ID assignment

When reading an SBGN-ML file, every element follows a consistent pattern:

• Model id_ = f"{xml_id}_model"
• Layout id_ = xml_id

Both xml_id_to_model_element and xml_id_to_layout_element are keyed by the raw xml_id.

Element type	Model id_	Layout id_	Registered	Notes
Compartment	f"{glyph_id}_model"	glyph_id	yes
EntityPool / Subunit	f"{glyph_id}_model"	glyph_id	yes
Activity	f"{glyph_id}_model"	glyph_id	yes
StateVariable	f"{glyph_id}_model"	glyph_id	yes	Frozen child
UnitOfInformation	f"{glyph_id}_model"	glyph_id	yes	Frozen child
Submap	f"{glyph_id}_model"	glyph_id	yes
Terminal / Tag	f"{glyph_id}_model"	glyph_id	yes
TerminalRef / TagRef	f"{arc_id}_model"	arc_id	yes	Frozen child
StoichiometricProcess	f"{glyph_id}_model"	glyph_id	yes
Reactant	f"{arc_id}_model"	arc_id	yes	Frozen child
Product	f"{arc_id}_model"	arc_id	yes	Frozen child
LogicalOperator	f"{glyph_id}_model"	glyph_id	yes
LogicalOperatorInput	f"{arc_id}_model"	arc_id	yes	Frozen child
Modulation	f"{arc_id}_model"	arc_id	yes
Phenotype	f"{glyph_id}_model"	glyph_id	yes	In model.processes

Map, model, and layout IDs come from <map id="...">:

• map_.id_ = map_id
• model.id_ = f"{map_id}_model"
• layout.id_ = f"{map_id}_layout"

These are only set for SBGN-ML 0.3. SBGN-ML 0.2 has no map id, so the builder falls back to UUID defaults.

API

momapy.sbgn.io.sbgnml

Classes for reading and writing SBGN-ML files.

Modules:

Name	Description
reader	SBGN-ML reader classes.
writer	SBGN-ML writer classes.

Classes:

Name	Description
SBGNML0_2Reader	Class for SBGN-ML 0.2 reader objects
SBGNML0_3Reader	Class for SBGN-ML 0.3 reader objects
SBGNML0_3Writer	Class for SBGN-ML 0.3 writer objects.

SBGNML0_2Reader

Bases: _SBGNMLReader

Class for SBGN-ML 0.2 reader objects

Methods:

Name	Description
check_file	Return true if the given file is an SBGN-ML 0.2 document, false otherwise
read	Read an SBGN-ML file and return a reader result object

check_file classmethod

check_file(file_path)

Return true if the given file is an SBGN-ML 0.2 document, false otherwise

Source code in src/momapy/sbgn/io/sbgnml/reader.py

@classmethod
def check_file(cls, file_path):
    """Return `true` if the given file is an SBGN-ML 0.2 document, `false` otherwise"""
    try:
        with open(file_path) as f:
            for line in f:
                if "http://sbgn.org/libsbgn/0.2" in line:
                    return True
        return False
    except Exception:
        return False

read classmethod

read(file_path: str | PathLike, return_type: Literal['map', 'model', 'layout'] = 'map', with_model: bool = True, with_layout: bool = True, with_annotations: bool = True, with_notes: bool = True, xsep: float = 0, ysep: float = 0) -> ReaderResult

Read an SBGN-ML file and return a reader result object

Source code in src/momapy/sbgn/io/sbgnml/reader.py

@classmethod
def read(
    cls,
    file_path: str | os.PathLike,
    return_type: typing.Literal["map", "model", "layout"] = "map",
    with_model: bool = True,
    with_layout: bool = True,
    with_annotations: bool = True,
    with_notes: bool = True,
    xsep: float = 0,
    ysep: float = 0,
) -> momapy.io.core.ReaderResult:
    """Read an SBGN-ML file and return a reader result object"""

    sbgnml_document = lxml.objectify.parse(file_path)
    sbgnml_sbgn = sbgnml_document.getroot()
    (
        obj,
        annotations,
        notes,
        id_to_element,
        source_id_to_model_element,
        source_id_to_layout_element,
        source_id_to_annotations,
        source_id_to_notes,
    ) = cls._make_main_obj(
        sbgnml_map=sbgnml_sbgn.map,
        return_type=return_type,
        with_model=with_model,
        with_layout=with_layout,
        with_annotations=with_annotations,
        with_notes=with_notes,
        xsep=xsep,
        ysep=ysep,
    )
    result = momapy.io.core.ReaderResult(
        obj=obj,
        element_to_notes=notes,
        element_to_annotations=annotations,
        id_to_element=id_to_element,
        source_id_to_model_element=source_id_to_model_element,
        source_id_to_layout_element=source_id_to_layout_element,
        source_id_to_annotations=source_id_to_annotations,
        source_id_to_notes=source_id_to_notes,
        file_path=file_path,
    )
    return result

SBGNML0_3Reader

Bases: _SBGNMLReader

Class for SBGN-ML 0.3 reader objects

Methods:

Name	Description
check_file	Return true if the given file is an SBGN-ML 0.3 document, false otherwise
read	Read an SBGN-ML file and return a reader result object

check_file classmethod

check_file(file_path)

