diff --git a/latest/_modules/index.html b/latest/_modules/index.html index 68965d9..18de717 100644 --- a/latest/_modules/index.html +++ b/latest/_modules/index.html @@ -84,6 +84,7 @@

All modules for which code is available

  • phenopacket_mapper.cli.quickstart_command
  • phenopacket_mapper.cli.validate_command
  • phenopacket_mapper.data_standards.DataModel2PhenopacketSchema
    • +
  • phenopacket_mapper.data_standards.cardinality
  • phenopacket_mapper.data_standards.code
  • phenopacket_mapper.data_standards.code_system
  • phenopacket_mapper.data_standards.data_model
    • diff --git a/latest/_modules/phenopacket_mapper/data_standards/cardinality.html b/latest/_modules/phenopacket_mapper/data_standards/cardinality.html new file mode 100644 index 0000000..e751035 --- /dev/null +++ b/latest/_modules/phenopacket_mapper/data_standards/cardinality.html @@ -0,0 +1,133 @@ + + + + + + + + phenopacket_mapper.data_standards.cardinality — phenopacket_mapper 0.0.1 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    +
      +
      • +
    • Module code
      • +
    • phenopacket_mapper.data_standards.cardinality
      • +
    • +
      • +
    +
    +
    +
    +
    + +

    Source code for phenopacket_mapper.data_standards.cardinality

    +from dataclasses import dataclass, field
+from typing import Union, Literal
+
+
+
    
+[docs]
+@dataclass(slots=True, frozen=True)
+class Cardinality:
+    min: int = field(default=0)
+    max: Union[int, Literal['n']] = field(default='n')
+
+    def __post_init__(self):
+        if not isinstance(self.min, int):
+            raise ValueError(f"Parameter min must be of type integer. (Not: {type(self.min)})")
+        elif self.min < 0:
+            raise ValueError(f"Parameter min must be a non-negative integer. (Not: {self.min})")
+        if not (isinstance(self.max, int) or self.max == 'n'):
+            raise ValueError(f"Parameter max must be of type or equal to the literal 'n'. "
+                             f"(Not: {self.min} ({type(self.min)}))")
+        elif self.max != 'n' and self.max < 1:  # has to be an integer
+            raise ValueError(f"Parameter max must be a positive integer. (Not: {self.min})")
+
+    def __str__(self):
+        return f"{self.min}..{self.max}"
    
+
+
    + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/latest/_modules/phenopacket_mapper/data_standards/data_model.html b/latest/_modules/phenopacket_mapper/data_standards/data_model.html index 396acbd..0a603fd 100644 --- a/latest/_modules/phenopacket_mapper/data_standards/data_model.html +++ b/latest/_modules/phenopacket_mapper/data_standards/data_model.html @@ -94,7 +94,8 @@

    Source code for phenopacket_mapper.data_standards.data_model

    import pandas as pd -from phenopacket_mapper.data_standards import CodeSystem +from phenopacket_mapper._api import DataNode +from phenopacket_mapper.data_standards import CodeSystem, Cardinality from phenopacket_mapper.data_standards.date import Date from phenopacket_mapper.data_standards.value_set import ValueSet from phenopacket_mapper.preprocessing import preprocess, preprocess_method @@ -103,10 +104,10 @@

    Source code for phenopacket_mapper.data_standards.data_model

    [docs] @dataclass(slots=True, frozen=True) -class DataField: +class DataField(DataNode): """This class defines fields used in the definition of a `DataModel` - A dataa field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a + A data field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a required flag, a specification, and an ordinal. The string for the `id` field is generated from the `name` field using the `str_to_valid_id` function from the @@ -117,38 +118,33 @@

    Source code for phenopacket_mapper.data_standards.data_model

    - The `id` field must be a valid Python identifier - The `id` field must start with a letter or the underscore character - The `id` field must cannot start with a number - - The `id` field can only contain lowercase alpha-numeric characters and underscores (a-z, 0-9, and _ ) + - The `id` field can only contain lowercase alphanumeric characters and underscores (a-z, 0-9, and _ ) - The `id` field cannot be any of the Python keywords (e.g. `in`, `is`, `not`, `class`, etc.). - The `id` field must be unique within a `DataModel` If the `value_set` is a single type, it can be passed directly as the `value_set` parameter. - e.g.: - >>> DataField(name="Field 1", specification=int) - DataField(name='Field 1', specification=ValueSet(elements=[<class 'int'>], name='', description=''), id='field_1', description='', section='', required=True, ordinal='') - :ivar name: Name of the field :ivar specification: Value set of the field, if the value set is only one type, can also pass that type directly :ivar id: The identifier of the field, adhering to the naming rules stated above :ivar description: Description of the field - :ivar section: Section of the field (Only applicable if the data model is divided into sections) :ivar required: Required flag of the field - :ivar ordinal: Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.) """ - # TODO: change section into path to data name: str = field() specification: Union[ValueSet, type, List[type]] = field() id: str = field(default=None) + required: bool = field(default=False) description: str = field(default='') - section: str = field(default='') - required: bool = field(default=True) - ordinal: str = field(default='') + cardinality: Cardinality = field(default_factory=Cardinality) def __post_init__(self): if not self.id: from phenopacket_mapper.utils import str_to_valid_id object.__setattr__(self, 'id', str_to_valid_id(self.name)) + if self.required: + object.__setattr__(self, 'cardinality', Cardinality(min=1, max=self.cardinality.max)) + if isinstance(self.specification, type): object.__setattr__(self, 'specification', ValueSet(elements=[self.specification])) if isinstance(self.specification, list): @@ -158,10 +154,10 @@

