "(0, 0, 0, 0, 1, 0, 0, 0)", + "8": "(0, 1, 0, 0, 0, 0, 0, 0)" + }, + "edges": [ + { + "s": 8, + "t": 8, + "p": 1, + "label": "\u03b5" + }, + { + "s": 3, + "t": 8, + "p": 1.0, + "label": "r2" + }, + { + "s": 5, + "t": 6, + "p": 0.3333333333333333, + "label": "r2" + }, + { + "s": 6, + "t": 6, + "p": 1, + "label": "\u03b5" + }, + { + "s": 2, + "t": 3, + "p": 0.5, + "label": "r1_T" + }, + { + "s": 7, + "t": 1, + "p": 0.5, + "label": "r2" + }, + { + "s": 5, + "t": 2, + "p": 0.3333333333333333, + "label": "r1_S" + }, + { + "s": 7, + "t": 3, + "p": 0.5, + "label": "r1_S" + }, + { + "s": 4, + "t": 4, + "p": 1, + "label": "\u03b5" + }, + { + "s": 1, + "t": 1, + "p": 1, + "label": "\u03b5" + }, + { + "s": 5, + "t": 7, + "p": 0.3333333333333333, + "label": "r1_T" + }, + { + "s": 2, + "t": 4, + "p": 0.5, + "label": "r2" + } + ], + "ordering": [ + "P(S{a},T{a})::cell", + "P(S{a},T{a})::out", + "P(S{a},T{i})::cell", + "P(S{a},T{i})::out", + "P(S{i},T{a})::cell", + "P(S{i},T{a})::out", + "P(S{i},T{i})::cell", + "P(S{i},T{i})::out" + ], + "initial": 5, + "bound": 1 +} \ No newline at end of file