Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/general_utils.py @ 380:03a7ba63813f draft

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Uploaded
author luca_milaz
date Fri, 05 Sep 2025 08:27:04 +0000
parents fe87d6fd7884
children 0a3ca20848f3
comparison
equal deleted inserted replaced
379:6f0aed06098c 380:03a7ba63813f
37 PDF = ("pdf",) # this is also a common output format for images, as it's required in publications. 37 PDF = ("pdf",) # this is also a common output format for images, as it's required in publications.
38 38
39 # Updated to include compressed variants 39 # Updated to include compressed variants
40 XML = ("xml", "xml.gz", "xml.zip", "xml.bz2") # SBML files are XML files, sometimes compressed 40 XML = ("xml", "xml.gz", "xml.zip", "xml.bz2") # SBML files are XML files, sometimes compressed
41 JSON = ("json", "json.gz", "json.zip", "json.bz2") # COBRA models can be stored as JSON files, sometimes compressed 41 JSON = ("json", "json.gz", "json.zip", "json.bz2") # COBRA models can be stored as JSON files, sometimes compressed
42 42 MAT = ("mat", "mat.gz", "mat.zip", "mat.bz2") # COBRA models can be stored as MAT files, sometimes compressed
43 TXT = ("txt",) # this is how most output data is written 43 YML = ("yml", "yml.gz", "yml.zip", "yml.bz2") # COBRA models can be stored as YML files, sometimes compressed
44
45 TXT = ("txt",) # this is how most output data is written
44 PICKLE = ("pickle", "pk", "p") # this is how all runtime data structures are saved 46 PICKLE = ("pickle", "pk", "p") # this is how all runtime data structures are saved
45 47
46 def __init__(self, *extensions): 48 def __init__(self, *extensions):
47 self.extensions = extensions 49 self.extensions = extensions
48 # Store original extension when set via fromExt 50 # Store original extension when set via fromExt
76 """ 78 """
77 (Private) converts to str representation. Good practice for usage with argparse. 79 (Private) converts to str representation. Good practice for usage with argparse.
78 Returns: 80 Returns:
79 str : the string representation of the file extension. 81 str : the string representation of the file extension.
80 """ 82 """
81 # If we have an original extension stored (for compressed files), use it 83 # If we have an original extension stored (for compressed files only), use it
82 if hasattr(self, '_original_extension') and self._original_extension: 84 if hasattr(self, '_original_extension') and self._original_extension:
83 return self._original_extension 85 return self._original_extension
84 86
85 # For XML and JSON without original extension, use the base extension 87 # For XML, JSON, MAT and YML without original extension, use the base extension
86 if self == FileFormat.XML: 88 if self == FileFormat.XML:
87 return "xml" 89 return "xml"
88 elif self == FileFormat.JSON: 90 elif self == FileFormat.JSON:
89 return "json" 91 return "json"
92 elif self == FileFormat.MAT:
93 return "mat"
94 elif self == FileFormat.YML:
95 return "yml"
90 96
91 return self.value[-1] 97 return self.value[-1]
92 98
93 class FilePath(): 99 class FilePath():
94 """ 100 """
612 if str(ext) in FileFormat.JSON.value: 618 if str(ext) in FileFormat.JSON.value:
613 # Compressed files are not automatically handled by cobra 619 # Compressed files are not automatically handled by cobra
614 if(ext == "json"): 620 if(ext == "json"):
615 return cobra.io.load_json_model(file_path.show()) 621 return cobra.io.load_json_model(file_path.show())
616 else: 622 else:
617 return self.extract_json_model(file_path, ext) 623 return self.extract_model(file_path, ext, "json")
624
625 if str(ext) in FileFormat.MAT.value:
626 # Compressed files are not automatically handled by cobra
627 if(ext == "mat"):
628 return cobra.io.load_matlab_model(file_path.show())
629 else:
630 return self.extract_model(file_path, ext, "mat")
631
632 if str(ext) in FileFormat.YML.value:
633 # Compressed files are not automatically handled by cobra
634 if(ext == "yml"):
635 return cobra.io.load_yaml_model(file_path.show())
636 else:
637 return self.extract_model(file_path, ext, "yml")
618 638
619 except Exception as e: raise DataErr(file_path, e.__str__()) 639 except Exception as e: raise DataErr(file_path, e.__str__())
620 raise DataErr(file_path, 640 raise DataErr(file_path,
621 f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.") 641 f"Fomat \"{file_path.ext}\" is not recognized, only JSON, XML, MAT and YAML (.yml) files are supported.")