    Source code for phenopacket_mapper.data_standards.data_model

    def __str__(self): ret = "DataField(\n" ret += f"\t\tid: {self.id},\n" - ret += f"\t\tsection: {self.section},\n" - ret += f"\t\tordinal, name: ({self.ordinal}, {self.name}),\n" - ret += f"\t\tvalue_set: {self.specification}, required: {self.required},\n" + ret += f"\t\tname: {self.name},\n" + ret += f"\t\trequired: {self.required}\n" ret += f"\t\tspecification: {self.specification}\n" + ret += f"\t\tcardinality: {str(self.cardinality)}\n" ret += "\t)" return ret @@ -174,6 +170,44 @@

    Source code for phenopacket_mapper.data_standards.data_model

    +[docs] +@dataclass(slots=True, frozen=True) +class DataSection: + """This class defines a section in a `DataModel` + + A section is a collection of `DataField` or `DataSection` objects. It is used to group related fields in a + `DataModel`. + + :ivar name: Name of the section + :ivar fields: List of `DataField` objects + """ + name: str = field() + id: str = field(default=None) + fields: Tuple[Union[DataField, 'DataSection', 'OrGroup'], ...] = field(default_factory=tuple) + required: bool = field(default=False) + cardinality: Cardinality = field(default_factory=Cardinality) + + def __post_init__(self): + if not self.id: + from phenopacket_mapper.utils import str_to_valid_id + object.__setattr__(self, 'id', str_to_valid_id(self.name)) + + if self.required: + object.__setattr__(self, 'cardinality', Cardinality(min=1, max=self.cardinality.max)) + + def __str__(self): + ret = "DataSection(\n" + ret += f"\t\tid: {self.id},\n" + ret += f"\t\tname: {self.name},\n" + ret += f"\t\trequired: {self.required}\n" + ret += f"\t\tcardinality: {str(self.cardinality)}\n" + for _field in self.fields: + ret += f"\t{str(_field)}\n" + ret += "\t)" + return ret
    + +
    [docs] @dataclass(slots=True) @@ -240,16 +274,12 @@

    Source code for phenopacket_mapper.data_standards.data_model

    be accessed using the `id` as an attribute of the `DataModel` object. E.g.: `data_model.date_of_birth`. This is useful in the data reading and mapping processes. - >>> data_model = DataModel("Test data model", (DataField(name="Field 1", specification=ValueSet()),)) - >>> data_model.field_1 - DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='') - :ivar data_model_name: Name of the data model :ivar fields: List of `DataField` objects :ivar resources: List of `CodeSystem` objects """ data_model_name: str = field() - fields: Tuple[DataField, ...] = field() + fields: Tuple[Union[DataField, DataSection, 'OrGroup'], ...] = field() resources: List[CodeSystem] = field(default_factory=list) def __post_init__(self): @@ -263,7 +293,8 @@

    Source code for phenopacket_mapper.data_standards.data_model

    raise AttributeError(f"'DataModel' object has no attribute '{var_name}'") def __str__(self): - ret = f"DataModel(name={self.data_model_name}\n" + ret = f"DataModel(\n" + ret += f"\tname: {self.data_model_name}\n" for _field in self.fields: ret += f"\t{str(_field)}\n" ret += "---\n" @@ -352,12 +383,9 @@

    Source code for phenopacket_mapper.data_standards.data_model

    file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = MappingProxyType({ DataField.name.__name__: 'data_field_name', - DataField.section.__name__: 'data_model_section', DataField.description.__name__: 'description', DataField.specification.__name__: 'value_set', DataField.required.__name__: 'required', - DataField.specification.__name__: 'specification', - DataField.ordinal.__name__: 'ordinal' }), parse_value_sets: bool = False, remove_line_breaks: bool = False, @@ -605,6 +633,39 @@

