biosimulators_utils.combine package

Submodules

biosimulators_utils.combine.data_model module

Data model for COMBINE/OMEX archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.combine.data_model.CombineArchive(contents=None)

Bases: CombineArchiveBase

A COMBINE/OMEX archive

contents

contents of the archive

Type:

list of CombineArchiveContent

get_master_content()

Get the master content of an archive

Returns:

master content

Return type:

list of CombineArchiveContent

is_equal(other)

Determine if two content items are equal

Parameters:

other (CombineArchiveContent) – another content item

Returns:

True, if two archives are equal

Return type:

bool

to_tuple()

Tuple representation of a COMBINE/OMEX archive

Returns:

tuple representation of a COMBINE/OMEX archive

Return type:

tuple of str

class biosimulators_utils.combine.data_model.CombineArchiveBase

Bases: ABC

A COMBINE/OMEX archive

class biosimulators_utils.combine.data_model.CombineArchiveContent(location=None, format=None, master=False)

Bases: CombineArchiveBase

A content item (e.g., file) in a COMBINE/OMEX archive

location

path to the content

Type:

str

format

URL for the specification of the format of the content

Type:

str

master

True, if the content is the “primary” content of the parent archive

Type:

bool

is_equal(other)

Determine if two content items are equal

Parameters:

other (CombineArchiveContent) – another content item

Returns:

True, if two content items are equal

Return type:

bool

to_tuple()

Tuple representation of a content item of a COMBINE/OMEX archive

Returns:

tuple representation of a content item of a COMBINE/OMEX archive

Return type:

tuple of str

class biosimulators_utils.combine.data_model.CombineArchiveContentFormat(value)

Bases: str, Enum

Format for the content of COMBINE/OMEX archives

ACTIONSCRIPT = 'http://purl.org/NET/mediatypes/text/x-actionscript'

ADOBE_FLASH = 'http://purl.org/NET/mediatypes/application/x-shockwave-flash'

AI = 'http://purl.org/NET/mediatypes/application/pdf'

BMP = 'http://purl.org/NET/mediatypes/image/bmp'

BNGL = 'http://purl.org/NET/mediatypes/text/bngl+plain'

BOURNE_SHELL = 'http://purl.org/NET/mediatypes/text/x-sh'

BioPAX = 'http://identifiers.org/combine.specifications/biopax'

C = 'http://purl.org/NET/mediatypes/text/x-c'

CPP_HEADER = 'http://purl.org/NET/mediatypes/text/x-c++hdr'

CPP_SOURCE = 'http://purl.org/NET/mediatypes/text/x-c++src'

CSS = 'http://purl.org/NET/mediatypes/text/css'

CSV = 'http://purl.org/NET/mediatypes/text/csv'

CellML = 'http://identifiers.org/combine.specifications/cellml'

CopasiML = 'http://purl.org/NET/mediatypes/application/x-copasi'

DLL = 'http://purl.org/NET/mediatypes/application/vnd.microsoft.portable-executable'

DOC = 'http://purl.org/NET/mediatypes/application/msword'

DOCX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.wordprocessingml.document'

EPS = 'http://purl.org/NET/mediatypes/application/postscript'

Escher = 'http://purl.org/NET/mediatypes/application/escher+json'

GENESIS = 'http://purl.org/NET/mediatypes/text/x-genesis'

GIF = 'http://purl.org/NET/mediatypes/image/gif'

GINML = 'http://purl.org/NET/mediatypes/application/ginml+xml'

GMSH_MESH = 'http://purl.org/NET/mediatypes/model/mesh'

GRAPHML = 'http://purl.org/NET/mediatypes/application/graphml+xml'

HDF5 = 'http://purl.org/NET/mediatypes/application/x-hdf'

HOC = 'http://purl.org/NET/mediatypes/text/x-hoc'

HTML = 'http://purl.org/NET/mediatypes/text/html'

ICO = 'http://purl.org/NET/mediatypes/image/x-icon'

INI = 'http://purl.org/NET/mediatypes/text/x-ini'

IPython_Notebook = 'http://purl.org/NET/mediatypes/application/x-ipynb+json'

JAVASCRIPT = 'http://purl.org/NET/mediatypes/text/javascript'

JAVA_ARCHIVE = 'http://purl.org/NET/mediatypes/application/java-archive'

JAVA_CLASS = 'http://purl.org/NET/mediatypes/application/java-vm'