622 642
623 643
624 def extract_json_model(file_path:FilePath, ext :FileFormat) -> cobra.Model: 644 def extract_model(file_path:FilePath, ext :FileFormat, model_encoding:Literal["json", "mat", "yml"]) -> cobra.Model:
625 """ 645 """
626 Extract json COBRA model from a compressed file (zip, gz, bz2). 646 Extract JSON, MAT and YAML COBRA model from a compressed file (zip, gz, bz2).
627 647
628 Args: 648 Args:
629 file_path: File path of the model 649 file_path: File path of the model
630 ext: File extensions of class FileFormat (should be .zip, .gz or .bz2) 650 ext: File extensions of class FileFormat (should be .zip, .gz or .bz2)
631 651
640 try: 660 try:
641 if '.zip' in ext_str: 661 if '.zip' in ext_str:
642 with zipfile.ZipFile(file_path.show(), 'r') as zip_ref: 662 with zipfile.ZipFile(file_path.show(), 'r') as zip_ref:
643 with zip_ref.open(zip_ref.namelist()[0]) as json_file: 663 with zip_ref.open(zip_ref.namelist()[0]) as json_file:
644 content = json_file.read().decode('utf-8') 664 content = json_file.read().decode('utf-8')
645 return cobra.io.load_json_model(StringIO(content)) 665 if model_encoding == "json":
666 return cobra.io.load_json_model(StringIO(content))
667 elif model_encoding == "mat":
668 return cobra.io.load_matlab_model(StringIO(content))
669 elif model_encoding == "yml":
670 return cobra.io.load_yaml_model(StringIO(content))
671 else:
672 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
646 elif '.gz' in ext_str: 673 elif '.gz' in ext_str:
647 with gzip.open(file_path.show(), 'rt', encoding='utf-8') as gz_ref: 674 with gzip.open(file_path.show(), 'rt', encoding='utf-8') as gz_ref:
648 return cobra.io.load_json_model(gz_ref) 675 if model_encoding == "json":
676 return cobra.io.load_json_model(gz_ref)
677 elif model_encoding == "mat":
678 return cobra.io.load_matlab_model(gz_ref)
679 elif model_encoding == "yml":
680 return cobra.io.load_yaml_model(gz_ref)
681 else:
682 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
649 elif '.bz2' in ext_str: 683 elif '.bz2' in ext_str:
650 with bz2.open(file_path.show(), 'rt', encoding='utf-8') as bz2_ref: 684 with bz2.open(file_path.show(), 'rt', encoding='utf-8') as bz2_ref:
651 return cobra.io.load_json_model(bz2_ref) 685 if model_encoding == "json":
686 return cobra.io.load_json_model(bz2_ref)
687 elif model_encoding == "mat":
688 return cobra.io.load_matlab_model(bz2_ref)
689 elif model_encoding == "yml":
690 return cobra.io.load_yaml_model(bz2_ref)
691 else:
692 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
652 else: 693 else:
653 raise ValueError(f"Compression format not supported: {ext_str}. Supported: .zip, .gz and .bz2") 694 raise ValueError(f"Compression format not supported: {ext_str}. Supported: .zip, .gz and .bz2")
654 695
655 except Exception as e: 696 except Exception as e:
656 raise Exception(f"Error during model extraction: {str(e)}") 697 raise Exception(f"Error during model extraction: {str(e)}")