    Source code for phenopacket_mapper.data_standards.data_model

    +[docs] +@dataclass(slots=True, frozen=True) +class OrGroup(DataNode): + fields: Tuple[Union[DataField, DataSection, 'OrGroup'], ...] + name: str = field(default='Or Group') + id: str = field(default=None) + description: str = field(default='') + required: bool = field(default=False) + cardinality: Cardinality = field(default_factory=Cardinality) + + def __post_init__(self): + if not self.id: + from phenopacket_mapper.utils import str_to_valid_id + object.__setattr__(self, 'id', str_to_valid_id(self.name)) + + if self.required: + object.__setattr__(self, 'cardinality', Cardinality(min=1, max=self.cardinality.max)) + + + def __str__(self): + ret = "OrGroup(\n" + ret += f"\t\tid: {self.id},\n" + ret += f"\t\tname: {self.name},\n" + ret += f"\t\trequired: {self.required}\n" + ret += f"\t\tcardinality: {self.cardinality}\n" + for _field in self.fields: + ret += f"\t{str(_field)}\n" + ret += "\t)" + return ret
    + + + if __name__ == "__main__": df = DataField(name="Field 1", specification=int) print(df.specification == ValueSet([int])) diff --git a/latest/_modules/phenopacket_mapper/mapping/mapper.html b/latest/_modules/phenopacket_mapper/mapping/mapper.html index 272b78a..22de44f 100644 --- a/latest/_modules/phenopacket_mapper/mapping/mapper.html +++ b/latest/_modules/phenopacket_mapper/mapping/mapper.html @@ -110,9 +110,15 @@

    Source code for phenopacket_mapper.mapping.mapper

    for e in self.elements.values(): self.check_data_fields_in_model(e) -
    -[docs] - def check_data_fields_in_model(self, element: Union[PhenopacketBuildingBlock, DataField]): + +
    +[docs] + def check_fields_adheres_to_phenopacket_allowed_values(self): + """Check if the fields in the mapping adhere to the values in the Phenopacket schema + + Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema. + Otherwise give precise error messages. + """ if isinstance(element, DataField): field = element if field not in self.data_model: diff --git a/latest/_modules/phenopacket_mapper/pipeline/input.html b/latest/_modules/phenopacket_mapper/pipeline/input.html index c686c92..3f1df0e 100644 --- a/latest/_modules/phenopacket_mapper/pipeline/input.html +++ b/latest/_modules/phenopacket_mapper/pipeline/input.html @@ -102,11 +102,9 @@

    Source code for phenopacket_mapper.pipeline.input

    file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = MappingProxyType({ DataField.name.__name__: 'data_field_name', - DataField.section.__name__: 'data_model_section', DataField.description.__name__: 'description', DataField.specification.__name__: 'value_set', DataField.required.__name__: 'required', - DataField.ordinal.__name__: 'ordinal' }), parse_value_sets: bool = False, remove_line_breaks: bool = False, diff --git a/latest/_sources/apidocs/phenopacket_mapper.data_standards.cardinality.rst.txt b/latest/_sources/apidocs/phenopacket_mapper.data_standards.cardinality.rst.txt new file mode 100644 index 0000000..7e3528e --- /dev/null +++ b/latest/_sources/apidocs/phenopacket_mapper.data_standards.cardinality.rst.txt @@ -0,0 +1,7 @@ +phenopacket\_mapper.data\_standards.cardinality module +====================================================== + +.. automodule:: phenopacket_mapper.data_standards.cardinality + :members: + :undoc-members: + :show-inheritance: diff --git a/latest/apidocs/phenopacket_mapper.data_standards.cardinality.html b/latest/apidocs/phenopacket_mapper.data_standards.cardinality.html new file mode 100644 index 0000000..07bb202 --- /dev/null +++ b/latest/apidocs/phenopacket_mapper.data_standards.cardinality.html @@ -0,0 +1,127 @@ + + + + + + + + + phenopacket_mapper.data_standards.cardinality module — phenopacket_mapper 0.0.1 documentation + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    phenopacket_mapper.data_standards.cardinality module

    +
    +
    +class phenopacket_mapper.data_standards.cardinality.Cardinality(min: int = 0, max: int | Literal['n'] = 'n')[source]
    +

    Bases: object

    +
    +
    +min: int
    +
    + +
    +
    +max: int | Literal['n']
    +
    + +
    + +
    + + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html index 6692656..b8aa79b 100644 --- a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html +++ b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html @@ -104,10 +104,10 @@ DataModelInstance class is used to define an instance of a DataModel, i.e. a record in a dataset.

