Skip to content

File Description

mzmlpy.elems.file_desc.FileDescription dataclass 

FileDescription(element: ElementTree.Element)

Bases: _DataTreeWrapper

Top-level file description element containing content type, source files, and contacts.

file_content property 

file_content: FileContent | None

return file content as FileContent object if present

source_files property 

source_files: list[SourceFile]

return source files as tuple of SourceFile objects

contact property 

contact: list[Contact]

return a list of contacts if present

ns cached property 

ns: str

Get XML namespace from the element tag.

get_source_file 

get_source_file(id: str) -> SourceFile | None

Get a source file by its id attribute.

Source code in src/mzmlpy/elems/file_desc.py 
173
174
175
176
177
178
def get_source_file(self, id: str) -> SourceFile | None:
    """Get a source file by its ``id`` attribute."""
    for sf in self.source_files:
        if sf.id == id:
            return sf
    return None

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
63
64
65
66
67
68
69
70
def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
72
73
74
def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

FileContent

mzmlpy.elems.file_desc.FileContent dataclass 

FileContent(element: ElementTree.Element)

Bases: _ParamGroup

CV parameters describing the overall content of the mzML file (e.g. MS1 spectrum, centroid spectrum).

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
63
64
65
66
67
68
69
70
def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
72
73
74
def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
100
101
102
103
104
105
def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
107
108
109
def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

cv_float 

cv_float(id: str) -> float | None

Return a cvParam's value as a float, or None if the term is absent or has no value.

Raises ValueError naming the term and its bad value if the value is present but not numeric — more actionable than a bare "could not convert string to float".

Source code in src/mzmlpy/elems/dtree_wrapper.py 
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
def cv_float(self, id: str) -> float | None:
    """Return a cvParam's value as a float, or None if the term is absent or has no value.

    Raises ValueError naming the term and its bad value if the value is present but not
    numeric — more actionable than a bare "could not convert string to float".
    """
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return float(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-numeric value {cv_param.value!r}"
        ) from e

cv_int 

cv_int(id: str) -> int | None

Return a cvParam's value as an int, or None if absent or valueless (see :meth:cv_float).

Source code in src/mzmlpy/elems/dtree_wrapper.py 
127
128
129
130
131
132
133
134
135
136
137
def cv_int(self, id: str) -> int | None:
    """Return a cvParam's value as an int, or None if absent or valueless (see :meth:`cv_float`)."""
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return int(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-integer value {cv_param.value!r}"
        ) from e

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
167
168
169
170
171
172
def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
174
175
176
def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
187
188
189
190
191
192
def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
194
195
196
def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

SourceFile

mzmlpy.elems.file_desc.SourceFile dataclass 

SourceFile(element: ElementTree.Element)

Bases: _ParamGroup

A single source file referenced by the mzML document.

Attributes are accessed via CV parameters (checksum type and value) as well as XML attributes (id, name, location).

id property 

id: str | None

Get the source file's id attribute.

name property 

name: str | None

Get the source file's name attribute.

location property 

location: str | None

Get the source file's location attribute (e.g. a directory URI).

checksum_type property 

checksum_type: Literal['MD5', 'SHA1', 'SHA256'] | None

Get checksum type if present.

checksum property 

checksum: str | None

Get checksum value if present.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
63
64
65
66
67
68
69
70
def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
72
73
74
def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
100
101
102
103
104
105
def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
107
108
109
def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

cv_float 

cv_float(id: str) -> float | None

Return a cvParam's value as a float, or None if the term is absent or has no value.

Raises ValueError naming the term and its bad value if the value is present but not numeric — more actionable than a bare "could not convert string to float".

Source code in src/mzmlpy/elems/dtree_wrapper.py 
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
def cv_float(self, id: str) -> float | None:
    """Return a cvParam's value as a float, or None if the term is absent or has no value.

    Raises ValueError naming the term and its bad value if the value is present but not
    numeric — more actionable than a bare "could not convert string to float".
    """
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return float(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-numeric value {cv_param.value!r}"
        ) from e

cv_int 

cv_int(id: str) -> int | None

Return a cvParam's value as an int, or None if absent or valueless (see :meth:cv_float).

Source code in src/mzmlpy/elems/dtree_wrapper.py 
127
128
129
130
131
132
133
134
135
136
137
def cv_int(self, id: str) -> int | None:
    """Return a cvParam's value as an int, or None if absent or valueless (see :meth:`cv_float`)."""
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return int(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-integer value {cv_param.value!r}"
        ) from e

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
167
168
169
170
171
172
def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
174
175
176
def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
187
188
189
190
191
192
def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
194
195
196
def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)

Contact

mzmlpy.elems.file_desc.Contact dataclass 

Contact(element: ElementTree.Element)

Bases: _ParamGroup

Contact information for a person or organization associated with the mzML file.

name property 

name: str | None

Get the contact's name, if present.

organization property 

organization: str | None

Get the contact's organization, if present.

address property 

address: str | None

Get the contact's address, if present.

