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 = "http://identifiers.org/combine.specifications/sed-ml"
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)
def _add_file_metadata(location: str, description: str = ""):
"""Add metadata to the added file"""
omex_description = libcombine.OmexDescription()
omex_description.setAbout(location)
omex_description.setDescription(description)
omex_description.setCreated(
libcombine.OmexDescription.getCurrentDateAndTime())
archive.addMetadata(location, omex_description)
def add_meta_data(archive, archive_name, meta_data):
for file in meta_data.keys():
# Create meta data for archive
des = libcombine.OmexDescription()
des.setAbout('.' if file.split('.')[0] == archive_name else "./{0}.xml".format(file))
des.setCreated(libcombine.OmexDescription.getCurrentDateAndTime())
if meta_data[file]["description"]:
des.setDescription(meta_data[file]["description"])
# Create creator for the meta data
for creator_data in meta_data[file]["creators"]:
# Add creator to meta data
des.addCreator(create_creator(**creator_data))
# Add meta data to archive
archive.addMetadata('.' if file.split('.')[0] == archive_name else
"./{0}.xml".format(file), des)
def create_combine_archive(
yaml_file: str,
filename: str,
family_name: Optional[str] = None,
given_name: Optional[str] = None,
email: Optional[str] = None,
organization: Optional[str] = None,
) -> None:
"""Create COMBINE archive (http://co.mbine.org/documents/archive) based
on PEtab YAML file.
Arguments:
yaml_file: Path to PEtab YAML file
family_name: Family name of archive creator
given_name: Given name of archive creator
email: E-mail address of archive creator
organization: Organization of archive creator
"""
path_prefix = os.path.dirname(yaml_file)
yaml_config = yaml.load_yaml(yaml_file)
# function-level import, because module-level import interfered with
# other SWIG interfaces
try:
import libcombine
except ImportError:
raise ImportError("To use PEtab's COMBINE functionality, libcombine "
"(python-libcombine) must be installed.")
def _add_file_metadata(location: str, description: str = ""):
"""Add metadata to the added file"""
omex_description = libcombine.OmexDescription()
omex_description.setAbout(location)
omex_description.setDescription(description)
omex_description.setCreated(
libcombine.OmexDescription.getCurrentDateAndTime())
archive.addMetadata(location, omex_description)
archive = libcombine.CombineArchive()
# Add PEtab files and metadata
archive.addFile(yaml_file, os.path.basename(yaml_file),
libcombine.KnownFormats.lookupFormat("yaml"), True)
_add_file_metadata(location=os.path.basename(yaml_file),
description="PEtab YAML file")
# Add parameter file(s) that describe a single parameter table.
# Works for a single file name, or a list of file names.
for parameter_subset_file in (list(
np.array(yaml_config[PARAMETER_FILE]).flat)):
archive.addFile(os.path.join(path_prefix, parameter_subset_file),
parameter_subset_file,
libcombine.KnownFormats.lookupFormat("tsv"), False)
_add_file_metadata(location=parameter_subset_file,
description="PEtab parameter file")
for problem in yaml_config[PROBLEMS]:
for sbml_file in problem[SBML_FILES]:
archive.addFile(os.path.join(path_prefix, sbml_file), sbml_file,
libcombine.KnownFormats.lookupFormat("sbml"),
False)
_add_file_metadata(location=sbml_file, description="SBML model")
for field in [
MEASUREMENT_FILES, OBSERVABLE_FILES, VISUALIZATION_FILES,
CONDITION_FILES
]:
if field not in problem:
continue
for file in problem[field]:
archive.addFile(os.path.join(path_prefix, file), file,
libcombine.KnownFormats.lookupFormat("tsv"),
False)
desc = field.split("_")[0]
_add_file_metadata(location=file,
description=f"PEtab {desc} file")
# Add archive metadata
description = libcombine.OmexDescription()
description.setAbout(".")