    -class phenopacket_mapper.data_standards.data_model.DataField(name: str, specification: ValueSet | type | List[type], id: str = None, description: str = '', section: str = '', required: bool = True, ordinal: str = '')[source]
    -

    Bases: object

    +class phenopacket_mapper.data_standards.data_model.DataField(name: str, specification: ~phenopacket_mapper.data_standards.value_set.ValueSet | type | ~typing.List[type], id: str = None, required: bool = False, description: str = '', cardinality: ~phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source] +

    Bases: DataNode

    This class defines fields used in the definition of a DataModel

    -

    A dataa field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a +

    A data field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a required flag, a specification, and an ordinal.

    The string for the id field is generated from the name field using the str_to_valid_id function from the phenopacket_mapper.utils module. This attempts to convert the name field. Sometimes this might not work as @@ -116,13 +116,10 @@ - The id field must be a valid Python identifier - The id field must start with a letter or the underscore character - The id field must cannot start with a number -- The id field can only contain lowercase alpha-numeric characters and underscores (a-z, 0-9, and _ ) +- The id field can only contain lowercase alphanumeric characters and underscores (a-z, 0-9, and _ ) - The id field cannot be any of the Python keywords (e.g. in, is, not, class, etc.). - The id field must be unique within a DataModel

    If the value_set is a single type, it can be passed directly as the value_set parameter.

    -

    e.g.: ->>> DataField(name=”Field 1”, specification=int) -DataField(name=’Field 1’, specification=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, ordinal=’’)

    Variables:
      @@ -130,9 +127,7 @@

    • specification – Value set of the field, if the value set is only one type, can also pass that type directly

    • id – The identifier of the field, adhering to the naming rules stated above

    • description – Description of the field

      • -

    • section – Section of the field (Only applicable if the data model is divided into sections)

    • required – Required flag of the field

      • -

    • ordinal – Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)

    @@ -151,24 +146,61 @@ id: str
    +
    +
    +required: bool
    +
    +
    description: str
    -
    -section: str
    +
    +cardinality: Cardinality
    + + +
    +
    +class phenopacket_mapper.data_standards.data_model.DataSection(name: str, id: str = None, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField | ~phenopacket_mapper.data_standards.data_model.DataSection | ~phenopacket_mapper.data_standards.data_model.OrGroup, ...] = <factory>, required: bool = False, cardinality: ~phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source]
    +

    Bases: object

    +

    This class defines a section in a DataModel

    +

    A section is a collection of DataField or DataSection objects. It is used to group related fields in a +DataModel.

    +
    +
    Variables:
    +
      +

    • name – Name of the section

      • +

    • fields – List of DataField objects

      • +
    +
    +
    -
    -required: bool
    +
    +name: str
    +
    + +
    +
    +id: str
    +
    + +
    +
    +fields: Tuple[DataField | DataSection | OrGroup, ...]
    -
    -ordinal: str
    +
    +required: bool
    +
    + +
    +
    +cardinality: Cardinality
    @@ -220,7 +252,7 @@
    -class phenopacket_mapper.data_standards.data_model.DataModel(data_model_name: str, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField, ...], resources: ~typing.List[~phenopacket_mapper.data_standards.code_system.CodeSystem] = <factory>)[source]
    +class phenopacket_mapper.data_standards.data_model.DataModel(data_model_name: str, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField | ~phenopacket_mapper.data_standards.data_model.DataSection | ~phenopacket_mapper.data_standards.data_model.OrGroup, ...], resources: ~typing.List[~phenopacket_mapper.data_standards.code_system.CodeSystem] = <factory>)[source]

    Bases: object

    This class defines a data model for medical data using DataField

    A data model can be used to import data and map it to the Phenopacket schema. It is made up of a list of DataField

    @@ -228,11 +260,6 @@ E.g.: DataField(name=’Date of Birth’, …) will have an id of ‘date_of_birth’. The DataField objects can be accessed using the id as an attribute of the DataModel object. E.g.: data_model.date_of_birth. This is useful in the data reading and mapping processes.

    -
    >>> data_model = DataModel("Test data model", (DataField(name="Field 1", specification=ValueSet()),))
->>> data_model.field_1
-DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')
-
    -
    Variables:
      @@ -249,7 +276,7 @@
      -fields: Tuple[DataField, ...]
      +fields: Tuple[DataField | DataSection | OrGroup, ...]
      @@ -309,7 +336,7 @@
      -static from_file(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'section': 'data_model_section', 'description': 'description', 'specification': 'specification', 'required': 'required', 'ordinal': 'ordinal'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]
      +static from_file(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'description': 'description', 'specification': 'value_set', 'required': 'required'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]

      Reads a Data Model from a file

      Parameters:
      @@ -477,6 +504,42 @@
      +
      +
      +class phenopacket_mapper.data_standards.data_model.OrGroup(fields: Tuple[Union[phenopacket_mapper.data_standards.data_model.DataField, phenopacket_mapper.data_standards.data_model.DataSection, ForwardRef('OrGroup')], ...], name: str = 'Or Group', id: str = None, description: str = '', required: bool = False, cardinality: phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source]
      +

