Source code for phenopacket_mapper.utils.parsing.parse_date
-from datetime import datetime
-from typing import Literal, Dict, Tuple
+import warnings
+from datetime import datetime
+from typing import Literal, Dict, Tuple, Optional
from phenopacket_mapper.data_standards import Date
from phenopacket_mapper.utils.parsing import parse_int
@@ -89,7 +90,7 @@ Source code for phenopacket_mapper.utils.parsing.parse_date
date_str: str,
default_first: Literal["day", "month"] = "day",
compliance: Literal['soft', 'hard'] = 'soft',
-) -> Date:
+) -> Optional[Date]:
"""Parse a date string into a Date object
There is a lot of variation in how dates are formatted, and this function attempts to handle as many of them as
@@ -172,7 +173,8 @@ Source code for phenopacket_mapper.utils.parsing.parse_date
if compliance == 'hard':
raise ValueError(f"Invalid date string '{date_str}': no separators found")
else:
- return date_str
+ warnings.warn(f"Invalid date string '{date_str}': could not be parsed, returning None")
+ return None
diff --git a/latest/_modules/phenopacket_mapper/utils/parsing/parse_primitive_data_value.html b/latest/_modules/phenopacket_mapper/utils/parsing/parse_primitive_data_value.html
index acaa1ae..bc255f6 100644
--- a/latest/_modules/phenopacket_mapper/utils/parsing/parse_primitive_data_value.html
+++ b/latest/_modules/phenopacket_mapper/utils/parsing/parse_primitive_data_value.html
@@ -76,7 +76,7 @@
Source code for phenopacket_mapper.utils.parsing.parse_primitive_data_value
-from typing import Literal, Union
+from typing import Union
diff --git a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html
index 0ec1143..31758a6 100644
--- a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html
+++ b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html
@@ -226,7 +226,7 @@
-
-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, ...], 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
@@ -255,7 +255,7 @@
diff --git a/latest/apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.html b/latest/apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.html
index 56b4add..eb0baa8 100644
--- a/latest/apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.html
+++ b/latest/apidocs/phenopacket_mapper.data_standards.data_models.rarelink_datamodel.html
@@ -95,8 +95,8 @@
-
-phenopacket_mapper.data_standards.data_models.rarelink_datamodel module
+
+phenopacket_mapper.data_standards.data_models.rarelink_datamodel module
diff --git a/latest/apidocs/phenopacket_mapper.data_standards.html b/latest/apidocs/phenopacket_mapper.data_standards.html
index b255ea7..c9aad4b 100644
--- a/latest/apidocs/phenopacket_mapper.data_standards.html
+++ b/latest/apidocs/phenopacket_mapper.data_standards.html
@@ -195,7 +195,7 @@
-
-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, ...], 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
@@ -224,7 +224,7 @@
@@ -503,6 +503,77 @@
+
+-
+class phenopacket_mapper.data_standards.DataSet(data_model: DataModel, data: List[DataModelInstance])[source]
+Bases: object
+This class defines a dataset as defined by a DataModel
+This class is used to define a dataset as defined by a DataModel. It is a collection of DataModelInstance
+objects.
+
+- Variables:
+
+data_model – The DataModel object that defines the data model for this dataset
data – A list of DataModelInstance objects, each adhering to the DataField definition in the DataModel
+
+
+
+
+-
+data: List[DataModelInstance]
+
+
+
+-
+property height
+
+
+
+-
+property width
+
+
+
+
+
+-
+preprocess(fields: str | DataField | List[str | DataField], mapping: Dict | Callable, **kwargs)[source]
+Preprocesses a field in the dataset
+Preprocessing happens in place, i.e. the values in the dataset are modified directly.
+If fields is a list of fields, the mapping must be a method that can handle a list of values being passed as
+value to it. E.g.:
+```python
+def preprocess_method(values, method, **kwargs):
+field1, field2 = values
+# do something with values
+return “preprocessed_values” + kwargs[“arg1”] + kwargs[“arg2”]
+dataset.preprocess([“field_1”, “field_2”], preprocess_method, arg1=”value1”, arg2=”value2”)
+```
+
+- Parameters:
+
+fields – Data fields to be preprocessed, will be passed onto mapping
mapping – A dictionary or method to use for preprocessing
+
+
+
+
+
+
+
-
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]
diff --git a/latest/apidocs/phenopacket_mapper.html b/latest/apidocs/phenopacket_mapper.html
index bf590e2..d1af70e 100644
--- a/latest/apidocs/phenopacket_mapper.html
+++ b/latest/apidocs/phenopacket_mapper.html
@@ -141,6 +141,7 @@ SubpackagesDataField
DataModelInstanceDataFieldValueDataSetCodeSystemDateValueSetBases: object
A class to build a Jupyter notebook programmatically.
