Mercurial > repos > sybila > ebcsgen_sbml_export

annotate ebcsgen_sbml_export.py @ 0:2f3f67415022 draft

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
author sybila
date Sat, 08 Oct 2022 12:55:26 +0000
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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diff changeset
1 import argparse
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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3 from eBCSgen.Errors.ModelParsingError import ModelParsingError
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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4 from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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5 from eBCSgen.Parsing.ParseBCSL import Parser
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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7 import libsbml
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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10 args_parser = argparse.ArgumentParser(description='Export SBML model with usage of SBML-multi package')
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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12 args_parser._action_groups.pop()
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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13 required = args_parser.add_argument_group('required arguments')
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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15 required.add_argument('--model', type=str, required=True)
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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16 required.add_argument('--output', type=str, required=True)
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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18 args = args_parser.parse_args()
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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20 model_parser = Parser("model")
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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21 model_str = open(args.model, "r").read()
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
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2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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23 model = model_parser.parse(model_str)
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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24 if model.success:
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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25 document = model.data.export_sbml()
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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26 libsbml.writeSBMLToFile(document, args.output)
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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27 else:
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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28 if "error" in model.data:
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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29 raise UnspecifiedParsingError(model.data["error"])
2f3f67415022 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
sybila
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30 raise ModelParsingError(model.data, model_str)