      Bases: DataNode

      +
      +
      +fields: Tuple[DataField | DataSection | OrGroup, ...]
      +
      + +
      +
      +name: str
      +
      + +
      +
      +id: str
      +
      + +
      +
      +description: str
      +
      + +
      +
      +required: bool
      +
      + +
      +
      +cardinality: Cardinality
      +
      + +
      + diff --git a/latest/apidocs/phenopacket_mapper.data_standards.html b/latest/apidocs/phenopacket_mapper.data_standards.html index ae1432e..38b3ff6 100644 --- a/latest/apidocs/phenopacket_mapper.data_standards.html +++ b/latest/apidocs/phenopacket_mapper.data_standards.html @@ -96,6 +96,22 @@

      phenopacket_mapper.data_standards package

      This submodule defines the data standards used in the project.

      +
      +
      +class phenopacket_mapper.data_standards.Cardinality(min: int = 0, max: int | Literal['n'] = 'n')[source]
      +

      Bases: object

      +
      +
      +min: int
      +
      + +
      +
      +max: int | Literal['n']
      +
      + +
      +
      class phenopacket_mapper.data_standards.Coding(system: str | CodeSystem, code: str, display: str = '', text: str = '')[source]
      @@ -195,7 +211,7 @@
      -class phenopacket_mapper.data_standards.DataModel(data_model_name: str, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField, ...], resources: ~typing.List[~phenopacket_mapper.data_standards.code_system.CodeSystem] = <factory>)[source]
      +class phenopacket_mapper.data_standards.DataModel(data_model_name: str, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField | ~phenopacket_mapper.data_standards.data_model.DataSection | ~phenopacket_mapper.data_standards.data_model.OrGroup, ...], resources: ~typing.List[~phenopacket_mapper.data_standards.code_system.CodeSystem] = <factory>)[source]

      Bases: object

      This class defines a data model for medical data using DataField

      A data model can be used to import data and map it to the Phenopacket schema. It is made up of a list of DataField

      @@ -203,11 +219,6 @@ E.g.: DataField(name=’Date of Birth’, …) will have an id of ‘date_of_birth’. The DataField objects can be accessed using the id as an attribute of the DataModel object. E.g.: data_model.date_of_birth. This is useful in the data reading and mapping processes.

      -
      >>> data_model = DataModel("Test data model", (DataField(name="Field 1", specification=ValueSet()),))
->>> data_model.field_1
-DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')
-
      -
      Variables:
        @@ -224,7 +235,7 @@
        -fields: Tuple[DataField, ...]
        +fields: Tuple[DataField | DataSection | OrGroup, ...]
        @@ -284,7 +295,7 @@
        -static from_file(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'section': 'data_model_section', 'description': 'description', 'specification': 'specification', 'required': 'required', 'ordinal': 'ordinal'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]
        +static from_file(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'description': 'description', 'specification': 'value_set', 'required': 'required'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]

        Reads a Data Model from a file

        Parameters:
        @@ -330,10 +341,10 @@
        -class phenopacket_mapper.data_standards.DataField(name: str, specification: ValueSet | type | List[type], id: str = None, description: str = '', section: str = '', required: bool = True, ordinal: str = '')[source]
        -

        Bases: object

        +class phenopacket_mapper.data_standards.DataField(name: str, specification: ~phenopacket_mapper.data_standards.value_set.ValueSet | type | ~typing.List[type], id: str = None, required: bool = False, description: str = '', cardinality: ~phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source] +

        Bases: DataNode

        This class defines fields used in the definition of a DataModel

        -

        A dataa field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a +

        A data field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a required flag, a specification, and an ordinal.

        The string for the id field is generated from the name field using the str_to_valid_id function from the phenopacket_mapper.utils module. This attempts to convert the name field. Sometimes this might not work as @@ -342,13 +353,10 @@ - The id field must be a valid Python identifier - The id field must start with a letter or the underscore character - The id field must cannot start with a number -- The id field can only contain lowercase alpha-numeric characters and underscores (a-z, 0-9, and _ ) +- The id field can only contain lowercase alphanumeric characters and underscores (a-z, 0-9, and _ ) - The id field cannot be any of the Python keywords (e.g. in, is, not, class, etc.). - The id field must be unique within a DataModel

        If the value_set is a single type, it can be passed directly as the value_set parameter.