url property 

url: str | None

Get the contact's URL, if present.

email property 

email: str | None

Get the contact's email address, if present.

phone_number property 

phone_number: str | None

Get the contact's phone number, if present.

toll_free_phone_number property 

toll_free_phone_number: str | None

Get the contact's toll-free phone number, if present.

fax_number property 

fax_number: str | None

Get the contact's fax number, if present.

role property 

role: str | None

Get the contact's role, if present.

ns cached property 

ns: str

Get XML namespace from the element tag.

cv_params cached property 

cv_params: list[CvParam]

Parse cvParams from the XML element.

accessions cached property 

accessions: set[str]

Get a set of all accession numbers from the cvParams.

names cached property 

names: set[str]

Get a set of all names from the cvParams.

user_params property 

user_params: list[UserParam]

Parse userParams from the XML element.

ref_params property 

ref_params: list[ReferenceableParamGroupRef]

Get a list of all referenceable parameters from the XML element.

serialize 

serialize() -> dict

return the full element content

Source code in src/mzmlpy/elems/dtree_wrapper.py 
63
64
65
66
67
68
69
70
def serialize(self) -> dict:
    """return the full element content"""
    return {
        "tag": self.element.tag,
        "attributes": self.element.attrib,
        "text": self.element.text,
        "children": [_DataTreeWrapper(child).serialize() for child in self.element],
    }

get_attribute 

get_attribute(attr_name: str) -> str | None

Get an attribute value from the element.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
72
73
74
def get_attribute(self, attr_name: str) -> str | None:
    """Get an attribute value from the element."""
    return self.element.attrib.get(attr_name)

get_cvparm 

get_cvparm(id: str) -> CvParam | None

Get a cvParam by accession or name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
100
101
102
103
104
105
def get_cvparm(self, id: str) -> CvParam | None:
    """Get a cvParam by accession or name."""
    for cv_param in self.cv_params:
        if cv_param.accession == id or cv_param.name == id:
            return cv_param
    return None

has_cvparm 

has_cvparm(id: str) -> bool

Check if a cvParam with the given accession or name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
107
108
109
def has_cvparm(self, id: str) -> bool:
    """Check if a cvParam with the given accession or name exists."""
    return any(cv_param.accession == id or cv_param.name == id for cv_param in self.cv_params)

cv_float 

cv_float(id: str) -> float | None

Return a cvParam's value as a float, or None if the term is absent or has no value.

Raises ValueError naming the term and its bad value if the value is present but not numeric — more actionable than a bare "could not convert string to float".

Source code in src/mzmlpy/elems/dtree_wrapper.py 
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
def cv_float(self, id: str) -> float | None:
    """Return a cvParam's value as a float, or None if the term is absent or has no value.

    Raises ValueError naming the term and its bad value if the value is present but not
    numeric — more actionable than a bare "could not convert string to float".
    """
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return float(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-numeric value {cv_param.value!r}"
        ) from e

cv_int 

cv_int(id: str) -> int | None

Return a cvParam's value as an int, or None if absent or valueless (see :meth:cv_float).

Source code in src/mzmlpy/elems/dtree_wrapper.py 
127
128
129
130
131
132
133
134
135
136
137
def cv_int(self, id: str) -> int | None:
    """Return a cvParam's value as an int, or None if absent or valueless (see :meth:`cv_float`)."""
    cv_param = self.get_cvparm(id)
    if cv_param is None or cv_param.value is None:
        return None
    try:
        return int(cv_param.value)
    except ValueError as e:
        raise ValueError(
            f"CV param {cv_param.name or id!r} ({id}) has a non-integer value {cv_param.value!r}"
        ) from e

get_user_param 

get_user_param(name: str) -> UserParam | None

Get a userParam by name.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
167
168
169
170
171
172
def get_user_param(self, name: str) -> UserParam | None:
    """Get a userParam by name."""
    for user_param in self.user_params:
        if user_param.name == name:
            return user_param
    return None

has_user_param 

has_user_param(name: str) -> bool

Check if a userParam with the given name exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
174
175
176
def has_user_param(self, name: str) -> bool:
    """Check if a userParam with the given name exists."""
    return any(user_param.name == name for user_param in self.user_params)

get_ref_param 

get_ref_param(
    ref: str,
) -> ReferenceableParamGroupRef | None

Get a referenceable parameter by ref.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
187
188
189
190
191
192
def get_ref_param(self, ref: str) -> ReferenceableParamGroupRef | None:
    """Get a referenceable parameter by ref."""
    for ref_param in self.ref_params:
        if ref_param.ref == ref:
            return ref_param
    return None

has_ref_param 

has_ref_param(ref: str) -> bool

Check if a referenceable parameter with the given ref exists.

Source code in src/mzmlpy/elems/dtree_wrapper.py 
194
195
196
def has_ref_param(self, ref: str) -> bool:
    """Check if a referenceable parameter with the given ref exists."""
    return any(ref_param.ref == ref for ref_param in self.ref_params)