JAVA_SOURCE = 'http://purl.org/NET/mediatypes/text/x-java'

JPEG = 'http://purl.org/NET/mediatypes/image/jpeg'

JSON = 'http://purl.org/NET/mediatypes/application/json'

Kappa = 'http://purl.org/NET/mediatypes/text/x-kappa'

LEMS = 'http://purl.org/NET/mediatypes/application/lems+xml'

MAPLE_WORKSHEET = 'http://purl.org/NET/mediatypes/application/x-maple'

MARKDOWN = 'http://purl.org/NET/mediatypes/text/markdown'

MASS = 'http://purl.org/NET/mediatypes/application/mass+json'

MATHEMATICA_NOTEBOOK = 'http://purl.org/NET/mediatypes/application/vnd.wolfram.mathematica'

MATLAB = 'http://purl.org/NET/mediatypes/text/x-matlab'

MATLAB_DATA = 'http://purl.org/NET/mediatypes/application/x-matlab-data'

MATLAB_FIGURE = 'http://purl.org/NET/mediatypes/application/matlab-fig'

MorpheusML = 'http://purl.org/NET/mediatypes/application/morpheusml+xml'

NCS = 'http://purl.org/NET/mediatypes/text/x-ncs'

NEURON_SESSION = 'http://purl.org/NET/mediatypes/text/x-nrn-ses'

NMODL = 'http://purl.org/NET/mediatypes/text/x-nmodl'

NeuroML = 'http://identifiers.org/combine.specifications/neuroml'

NuML = 'http://purl.org/NET/mediatypes/application/numl+xml'

ODE = 'http://purl.org/NET/mediatypes/text/x-ode'

ODT = 'http://purl.org/NET/mediatypes/application/vnd.oasis.opendocument.text'

OMEX = 'http://identifiers.org/combine.specifications/omex'

OMEX_MANIFEST = 'http://identifiers.org/combine.specifications/omex-manifest'

OMEX_METADATA = 'http://identifiers.org/combine.specifications/omex-metadata'

OTHER = 'http://purl.org/NET/mediatypes/application/octet-stream'

OWL = 'http://purl.org/NET/mediatypes/application/rdf+xml'

PDF = 'http://purl.org/NET/mediatypes/application/PDF'

PERL = 'http://purl.org/NET/mediatypes/text/x-perl'

PHP = 'http://purl.org/NET/mediatypes/application/x-httpd-php'

PNG = 'http://purl.org/NET/mediatypes/image/png'

POSTSCRIPT = 'http://purl.org/NET/mediatypes/application/postscript'

PPT = 'http://purl.org/NET/mediatypes/application/vnd.ms-powerpoint'

PPTX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.presentationml.presentation'

PSD = 'http://purl.org/NET/mediatypes/image/vnd.adobe.photoshop'

Python = 'http://purl.org/NET/mediatypes/application/x-python-code'

QUICKTIME = 'http://purl.org/NET/mediatypes/video/quicktime'

R = 'http://purl.org/NET/mediatypes/text/x-r'

RBA = 'http://purl.org/NET/mediatypes/application/rba+zip'

RDF_XML = 'http://purl.org/NET/mediatypes/application/rdf+xml'

RST = 'http://purl.org/NET/mediatypes/text/x-rst'

RUBY = 'http://purl.org/NET/mediatypes/text/x-ruby'

R_Project = 'http://purl.org/NET/mediatypes/application/x-r-project'

SBGN = 'http://identifiers.org/combine.specifications/sbgn'

SBML = 'http://identifiers.org/combine.specifications/sbml'

SBOL = 'http://identifiers.org/combine.specifications/sbol'

SBOL_VISUAL = 'http://identifiers.org/combine.specifications/sbol-visual'

SED_ML = 'http://identifiers.org/combine.specifications/sed-ml'

SHOCKWAVE_FLASH = 'http://purl.org/NET/mediatypes/application/x-shockwave-flash'

SLI = 'http://purl.org/NET/mediatypes/text/x-sli'

SO = 'http://purl.org/NET/mediatypes/application/x-sharedlib'

SQL = 'http://purl.org/NET/mediatypes/application/sql'

SVG = 'http://purl.org/NET/mediatypes/image/svg+xml'

SVGZ = 'http://purl.org/NET/mediatypes/image/svg+xml-compressed'

Scilab = 'http://purl.org/NET/mediatypes/application/x-scilab'

