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fix: matlab loading and sbml validation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,73 +1,83 @@ | ||
| import cobra | ||
| import json | ||
| from pathlib import Path | ||
|
|
||
| def loadYaml(model_name): | ||
| print('load yaml') | ||
| is_valid = False | ||
| description = 'Check if the model in YAML can be loaded with cobrapy.' | ||
| print(description) | ||
| status = False | ||
| errors = '' | ||
| try: | ||
| cobra.io.load_yaml_model(model_name + '.yml') | ||
| is_valid = True | ||
| status = True | ||
| except FileNotFoundError: | ||
| errors = "File missing" | ||
| except Exception as e: | ||
| errors = json.dumps(str(e)) | ||
| print(e) | ||
| return 'cobrapy-load-yaml', cobra.__version__, is_valid, errors | ||
| return 'cobrapy-load-yaml', description, cobra.__version__, status, errors | ||
|
|
||
| def loadSbml(model_name): | ||
| print('load sbml') | ||
| is_valid = False | ||
| description = 'Check if the model in SBML format can be loaded with cobrapy.' | ||
| print(description) | ||
| status = False | ||
| errors = '' | ||
| try: | ||
| cobra.io.read_sbml_model(model_name + '.xml') | ||
| is_valid = True | ||
| status = True | ||
| except FileNotFoundError: | ||
| errors = "File missing" | ||
| except Exception as e: | ||
| errors = json.dumps(str(e)) | ||
| print(e) | ||
| return 'cobrapy-load-sbml', cobra.__version__, is_valid, errors | ||
| return 'cobrapy-load-sbml', description, cobra.__version__, status, errors | ||
|
|
||
| def loadMatlab(model_name): | ||
| print('load matlab') | ||
| is_valid = False | ||
| description = 'Check if the model in Matlab format can be loaded with cobrapy.' | ||
| print(description) | ||
| status = False | ||
| errors = '' | ||
| try: | ||
| cobra.io.load_matlab_model(model_name + '.mat') | ||
| is_valid = True | ||
| data_dir = Path(".") / ".." | ||
| data_dir = data_dir.resolve() | ||
| model_path = data_dir / "{}.mat".format(model_name) | ||
| cobra.io.load_matlab_model(str(model_path.resolve())) | ||
| status = True | ||
| except FileNotFoundError: | ||
| errors = "File missing" | ||
| except Exception as e: | ||
| errors = json.dumps(str(e)) | ||
| print(e) | ||
| return 'cobrapy-load-matlab', cobra.__version__, is_valid, errors | ||
| return 'cobrapy-load-matlab', description, cobra.__version__, status, errors | ||
|
|
||
| def loadJson(model_name): | ||
| print('load json') | ||
| is_valid = False | ||
| description = 'Check if the model in JSON format can be loaded with cobrapy.' | ||
| print(description) | ||
| status = False | ||
| errors = '' | ||
| try: | ||
| cobra.io.load_json_model(model_name + '.json') | ||
| is_valid = True | ||
| status = True | ||
| except FileNotFoundError: | ||
| errors = "File missing" | ||
| except Exception as e: | ||
| errors = json.dumps(str(e)) | ||
| print(e) | ||
| return 'cobrapy-load-json', cobra.__version__, is_valid, errors | ||
| return 'cobrapy-load-json', description, cobra.__version__, status, errors | ||
|
|
||
|
|
||
| def validateSbml(model_name): | ||
| print('validate sbml with cobrapy') | ||
| is_valid = False | ||
| description = 'Check with cobrapy if the model in SBML format is valid.' | ||
| print(description) | ||
| status = False | ||
| errors = '' | ||
| try: | ||
| _, result = cobra.io.sbml.validate_sbml_model(model_name + '.xml') | ||
| if result == {}: | ||
| is_valid = True | ||
| if result['SBML_FATAL'] == [] and result['SBML_ERROR'] == [] and result['SBML_SCHEMA_ERROR'] == [] and result['COBRA_FATAL'] == [] and result['COBRA_ERROR'] == []: | ||
| status = True | ||
| else: | ||
| raise Exception(result) | ||
| except Exception as e: | ||
| errors = json.dumps(str(e)) | ||
| print(e) | ||
| return 'cobrapy-validate-sbml', cobra.__version__, is_valid, errors | ||
| return 'cobrapy-validate-sbml', description, cobra.__version__, status, errors |
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