description.setDescription("PEtab archive")
description.setCreated(libcombine.OmexDescription.getCurrentDateAndTime())
# Add creator info
creator = libcombine.VCard()
if family_name:
creator.setFamilyName(family_name)
if given_name:
creator.setGivenName(given_name)
if email:
creator.setEmail(email)
if organization:
creator.setOrganization(organization)
description.addCreator(creator)
archive.addMetadata(".", description)
archive.writeToFile(filename)
def _addEntriesToArchive(omexPath, entries, workingDir, add_entries):
"""
:param archive:
:param entries:
:param workingDir:
:return:
"""
omexPath = os.path.abspath(omexPath)
print('omexPath:', omexPath)
print('workingDir:', workingDir)
if not os.path.exists(workingDir):
raise IOError(
"Working directory does not exist: {}".format(workingDir))
if add_entries is False:
if os.path.exists(omexPath):
# delete the old omex file
warnings.warn(
"Combine archive is overwritten: {}".format(omexPath))
os.remove(omexPath)
archive = libcombine.CombineArchive()
if add_entries is True:
# use existing entries
if os.path.exists(omexPath):
# init archive from existing content
if archive.initializeFromArchive(omexPath) is None:
raise IOError("Combine Archive is invalid: ", omexPath)
# timestamp
time_now = libcombine.OmexDescription.getCurrentDateAndTime()
print('*' * 80)
for entry in entries:
print(entry)
location = entry.location
path = os.path.join(workingDir, location)
if not os.path.exists(path):
raise IOError(
"File does not exist at given location: {}".format(path))
archive.addFile(path, location, entry.format, entry.master)
if entry.description or entry.creators:
omex_d = libcombine.OmexDescription()
omex_d.setAbout(location)
omex_d.setCreated(time_now)
if entry.description:
omex_d.setDescription(entry.description)
if entry.creators:
for c in entry.creators:
creator = libcombine.VCard()
creator.setFamilyName(c.familyName)
creator.setGivenName(c.givenName)
creator.setEmail(c.email)
creator.setOrganization(c.organization)
omex_d.addCreator(creator)
archive.addMetadata(location, omex_d)
archive.writeToFile(omexPath)
archive.cleanUp()
def create_omex(folder, omex_file, strict=True):
""" Creates a combine archive from folder
:param folder:
:param omex_file:
:param strict: strict creation, raises Errors instead of warnings
:return:
"""
print('*' * 100)
print('Create OMEX:')
print('\t', folder)
print('*' * 100)
if not os.path.exists(folder):
raise IOError("Input folder does not exist:", folder)
# delete the old omex file
if os.path.exists(omex_file):
os.remove(omex_file)
json_manifest = os.path.join(folder, 'manifest.json')
# print(json_manifest)
with open(json_manifest, "r") as f:
json_entries = json.load(f)
json_entries = json_entries['entries']
# pprint.pprint(json_entries)
# ----------------------------------
# Create metadata file
# ----------------------------------
# create the metadata file
# <content format = "http://identifiers.org/combine.specifications/omex-metadata" location = "metadata.rdf" / >
time_now = libcombine.OmexDescription.getCurrentDateAndTime()
metadata_xml = []
for entry in json_entries:
location = entry['location']
# add metadata for location
description = entry.get("description", None)
creators = entry.get("creators", None)
if description or creators:
# Create an omex description
omex_d = libcombine.OmexDescription()
omex_d.setAbout(location)
omex_d.setCreated(time_now)
if description:
omex_d.setDescription(description)
if creators:
for c in creators:
creator = libcombine.VCard()
creator.setFamilyName(c.get("familyName", ""))
creator.setGivenName(c.get("givenName", ""))
creator.setEmail(c.get("email", ""))
creator.setOrganization(c.get("organisation"))
omex_d.addCreator(creator)
metadata_xml.append(omex_d.toXML())
# store the metadata file
# FIXME: bad hack for now, but seems to work
contents = [(item.split("\n"))[2:-2] for item in metadata_xml]
start_str = "<?xml version='1.0' encoding='UTF-8'?>\n" \
"<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#'>"
content_str = "\n".join(["\n".join(lines) for lines in contents])
end_str = "</rdf:RDF>"
metadata_str = "\n".join([start_str, content_str, end_str])
f_metadata = os.path.join(folder, "metadata.rdf")
with open(f_metadata, "w") as f:
f.write(metadata_str)
# ----------------------------------
# create manifest.xml
# ----------------------------------
f_manifest = os.path.join(folder, "manifest.xml")
with open(f_manifest, "w") as f:
f.write("<omexManifest>\n")
for entry in json_entries:
location = entry['location']
path = os.path.join(folder, location)
if not os.path.exists(path) and not path.endswith('manifest.xml'):
msg = "File does not exist at given location: {}".format(path)
if strict:
raise IOError(msg)
else:
warnings.warn(msg)
# add file to archive
format = entry['format']
master = entry.get('master', False)
# archive.addFile(path, location, format, master)
f.write('<content location="{}" format="{}" master="{}"/>\n'.format(location, format, master))
f.write("</omexManifest>\n")
# ----------------------------------
# create omex
# ----------------------------------
zip_dir(folder, omex_file)
print('Archive created:', omex_file)