SimBiology_Project = 'http://purl.org/NET/mediatypes/application/x-sbproj'

Smoldyn = 'http://purl.org/NET/mediatypes/text/smoldyn+plain'

TEXT = 'http://purl.org/NET/mediatypes/text/plain'

TIFF = 'http://purl.org/NET/mediatypes/image/tiff'

TSV = 'http://purl.org/NET/mediatypes/text/tab-separated-values'

VCML = 'http://purl.org/NET/mediatypes/application/vcml+xml'

Vega = 'http://purl.org/NET/mediatypes/application/vnd.vega.v5+json'

Vega_Lite = 'http://purl.org/NET/mediatypes/application/vnd.vegalite.v3+json'

WEBP = 'http://purl.org/NET/mediatypes/image/webp'

XLS = 'http://purl.org/NET/mediatypes/application/vnd.ms-excel'

XLSX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'

XML = 'http://purl.org/NET/mediatypes/application/xml'

XPP = 'http://purl.org/NET/mediatypes/text/x-ode'

XPP_AUTO = 'http://purl.org/NET/mediatypes/text/x-ode-auto'

XPP_SET = 'http://purl.org/NET/mediatypes/text/x-ode-set'

XSL = 'http://purl.org/NET/mediatypes/application/xslfo+xml'

XUL = 'http://purl.org/NET/mediatypes/text/xul'

XYZ = 'http://purl.org/NET/mediatypes/chemical/x-xyz'

YAML = 'http://purl.org/NET/mediatypes/application/x-yaml'

ZGINML = 'http://purl.org/NET/mediatypes/application/zginml+zip'

ZIP = 'http://purl.org/NET/mediatypes/application/zip'

pharmML = 'http://purl.org/NET/mediatypes/application/pharmml+xml'

class biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern(value)

Bases: str, Enum

Format for the content of COMBINE/OMEX archives

ACTIONSCRIPT = '^https?://purl\\.org/NET/mediatypes/text/x-actionscript$'

ADOBE_FLASH = '^https?://purl\\.org/NET/mediatypes/(application/x-shockwave-flash|application/vnd\\.adobe\\.flash-movie)$'

AI = '^https?://purl\\.org/NET/mediatypes/(application/pdf|application/postscript)$'

BMP = '^https?://purl\\.org/NET/mediatypes/image/bmp$'

BNGL = '^https?://purl\\.org/NET/mediatypes/text/bngl\\+plain($|\\.)'

BOURNE_SHELL = '^https?://purl\\.org/NET/mediatypes/(text/x-sh|application/x-sh)$'

BioPAX = '^https?://identifiers\\.org/combine\\.specifications/biopax($|\\.)'

C = '^https?://purl\\.org/NET/mediatypes/text/x-c$'

CPP_HEADER = '^https?://purl\\.org/NET/mediatypes/text/x-c\\+\\+hdr$'

CPP_SOURCE = '^https?://purl\\.org/NET/mediatypes/text/x-c\\+\\+src$'

CSS = '^https?://purl\\.org/NET/mediatypes/text/css$'

CSV = '^https?://purl\\.org/NET/mediatypes/text/csv$'

CellML = '^https?://identifiers\\.org/combine\\.specifications/cellml($|\\.)'

CopasiML = '^https?://purl\\.org/NET/mediatypes/application/x-copasi$'

DLL = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.microsoft\\.portable-executable$'

DOC = '^https?://purl\\.org/NET/mediatypes/application/msword$'

DOCX = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.openxmlformats-officedocument\\.wordprocessingml\\.document$'

EPS = '^https?://purl\\.org/NET/mediatypes/(application/postscript|application/eps|application/x-eps|image/eps|image/x-eps)$'

Escher = '^https?://purl\\.org/NET/mediatypes/application/escher\\+json$'

GENESIS = '^https?://purl\\.org/NET/mediatypes/text/x-genesis$'

GIF = '^https?://purl\\.org/NET/mediatypes/image/gif$'

GINML = '^https?://purl\\.org/NET/mediatypes/application/ginml\\+xml$'

GMSH_MESH = '^https?://purl\\.org/NET/mediatypes/model/mesh$'

GRAPHML = '^https?://purl\\.org/NET/mediatypes/(application/graphml\\+xml|application/x-graphml\\+xml)$'

HDF5 = '^https?://purl\\.org/NET/mediatypes/application/x-hdf5?$'

HOC = '^https?://purl\\.org/NET/mediatypes/text/x-hoc$'