        -

        e.g.: ->>> DataField(name=”Field 1”, specification=int) -DataField(name=’Field 1’, specification=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, ordinal=’’)

        Variables:
          @@ -356,9 +364,7 @@

        • specification – Value set of the field, if the value set is only one type, can also pass that type directly

        • id – The identifier of the field, adhering to the naming rules stated above

        • description – Description of the field

          • -

        • section – Section of the field (Only applicable if the data model is divided into sections)

        • required – Required flag of the field

          • -

        • ordinal – Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)

        @@ -378,23 +384,18 @@
        -
        -description: str
        -
        - -
        -
        -section: str
        +
        +required: bool
        -
        -required: bool
        +
        +description: str
        -
        -ordinal: str
        +
        +cardinality: Cardinality
        @@ -568,6 +569,84 @@
      +
      +
      +class phenopacket_mapper.data_standards.DataSection(name: str, id: str = None, fields: ~typing.Tuple[~phenopacket_mapper.data_standards.data_model.DataField | ~phenopacket_mapper.data_standards.data_model.DataSection | ~phenopacket_mapper.data_standards.data_model.OrGroup, ...] = <factory>, required: bool = False, cardinality: ~phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source]
      +

      Bases: object

      +

      This class defines a section in a DataModel

      +

      A section is a collection of DataField or DataSection objects. It is used to group related fields in a +DataModel.

      +
      +
      Variables:
      +
        +

      • name – Name of the section

        • +

      • fields – List of DataField objects

        • +
      +
      +
      +
      +
      +name: str
      +
      + +
      +
      +id: str
      +
      + +
      +
      +fields: Tuple[DataField | DataSection | OrGroup, ...]
      +
      + +
      +
      +required: bool
      +
      + +
      +
      +cardinality: Cardinality
      +
      + +
      + +
      +
      +class phenopacket_mapper.data_standards.OrGroup(fields: Tuple[Union[phenopacket_mapper.data_standards.data_model.DataField, phenopacket_mapper.data_standards.data_model.DataSection, ForwardRef('OrGroup')], ...], name: str = 'Or Group', id: str = None, description: str = '', required: bool = False, cardinality: phenopacket_mapper.data_standards.cardinality.Cardinality = <factory>)[source]
      +

      Bases: DataNode

      +
      +
      +fields: Tuple[DataField | DataSection | OrGroup, ...]
      +
      + +
      +
      +name: str
      +
      + +
      +
      +id: str
      +
      + +
      +
      +description: str
      +
      + +
      +
      +required: bool
      +
      + +
      +
      +cardinality: Cardinality
      +
      + +
      +
      class phenopacket_mapper.data_standards.CodeSystem(name: str, namespace_prefix: str, url: str = None, iri_prefix: str = None, version: str = '0.0.0', synonyms: ~typing.List[str] = <factory>)[source]
      @@ -913,10 +992,12 @@

      Submodulesphenopacket_mapper.data_standards.data_model module
    • phenopacket_mapper.data_standards.date module

      • @@ -135,6 +138,7 @@

      Subpackagesphenopacket_mapper.data_standards package

      Bases: object

      -
      -check_data_fields_in_model(element: PhenopacketBuildingBlock | DataField)[source]
      -
      +
      +check_fields_adheres_to_phenopacket_allowed_values()[source]
      +

      Check if the fields in the mapping adhere to the values in the Phenopacket schema

      +

      Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema. +Otherwise give precise error messages.

      +
      diff --git a/latest/apidocs/phenopacket_mapper.mapping.mapper.html b/latest/apidocs/phenopacket_mapper.mapping.mapper.html index 91426a8..64b20ac 100644 --- a/latest/apidocs/phenopacket_mapper.mapping.mapper.html +++ b/latest/apidocs/phenopacket_mapper.mapping.mapper.html @@ -83,9 +83,12 @@ class phenopacket_mapper.mapping.mapper.PhenopacketMapper(data_model: DataModel, **kwargs)[source]

      Bases: object

      -
      -check_data_fields_in_model(element: PhenopacketBuildingBlock | DataField)[source]
      -
      +
      +check_fields_adheres_to_phenopacket_allowed_values()[source]
      +

      Check if the fields in the mapping adhere to the values in the Phenopacket schema

      +

      Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema. +Otherwise give precise error messages.

      +
      diff --git a/latest/apidocs/phenopacket_mapper.pipeline.html b/latest/apidocs/phenopacket_mapper.pipeline.html index 5513bc2..2ec76b2 100644 --- a/latest/apidocs/phenopacket_mapper.pipeline.html +++ b/latest/apidocs/phenopacket_mapper.pipeline.html @@ -98,7 +98,7 @@

      This module includes the pipeline for mapping data to phenopackets.