-
-- Parameters:
-notebook_content – A dictionary representing the notebook structure.
-
-
add_markdown_cell(text)[source]
diff --git a/latest/apidocs/phenopacket_mapper.utils.html b/latest/apidocs/phenopacket_mapper.utils.html
index 3f6ac49..d83a381 100644
--- a/latest/apidocs/phenopacket_mapper.utils.html
+++ b/latest/apidocs/phenopacket_mapper.utils.html
@@ -101,11 +101,6 @@
class phenopacket_mapper.utils.NotebookBuilder[source]
Bases: object
A class to build a Jupyter notebook programmatically.
-
-- Parameters:
-notebook_content – A dictionary representing the notebook structure.
-
-
add_markdown_cell(text)[source]
diff --git a/latest/apidocs/phenopacket_mapper.utils.parsing.html b/latest/apidocs/phenopacket_mapper.utils.parsing.html
index 89e9d6f..c1f0d08 100644
--- a/latest/apidocs/phenopacket_mapper.utils.parsing.html
+++ b/latest/apidocs/phenopacket_mapper.utils.parsing.html
@@ -243,7 +243,7 @@
-
-phenopacket_mapper.utils.parsing.parse_date(date_str: str, default_first: Literal['day', 'month'] = 'day', compliance: Literal['soft', 'hard'] = 'soft') Date[source]
+phenopacket_mapper.utils.parsing.parse_date(date_str: str, default_first: Literal['day', 'month'] = 'day', compliance: Literal['soft', 'hard'] = 'soft') Date | None[source]
Parse a date string into a Date object
There is a lot of variation in how dates are formatted, and this function attempts to handle as many of them as
possible. The function will first attempt to parse the date string as an ISO 8601 formatted string. If that fails,
diff --git a/latest/apidocs/phenopacket_mapper.utils.parsing.parse_date.html b/latest/apidocs/phenopacket_mapper.utils.parsing.parse_date.html
index 5f59987..17a579e 100644
--- a/latest/apidocs/phenopacket_mapper.utils.parsing.parse_date.html
+++ b/latest/apidocs/phenopacket_mapper.utils.parsing.parse_date.html
@@ -80,7 +80,7 @@
phenopacket_mapper.utils.parsing.parse_date module
-
-phenopacket_mapper.utils.parsing.parse_date.parse_date(date_str: str, default_first: Literal['day', 'month'] = 'day', compliance: Literal['soft', 'hard'] = 'soft') Date[source]
+phenopacket_mapper.utils.parsing.parse_date.parse_date(date_str: str, default_first: Literal['day', 'month'] = 'day', compliance: Literal['soft', 'hard'] = 'soft') Date | None[source]
Parse a date string into a Date object
There is a lot of variation in how dates are formatted, and this function attempts to handle as many of them as
possible. The function will first attempt to parse the date string as an ISO 8601 formatted string. If that fails,
diff --git a/latest/genindex.html b/latest/genindex.html
index 6e19bcb..e295631 100644
--- a/latest/genindex.html
+++ b/latest/genindex.html
@@ -194,15 +194,25 @@
D
- data (phenopacket_mapper.data_standards.data_model.DataSet attribute)
+
+
- data_frame (phenopacket_mapper.data_standards.data_model.DataSet property)
+
+
- data_model (phenopacket_mapper.data_standards.data_model.DataModelInstance attribute)
- data_model_name (phenopacket_mapper.data_standards.data_model.DataModel attribute)
@@ -229,18 +239,22 @@
D
- (class in phenopacket_mapper.data_standards.data_model)
- - DataModel2PhenopacketSchema (class in phenopacket_mapper.data_standards.DataModel2PhenopacketSchema)
-
+ - DataModel2PhenopacketSchema (class in phenopacket_mapper.data_standards.DataModel2PhenopacketSchema)
+
- DataModelInstance (class in phenopacket_mapper.data_standards)
- - DataSet (class in phenopacket_mapper.data_standards.data_model)
+
- DataSet (class in phenopacket_mapper.data_standards)
+
+
- Date (class in phenopacket_mapper.data_standards)
@@ -392,9 +406,17 @@ H
- head() (phenopacket_mapper.data_standards.data_model.DataSet method)