HTML = '^https?://purl\\.org/NET/mediatypes/(text/html|application/xhtml\\+xml)$'

ICO = '^https?://purl\\.org/NET/mediatypes/(image/x-icon|image/vnd\\.microsoft\\.icon)$'

INI = '^https?://purl\\.org/NET/mediatypes/text/x-ini$'

IPython_Notebook = '^https?://purl\\.org/NET/mediatypes/application/x-ipynb\\+json$'

JAVASCRIPT = '^https?://purl\\.org/NET/mediatypes/(text/javascript|text/x-javascript|application/javascript|application/x-javascript)$'

JAVA_ARCHIVE = '^https?://purl\\.org/NET/mediatypes/(application/java-archive|application/x-java-archive|application/jar|application/x-jar)$'

JAVA_CLASS = '^https?://purl\\.org/NET/mediatypes/(application/java-vm|application/x-java-vm|application/java|application/x-java)$'

JAVA_SOURCE = '^https?://purl\\.org/NET/mediatypes/(text/x-java|text/x-java-source)$'

JPEG = '^https?://purl\\.org/NET/mediatypes/image/jpeg$'

JSON = '^https?://purl\\.org/NET/mediatypes/application/json$'

Kappa = '^https?://purl\\.org/NET/mediatypes/text/x-kappa$'

LEMS = '^https?://purl\\.org/NET/mediatypes/application/lems\\+xml$'

MAPLE_WORKSHEET = '^https?://purl\\.org/NET/mediatypes/application/x-maple$'

MARKDOWN = '^https?://purl\\.org/NET/mediatypes/text/markdown$'

MASS = '^https?://purl\\.org/NET/mediatypes/application/mass\\+json$'

MATHEMATICA_NOTEBOOK = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.wolfram\\.mathematica$'

MATLAB = '^https?://purl\\.org/NET/mediatypes/text/x-matlab$'

MATLAB_DATA = '^https?://purl\\.org/NET/mediatypes/application/x-matlab-data$'

MATLAB_FIGURE = '^https?://purl\\.org/NET/mediatypes/application/matlab-fig$'

MorpheusML = '^https?://purl\\.org/NET/mediatypes/application/morpheusml\\+xml$'

NCS = '^https?://purl\\.org/NET/mediatypes/text/x-ncs$'

NEURON_SESSION = '^https?://purl\\.org/NET/mediatypes/text/x-nrn-ses$'

NMODL = '^https?://purl\\.org/NET/mediatypes/text/x-nmodl$'

NeuroML = '^https?://identifiers\\.org/combine\\.specifications/neuroml($|\\.)'

NuML = '^https?://purl\\.org/NET/mediatypes/application/numl\\+xml$'

ODE = '^https?://purl\\.org/NET/mediatypes/text/x-(ode|xpp)$'

ODT = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.oasis\\.opendocument\\.text$'

OMEX = '^https?://identifiers\\.org/combine\\.specifications/omex($|\\.)'

OMEX_MANIFEST = '^https?://identifiers\\.org/combine\\.specifications/omex-manifest($|\\.)'

OMEX_METADATA = '^https?://identifiers\\.org/combine\\.specifications/omex-metadata($|\\.)'

OTHER = '^https?://purl\\.org/NET/mediatypes/application/octet-stream$'

OWL = '^https?://purl\\.org/NET/mediatypes/application/rdf\\+xml$'

PDF = '^https?://purl\\.org/NET/mediatypes/application/pdf$'

PERL = '^https?://purl\\.org/NET/mediatypes/(text/x-perl|application/x-perl)$'

PHP = '^https?://purl\\.org/NET/mediatypes/(application/x-httpd-php|application/x-httpd-php-source|application/x-php|text/x-php)$'

PNG = '^https?://purl\\.org/NET/mediatypes/image/png$'

POSTSCRIPT = '^https?://purl\\.org/NET/mediatypes/application/postscript$'

PPT = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.ms-powerpoint$'

PPTX = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.openxmlformats-officedocument\\.presentationml\\.presentation$'

PSD = '^https?://purl\\.org/NET/mediatypes/(image/vnd\\.adobe\\.photoshop|image/psd|image/x-psd|application/photoshop|application/x-photoshop|application/psd|application/x-psd)$'

Python = '^https?://purl\\.org/NET/mediatypes/application/x-python-code$'

QUICKTIME = '^https?://purl\\.org/NET/mediatypes/(video/quicktime|image/mov)$'