      -phenopacket_mapper.pipeline.read_data_model(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'section': 'data_model_section', 'description': 'description', 'specification': 'value_set', 'required': 'required', 'ordinal': 'ordinal'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]
      +phenopacket_mapper.pipeline.read_data_model(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'description': 'description', 'specification': 'value_set', 'required': 'required'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]

      Reads a Data Model from a file

      Parameters:
      @@ -201,9 +201,12 @@ class phenopacket_mapper.pipeline.PhenopacketMapper(data_model: DataModel, **kwargs)[source]

      Bases: object

      -
      -check_data_fields_in_model(element: PhenopacketBuildingBlock | DataField)[source]
      -
      +
      +check_fields_adheres_to_phenopacket_allowed_values()[source]
      +

      Check if the fields in the mapping adhere to the values in the Phenopacket schema

      +

      Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema. +Otherwise give precise error messages.

      +
      diff --git a/latest/apidocs/phenopacket_mapper.pipeline.input.html b/latest/apidocs/phenopacket_mapper.pipeline.input.html index 39cc94f..e7113e0 100644 --- a/latest/apidocs/phenopacket_mapper.pipeline.input.html +++ b/latest/apidocs/phenopacket_mapper.pipeline.input.html @@ -98,7 +98,7 @@

      phenopacket_mapper.pipeline.input module

      -phenopacket_mapper.pipeline.input.read_data_model(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'section': 'data_model_section', 'description': 'description', 'specification': 'value_set', 'required': 'required', 'ordinal': 'ordinal'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]
      +phenopacket_mapper.pipeline.input.read_data_model(data_model_name: str, resources: List[CodeSystem], path: str | Path, file_type: Literal['csv', 'excel', 'unknown'] = 'unknown', column_names: Dict[str, str] = mappingproxy({'name': 'data_field_name', 'description': 'description', 'specification': 'value_set', 'required': 'required'}), parse_value_sets: bool = False, remove_line_breaks: bool = False, parse_ordinals: bool = True) → DataModel[source]

      Reads a Data Model from a file

      Parameters:
      diff --git a/latest/genindex.html b/latest/genindex.html index fa2df6d..24a3bb5 100644 --- a/latest/genindex.html +++ b/latest/genindex.html @@ -139,16 +139,38 @@

      A

      C

      + - - + + - + -
      • iso_8601_datestring() (phenopacket_mapper.data_standards.Date method)
          @@ -527,6 +573,18 @@

          M

          +
        • max (phenopacket_mapper.data_standards.Cardinality attribute) + +
          • +
        • min (phenopacket_mapper.data_standards.Cardinality attribute) + +
        • minute (phenopacket_mapper.data_standards.Date attribute) @@ -568,6 +626,8 @@

          M

        • phenopacket_mapper.cli.validate_command
        • phenopacket_mapper.data_standards +
          • +
        • phenopacket_mapper.data_standards.cardinality
        • phenopacket_mapper.data_standards.code
          • @@ -664,8 +724,16 @@

          N

        • (phenopacket_mapper.data_standards.CodeSystem attribute)
        • (phenopacket_mapper.data_standards.data_model.DataField attribute) +
          • +
        • (phenopacket_mapper.data_standards.data_model.DataSection attribute) +
          • +
        • (phenopacket_mapper.data_standards.data_model.OrGroup attribute)
        • (phenopacket_mapper.data_standards.DataField attribute) +
          • +
        • (phenopacket_mapper.data_standards.DataSection attribute) +
          • +
        • (phenopacket_mapper.data_standards.OrGroup attribute)
        • (phenopacket_mapper.data_standards.value_set.ValueSet attribute)
          • @@ -692,10 +760,10 @@

          N

          O

          @@ -874,6 +942,13 @@

          P

          +
        • + phenopacket_mapper.data_standards.cardinality + +
        • @@ -925,6 +1000,8 @@

          P

        • module
          • + + - - + - + + + +
          • phenopacket_mapper.data_standards.value_set @@ -932,8 +1009,6 @@

            P

          • module
          -           		-
          • str_to_valid_id() (in module phenopacket_mapper.utils)
              diff --git a/latest/objects.inv b/latest/objects.inv index 43a4f6f..a670339 100644 Binary files a/latest/objects.inv and b/latest/objects.inv differ diff --git a/latest/py-modindex.html b/latest/py-modindex.html index a8647ff..a9f9f76 100644 --- a/latest/py-modindex.html +++ b/latest/py-modindex.html @@ -149,6 +149,11 @@