+
+
- height (phenopacket_mapper.data_standards.data_model.DataSet property)
+
+
- hour (phenopacket_mapper.data_standards.Date attribute)
- -
- phenopacket_mapper.data_standards.data_models.rarelink_datamodel
-
-
- - module
-
@@ -912,8 +925,6 @@
P
- module
-
-
phenopacket_mapper.data_standards.value_set
@@ -921,6 +932,8 @@
P
- module
+
-
phenopacket_mapper.mapping
@@ -1125,6 +1138,8 @@
P
- (in module phenopacket_mapper.preprocessing.preprocess)
- (phenopacket_mapper.data_standards.data_model.DataSet method)
+
+ - (phenopacket_mapper.data_standards.DataSet method)
- preprocess_dict() (in module phenopacket_mapper.preprocessing)
@@ -1350,7 +1365,11 @@
W
- width (phenopacket_mapper.data_standards.data_model.DataSet property)
+
+
- write() (in module phenopacket_mapper.pipeline)
diff --git a/latest/objects.inv b/latest/objects.inv
index dd18cb0..df45ccf 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 3f25846..3336d25 100644
--- a/latest/py-modindex.html
+++ b/latest/py-modindex.html
@@ -174,11 +174,6 @@ Python Module Index
phenopacket_mapper.data_standards.data_models.erdri_cds
-
-
- phenopacket_mapper.data_standards.data_models.rarelink_datamodel
-
diff --git a/latest/searchindex.js b/latest/searchindex.js
index 6309d85..585c808 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 module": [[5, null]], "phenopacket_mapper.api_requests.orpha_api_request module": [[6, null]], "phenopacket_mapper.cli package": [[7, null]], "phenopacket_mapper.cli.main module": [[8, null]], "phenopacket_mapper.cli.mapping_command module": [[9, null]], "phenopacket_mapper.cli.quickstart_command module": [[10, null]], "phenopacket_mapper.cli.validate_command module": [[11, null]], "phenopacket_mapper.data_standards package": [[12, null]], "phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module": [[13, null]], "phenopacket_mapper.data_standards.code module": [[14, null]], "phenopacket_mapper.data_standards.code_system module": [[15, null]], "phenopacket_mapper.data_standards.data_model module": [[16, null]], "phenopacket_mapper.data_standards.data_models package": [[17, null]], "phenopacket_mapper.data_standards.data_models.erdri_cds module": [[18, null]], "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module": [[19, null]], "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_element 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]], "phenopacket_mapper.utils.create_ipynb_in_code module": [[36, null]], "phenopacket_mapper.utils.get_field_name module": [[37, null]], "phenopacket_mapper.utils.pandas_utils module": [[38, null]], "phenopacket_mapper.utils.parsing package": [[39, null]], "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module": [[40, null]], "phenopacket_mapper.utils.parsing.parse_coding module": [[41, null]], "phenopacket_mapper.utils.parsing.parse_data_type module": [[42, null]], "phenopacket_mapper.utils.parsing.parse_date module": [[43, null]], "phenopacket_mapper.utils.parsing.parse_ordinal module": [[44, null]], "phenopacket_mapper.utils.parsing.parse_primitive_data_value module": [[45, null]], "phenopacket_mapper.utils.parsing.parse_value module": [[46, null]], "phenopacket_mapper.utils.parsing.parse_value_set module": [[47, null]], "phenopacket_mapper.utils.str_to_valid_id module": [[48, null]]}, "docnames": ["apidocs/modules", "apidocs/phenopacket_mapper", "apidocs/phenopacket_mapper.api_requests", "apidocs/phenopacket_mapper.api_requests.api_request_super_class", "apidocs/phenopacket_mapper.api_requests.get", 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\ No newline at end of file
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