Return true if the given file is an SBGN-ML 0.3 document, false otherwise

Source code in src/momapy/sbgn/io/sbgnml/reader.py

@classmethod
def check_file(cls, file_path):
    """Return `true` if the given file is an SBGN-ML 0.3 document, `false` otherwise"""
    try:
        with open(file_path) as f:
            for line in f:
                if "http://sbgn.org/libsbgn/0.3" in line:
                    return True
        return False
    except Exception:
        return False

read classmethod

read(file_path: str | PathLike, return_type: Literal['map', 'model', 'layout'] = 'map', with_model: bool = True, with_layout: bool = True, with_annotations: bool = True, with_notes: bool = True, xsep: float = 0, ysep: float = 0) -> ReaderResult

Read an SBGN-ML file and return a reader result object

Source code in src/momapy/sbgn/io/sbgnml/reader.py

@classmethod
def read(
    cls,
    file_path: str | os.PathLike,
    return_type: typing.Literal["map", "model", "layout"] = "map",
    with_model: bool = True,
    with_layout: bool = True,
    with_annotations: bool = True,
    with_notes: bool = True,
    xsep: float = 0,
    ysep: float = 0,
) -> momapy.io.core.ReaderResult:
    """Read an SBGN-ML file and return a reader result object"""

    sbgnml_document = lxml.objectify.parse(file_path)
    sbgnml_sbgn = sbgnml_document.getroot()
    (
        obj,
        annotations,
        notes,
        id_to_element,
        source_id_to_model_element,
        source_id_to_layout_element,
        source_id_to_annotations,
        source_id_to_notes,
    ) = cls._make_main_obj(
        sbgnml_map=sbgnml_sbgn.map,
        return_type=return_type,
        with_model=with_model,
        with_layout=with_layout,
        with_annotations=with_annotations,
        with_notes=with_notes,
        xsep=xsep,
        ysep=ysep,
    )
    result = momapy.io.core.ReaderResult(
        obj=obj,
        element_to_notes=notes,
        element_to_annotations=annotations,
        id_to_element=id_to_element,
        source_id_to_model_element=source_id_to_model_element,
        source_id_to_layout_element=source_id_to_layout_element,
        source_id_to_annotations=source_id_to_annotations,
        source_id_to_notes=source_id_to_notes,
        file_path=file_path,
    )
    return result

SBGNML0_3Writer

Bases: _SBGNMLWriter

Class for SBGN-ML 0.3 writer objects.

Methods:

Name	Description
write	Write an SBGN map to an SBGN-ML file.

write classmethod

write(obj: SBGNMap, file_path: str | PathLike, element_to_annotations: dict | None = None, element_to_notes: dict | None = None, source_id_to_model_element: dict | None = None, source_id_to_layout_element: dict | None = None, with_render_information: bool = True, with_annotations: bool = True, with_notes: bool = True) -> None

Write an SBGN map to an SBGN-ML file.

Parameters:

Name	Type	Description	Default
obj	SBGNMap	The SBGN map to serialize.	required
file_path	str | PathLike	Destination file path.	required
element_to_annotations	dict | None	Optional per-element annotation dict.	None
element_to_notes	dict | None	Optional per-element notes dict.	None
source_id_to_model_element	dict | None	Optional source ID to model element mapping from ReaderResult.	None
source_id_to_layout_element	dict | None	Optional source ID to layout element mapping from ReaderResult.	None
with_render_information	bool	Ignored (kept for API compat).	True
with_annotations	bool	Whether to write annotations.	True
with_notes	bool	Whether to write notes.	True

Source code in src/momapy/sbgn/io/sbgnml/writer.py

@classmethod
def write(
    cls,
    obj: momapy.sbgn.SBGNMap,
    file_path: str | os.PathLike,
    element_to_annotations: dict | None = None,
    element_to_notes: dict | None = None,
    source_id_to_model_element: dict | None = None,
    source_id_to_layout_element: dict | None = None,
    with_render_information: bool = True,
    with_annotations: bool = True,
    with_notes: bool = True,
) -> None:
    """Write an SBGN map to an SBGN-ML file.

    Args:
        obj: The SBGN map to serialize.
        file_path: Destination file path.
        element_to_annotations: Optional per-element annotation dict.
        element_to_notes: Optional per-element notes dict.
        source_id_to_model_element: Optional source ID to model
            element mapping from ReaderResult.
        source_id_to_layout_element: Optional source ID to layout
            element mapping from ReaderResult.
        with_render_information: Ignored (kept for API compat).
        with_annotations: Whether to write annotations.
        with_notes: Whether to write notes.
    """
    momapy.utils.check_parent_dir_exists(file_path)
    if element_to_annotations is None:
        element_to_annotations = {}
    if element_to_notes is None:
        element_to_notes = {}
    writing_context = momapy.io.utils.WritingContext(
        map_=obj,
        element_to_annotations=element_to_annotations,
        element_to_notes=element_to_notes,
        source_id_to_model_element=source_id_to_model_element,
        source_id_to_layout_element=source_id_to_layout_element,
        with_annotations=with_annotations,
        with_notes=with_notes,
    )
    sbgnml_sbgn = momapy.sbgn.io.sbgnml._writing.make_lxml_element(
        "sbgn", nsmap=momapy.sbgn.io.sbgnml._writing.NSMAP
    )
    sbgnml_map = make_sbgnml_map(writing_context)
    sbgnml_sbgn.append(sbgnml_map)
    with open(file_path, "w", encoding="utf-8") as f:
        f.write(
            lxml.etree.tostring(
                sbgnml_sbgn, pretty_print=True, xml_declaration=True
            ).decode()
        )