              Python Module Index

          		    phenopacket_mapper.data_standards
              + phenopacket_mapper.data_standards.cardinality +
              diff --git a/latest/searchindex.js b/latest/searchindex.js index 038ae73..fd10e29 100644 --- a/latest/searchindex.js +++ b/latest/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API reference": [[0, null]], "About": [[49, "about"]], "Anaconda": [[50, "anaconda"], [50, "id2"]], "Contents:": [[49, null], [53, null]], "Create a Data Model in Code": [[54, null]], "Creating a virtual environment": [[50, "creating-a-virtual-environment"]], "Features": [[51, "features"]], "Indices and tables": [[49, "indices-and-tables"]], "Installation": [[50, null]], "Installing Git": [[50, "installing-git"]], "Installing Java": [[50, "installing-java"]], "Installing Python": [[50, "installing-python"]], "Installing the Phenopacket Mapper": [[50, "installing-the-phenopacket-mapper"]], "Introduction": [[51, null]], "Motivation": [[51, "motivation"]], "Phenopackets": [[51, "phenopackets"]], "Publications": [[51, "publications"]], "Quickstart": [[52, null]], "Read a Data Model from a File": [[55, null]], "Resources": [[51, "resources"]], "Standard Python": [[50, "standard-python"], [50, "id1"]], "Submodules": [[2, "submodules"], [7, "submodules"], [12, "submodules"], [17, "submodules"], [22, "submodules"], [26, "submodules"], [31, "submodules"], [35, "submodules"], [39, "submodules"]], "Subpackages": [[1, "subpackages"], [12, "subpackages"], [35, "subpackages"]], "TLDR": [[51, "tldr"]], "User Guides": [[53, null]], "Using pip": [[50, "using-pip"]], "Welcome to Phenopacket Mapper\u2019s documentation!": [[49, null]], "What are Phenopackets?": [[51, "what-are-phenopackets"]], "Why Phenopackets?": [[51, "why-phenopackets"]], "[WIP] Local installation": [[50, "wip-local-installation"]], "phenopacket_mapper package": [[1, null]], "phenopacket_mapper.api_requests package": [[2, null]], "phenopacket_mapper.api_requests.api_request_super_class module": [[3, null]], "phenopacket_mapper.api_requests.get module": [[4, null]], "phenopacket_mapper.api_requests.hpo_api_request 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"phenopacket_mapper.data_standards.date module": [[20, null]], "phenopacket_mapper.data_standards.value_set module": [[21, null]], "phenopacket_mapper.mapping package": [[22, null]], "phenopacket_mapper.mapping.map_field module": [[23, null]], "phenopacket_mapper.mapping.mapper module": [[24, null]], "phenopacket_mapper.mapping.phenopacket_building_block module": [[25, null]], "phenopacket_mapper.pipeline package": [[26, null]], "phenopacket_mapper.pipeline.input module": [[27, null]], "phenopacket_mapper.pipeline.mapper module": [[28, null]], "phenopacket_mapper.pipeline.output module": [[29, null]], "phenopacket_mapper.pipeline.validate module": [[30, null]], "phenopacket_mapper.preprocessing package": [[31, null]], "phenopacket_mapper.preprocessing.preprocess module": [[32, null]], "phenopacket_mapper.preprocessing.preprocess_dict module": [[33, null]], "phenopacket_mapper.preprocessing.preprocess_method module": [[34, null]], "phenopacket_mapper.utils package": [[35, null]], 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module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_building_block module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", 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[51, 52, 53], "your": 51, "yournam": 51, "z": [12, 17, 21], "zero": [12, 21]}, "titles": ["API reference", "phenopacket_mapper package", "phenopacket_mapper.api_requests package", "phenopacket_mapper.api_requests.api_request_super_class module", "phenopacket_mapper.api_requests.get module", "phenopacket_mapper.api_requests.hpo_api_request module", "phenopacket_mapper.api_requests.orpha_api_request module", "phenopacket_mapper.cli package", "phenopacket_mapper.cli.main module", "phenopacket_mapper.cli.mapping_command module", "phenopacket_mapper.cli.quickstart_command module", "phenopacket_mapper.cli.validate_command module", "phenopacket_mapper.data_standards package", "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module", "phenopacket_mapper.data_standards.cardinality module", "phenopacket_mapper.data_standards.code module", "phenopacket_mapper.data_standards.code_system module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_building_block module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", "phenopacket_mapper.utils package", "phenopacket_mapper.utils.create_ipynb_in_code module", "phenopacket_mapper.utils.get_field_name module", "phenopacket_mapper.utils.pandas_utils module", "phenopacket_mapper.utils.parsing package", "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module", "phenopacket_mapper.utils.parsing.parse_coding module", "phenopacket_mapper.utils.parsing.parse_data_type module", "phenopacket_mapper.utils.parsing.parse_date module", "phenopacket_mapper.utils.parsing.parse_ordinal module", "phenopacket_mapper.utils.parsing.parse_primitive_data_value module", "phenopacket_mapper.utils.parsing.parse_value module", "phenopacket_mapper.utils.parsing.parse_value_set module", "phenopacket_mapper.utils.str_to_valid_id module", "Welcome to Phenopacket Mapper\u2019s documentation!", "Installation", "Introduction", "Quickstart", "User Guides", "Create a Data Model in Code", "Read a Data Model from a File"], "titleterms": {"": 50, "about": 50, "anaconda": 51, "api": 0, "api_request": [2, 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