R = '^https?://purl\\.org/NET/mediatypes/text/x-r$'

RBA = '^https?://purl\\.org/NET/mediatypes/application/rba\\+zip$'

RDF_XML = '^https?://purl\\.org/NET/mediatypes/application/rdf\\+xml$'

RST = '^https?://purl\\.org/NET/mediatypes/text/x-rst$'

RUBY = '^https?://purl\\.org/NET/mediatypes/text/x-ruby$'

R_Project = '^https?://purl\\.org/NET/mediatypes/application/x-r-project$'

SBGN = '^https?://identifiers\\.org/combine\\.specifications/sbgn($|\\.)'

SBML = '^https?://identifiers\\.org/combine\\.specifications/sbml($|\\.)'

SBOL = '^https?://identifiers\\.org/combine\\.specifications/sbol($|\\.)'

SBOL_VISUAL = '^https?://identifiers\\.org/combine\\.specifications/sbol-visual($|\\.)'

SED_ML = '^https?://identifiers\\.org/combine\\.specifications/sed\\-?ml($|\\.)'

SHOCKWAVE_FLASH = '^https?://purl\\.org/NET/mediatypes/(application/x-shockwave-flash|application/vnd\\.adobe\\.flash-movie)$'

SLI = '^https?://purl\\.org/NET/mediatypes/text/x-sli$'

SO = '^https?://purl\\.org/NET/mediatypes/application/x-sharedlib$'

SQL = '^https?://purl\\.org/NET/mediatypes/application/sql$'

SVG = '^https?://purl\\.org/NET/mediatypes/image/svg\\+xml$'

SVGZ = '^https?://purl\\.org/NET/mediatypes/image/svg\\+xml-compressed$'

Scilab = '^https?://purl\\.org/NET/mediatypes/application/x-scilab$'

SimBiology_Project = '^https?://purl\\.org/NET/mediatypes/application/x-sbproj$'

Smoldyn = '^https?://purl\\.org/NET/mediatypes/text/smoldyn\\+plain$'

TEXT = '^https?://purl\\.org/NET/mediatypes/text/plain$'

TIFF = '^https?://purl\\.org/NET/mediatypes/image/tiff$'

TSV = '^https?://purl\\.org/NET/mediatypes/text/tab-separated-values$'

VCML = '^https?://purl\\.org/NET/mediatypes/application/vcml\\+xml$'

Vega = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.vega\\.v5\\+json$'

Vega_Lite = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.vegalite\\.v3\\+json$'

WEBP = '^https?://purl\\.org/NET/mediatypes/image/webp$'

XLS = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.ms-excel$'

XLSX = '^https?://purl\\.org/NET/mediatypes/application/vnd\\.openxmlformats-officedocument\\.spreadsheetml\\.sheet$'

XML = '^https?://purl\\.org/NET/mediatypes/application/xml$'

XPP = '^https?://purl\\.org/NET/mediatypes/text/x-(ode|xpp)$'

XPP_AUTO = '^https?://purl\\.org/NET/mediatypes/text/x-(ode|xpp)-auto$'

XPP_SET = '^https?://purl\\.org/NET/mediatypes/text/x-(ode|xpp)-set$'

XSL = '^https?://purl\\.org/NET/mediatypes/(application/xslfo\\+xml|text/xsl)$'

XUL = '^https?://purl\\.org/NET/mediatypes/text/xul$'

XYZ = '^https?://purl\\.org/NET/mediatypes/chemical/x-xyz$'

YAML = '^https?://purl\\.org/NET/mediatypes/application/x-yaml$'

ZGINML = '^https?://purl\\.org/NET/mediatypes/application/zginml\\+zip$'

ZIP = '^https?://purl\\.org/NET/mediatypes/application/zip$'

pharmML = '^https?://purl\\.org/NET/mediatypes/application/pharmml\\+xml$'

biosimulators_utils.combine.exceptions module

Exceptions for COMBINE/OMEX archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2021-01-12

Copyright:

2021, Center for Reproducible Biomedical Modeling

License:

MIT

exception biosimulators_utils.combine.exceptions.CombineArchiveExecutionError

Bases: BioSimulatorsException

Error that a SED document could not be executed

exception biosimulators_utils.combine.exceptions.NoSedmlError

Bases: BioSimulatorsException

Error that a COMBINE/OMEX archive does not contain any SED-ML files

biosimulators_utils.combine.exec module

Utilities for executing tasks in SED-ML files in COMBINE/OMEX archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

biosimulators_utils.combine.exec.exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir, apply_xml_model_changes=False, sed_doc_executer_supported_features=(<class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), sed_doc_executer_logged_features=(<class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), log_level=StandardOutputErrorCapturerLevel.c, config=None)

Execute the SED-ML files in a COMBINE/OMEX archive (execute tasks and save outputs)

Parameters:

• sed_doc_executer (types.FunctionType) –

  function to execute each SED document in the archive. The function must implement the following interface:

  def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
               apply_xml_model_changes=False,
               log=None, log_level=StandardOutputErrorCapturerLevel.c, indent=0, config=None):
      ''' Execute the tasks specified in a SED document and generate the specified outputs
  
      Args:
          doc (:obj:`SedDocument` of :obj:`str`): SED document or a path to SED-ML file which defines a SED document
          working_dir (:obj:`str`): working directory of the SED document (path relative to which models are located)
  
          out_path (:obj:`str`): path to store the outputs
  
              * CSV: directory in which to save outputs to files
                ``{out_path}/{rel_out_path}/{report.id}.csv``
              * HDF5: directory in which to save a single HDF5 file (``{out_path}/reports.h5``),
                with reports at keys ``{rel_out_path}/{report.id}`` within the HDF5 file
  
          rel_out_path (:obj:`str`, optional): path relative to :obj:`out_path` to store the outputs
          apply_xml_model_changes (:obj:`bool`, optional): if :obj:`True`, apply any model changes specified in the SED-ML file
          log (:obj:`SedDocumentLog`, optional): execution status of document
          log_level (:obj:`StandardOutputErrorCapturerLevel`, optional): level at which to log output
          indent (:obj:`int`, optional): degree to indent status messages
          config (:obj:`Config`, optional): BioSimulators common configuration
      '''
  

• archive_filename (str) – path to COMBINE/OMEX archive

• out_dir (str) –

  path to store the outputs of the archive

  • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

  • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

• apply_xml_model_changes (bool) – if True, apply any model changes specified in the SED-ML files before calling task_executer.

• sed_doc_executer_supported_features (list of type, optional) – list of the types of elements that the SED document executer supports. Default: tasks, reports, plots, data sets, curves, and surfaces.

• sed_doc_executer_logged_features (list of type, optional) – list of the types fo elements which that the SED document executer logs. Default: tasks, reports, plots, data sets, curves, and surfaces.

• log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output

• config (Config) – configuration

Returns:

• SedDocumentResults: results

• CombineArchiveLog: log

Return type:

tuple

biosimulators_utils.combine.io module

Utilities for reading and writing COMBINE/OMEX archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.combine.io.CombineArchiveReader

Bases: object

Reader for COMBINE/OMEX archives

errors

errors

Type:

nested list of str

warnings

warnings

Type:

nested list of str

NONE_DATETIME = '2000-01-01T00:00:00Z'

read_manifest(filename, archive_filename=None, config=None)

Read the contents of an OMEX manifest file

Parameters:

• filename (str) – path to OMEX manifest file

• archive_filename (str, option) – path to COMBINE archive

• config (Config, optional) – configuration

Returns:

contents of the OMEX manifest file

Return type:

list of CombineArchiveContent

run(in_file: str, out_dir: str, include_omex_metadata_files: bool = True, config: Config | None = None) → CombineArchive

Read an archive from a file

Parameters:

• in_file (str) – path to archive

• out_dir (str) – directory where the contents of the archive should be unpacked

• include_omex_metadata_files (bool, optional) – whether to include the OMEX metadata file as part of the contents of the archive

• config (Config, optional) – configuration

Returns:

description of archive

Return type:

CombineArchive

Raises:

ValueError – archive is invalid

class biosimulators_utils.combine.io.CombineArchiveWriter

Bases: object

Writer for COMBINE/OMEX archives

errors

errors

Type:

nested list of str

warnings

warnings

Type:

nested list of str

run(archive, in_dir, out_file)

Write an archive to a file

Parameters:

• archive (CombineArchive) – description of archive

• in_dir (str) – directory which contains the files in the archive

• out_file (str) – path to save archive

Raises:

AssertionError – if files could not be added to the archive or the archive could not be saved

write_manifest(contents, filename)

Write an OMEX manifest file

Parameters:

• contents (list of CombineArchiveContent) – contents of a COMBINE/OMEX archive

• filename (str) – path to OMEX manifest file

class biosimulators_utils.combine.io.CombineArchiveZipReader

Bases: object

Create a COMBINE/OMEX archive object from a plain zip archive. Set the format of files with the extension .sedml to CombineArchiveContentFormat.SED_ML.value.

classmethod run(in_file, out_dir=None)

Read an archive from a zip file

Parameters:

• in_file (str) – path to archive

• out_dir (str, optional) – directory where the contents of the archive should be unpacked

Returns:

description of the archive

Return type:

CombineArchive

Raises:

ValueError – archive is invalid

biosimulators_utils.combine.utils module

Utilities for working with COMBINE/OMEX archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

biosimulators_utils.combine.utils.get_sedml_contents(archive, include_all_sed_docs_when_no_sed_doc_is_master=True, always_include_all_sed_docs=False)

Get the SED-ML files in an archive

Parameters:

• archive (CombineArchive) – COMBINE/OMEX archive

• include_all_sed_docs_when_no_sed_doc_is_master (bool, optional) – if true and no SED document has master="true", return all SED documents.

• always_include_all_sed_docs (bool, optional) – if true, return all SED documents, regardless of whether they have master="true" or not.

Returns:

SED-ML files in a COMBINE/OMEX archive

Return type:

list of CombineArchiveContent

biosimulators_utils.combine.utils.get_summary_sedml_contents(archive, archive_dir, include_all_sed_docs_when_no_sed_doc_is_master=True, always_include_all_sed_docs=False, config=None)

Get a summary of the SED-ML content in a COMBINE/OMEX archive

Parameters:

• archive (CombineArchive) – COMBINE/OMEX archive

• archive_dir (str) – path where the content of the archive is located

• include_all_sed_docs_when_no_sed_doc_is_master (bool, optional) – if true and no SED document has master="true", return all SED documents.

• always_include_all_sed_docs (bool, optional) – if true, return all SED documents, regardless of whether they have master="true" or not.

• config (Config, optional) – whether to fail on missing includes

Returns:

summary of the SED-ML content in a COMBINE/OMEX archive

Return type:

str

biosimulators_utils.combine.validation module

Methods for validating COMBINE archives

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2021-04-16

Copyright:

2021, Center for Reproducible Biomedical Modeling

License:

MIT

biosimulators_utils.combine.validation.validate(archive: CombineArchive, archive_dirname: str, include_all_sed_docs_when_no_sed_doc_is_master: bool = True, always_include_all_sed_docs: bool = False, formats_to_validate: list[CombineArchiveContentFormat] = [CombineArchiveContentFormat.SED_ML], validate_models_with_languages: bool = True, config: Config | None = None)

Validate a COMBINE/OMEX archive and the SED-ML and model documents it contains

Parameters:

• archive (CombineArchive) – COMBINE/OMEX archive

• archive_dirname (str) – directory with the content of the archive

• include_all_sed_docs_when_no_sed_doc_is_master (bool, optional) – if true and no SED document has master="true", return all SED documents.

• always_include_all_sed_docs (bool, optional) – if true, return all SED documents, regardless of whether they have master="true" or not.

• formats_to_validate (list of CombineArchiveContentFormat, optional) – list for formats of files to validate

• validate_models_with_languages (bool, optional) – if True, validate models

• config (Config, optional) – configuration

Returns:

• nested list of str: nested list of errors with the archive

• nested list of str: nested list of warnings with the archive

Return type:

tuple

biosimulators_utils.combine.validation.validate_content(content, archive_dirname, formats_to_validate=[CombineArchiveContentFormat.SED_ML], validate_models_with_languages=True, config=None)

Validate an item of a COMBINE/OMEX archive

Parameters:

• content (CombineArchiveContent) – item of a COMBINE/OMEX archive

• archive_dirname (str) – directory with the content of the archive

• formats_to_validate (list of CombineArchiveContentFormat, optional) – list for formats of files to validate

• validate_models_with_languages (bool, optional) – if True, validate models

• config (Config, optional) – configuration

Returns:

• nested list of str: nested list of errors with the archive

• nested list of str: nested list of warnings with the archive

Return type:

tuple

biosimulators_utils.combine.validation.validate_format(format)

Validate a COMBINE of an element of a COMBINE/OMEX archive

Parameters:

format (str) – format

Returns:

nested list of errors with the archive

Return type:

nested list of str