Source code for create_omex

Creates the omex files from the given SED-ML files.

from __future__ import absolute_import, print_function

import os

import libcombine

[docs]EXAMPLES_DIR = os.path.dirname(os.path.realpath(__file__))
[docs]SEDML_DIR = os.path.join(EXAMPLES_DIR, "./sedml")
[docs]OMEX_DIR = os.path.join(EXAMPLES_DIR, "./omex")
[docs]def create_omex_from_sedml(sedml_file, omex_file): """Creates a combine archive from folder :param folder: :param omex_file: :return: """ print("*" * 100) print("Create OMEX:") print("\t", sedml_file) print("*" * 100) time_now = libcombine.OmexDescription.getCurrentDateAndTime() archive = libcombine.CombineArchive() # add the sedml file location = os.path.relpath(sedml_file) format = "" master = True archive.addFile(path, location, format, master) omex_d = libcombine.OmexDescription() omex_d.setAbout(location) omex_d.setCreated(time_now) archive.addMetadata(location, omex_d) # delete the old omex file if os.path.exists(omex_file): os.remove(omex_file) archive.writeToFile(omex_file) print("Archive created:", omex_file)
[docs]def printMetaDataFor(archive, location): """Prints metadata for given location. :param archive: CombineArchive instance :param location: :return: """ desc = archive.getMetadataForLocation(location) if desc.isEmpty(): print(" no metadata for '{0}'".format(location)) return None print(" metadata for '{0}':".format(location)) print(" Created : {0}".format(desc.getCreated().getDateAsString())) for i in range(desc.getNumModified()): print(" Modified : {0}".format(desc.getModified(i).getDateAsString())) print(" # Creators: {0}".format(desc.getNumCreators())) for i in range(desc.getNumCreators()): creator = desc.getCreator(i) print(" {0} {1}".format(creator.getGivenName(), creator.getFamilyName()))
[docs]def printArchive(fileName): """Prints content of combine archive :param fileName: path of archive :return: None """ archive = libcombine.CombineArchive() if archive.initializeFromArchive(fileName) is None: print("Invalid Combine Archive") return None print("*" * 80) print("Print archive:", fileName) print("*" * 80) printMetaDataFor(archive, ".") print("Num Entries: {0}".format(archive.getNumEntries())) for i in range(archive.getNumEntries()): entry = archive.getEntry(i) print( " {0}: location: {1} format: {2}".format( i, entry.getLocation(), entry.getFormat() ) ) printMetaDataFor(archive, entry.getLocation()) archive.cleanUp()
if __name__ == "__main__": # get sedml files
[docs] sedml_files = []
for subdir, dirs, files in os.walk(SEDML_DIR): for file in files: path = os.path.join(subdir, file) if os.path.isfile(path) and path.endswith(".xml"): sedml_files.append(path) for path in sorted(sedml_files): basename = os.path.basename(path) name = basename[:-4] # name without extension sedml_file = os.path.abspath(path) omex_file = os.path.join(OMEX_DIR, "{}.omex".format(name)) create_omex_from_sedml(sedml_file=sedml_file, omex_file=omex_file) printArchive(omex_file) print("\n\n")