Datasets
The Dataset classes define the data model behind Open Targets Gentropy. Every class inherits from the Dataset
class and contains a dataframe with a predefined schema that can be found in the respective classes.
gentropy.dataset.dataset.Dataset
dataclass
¶
Bases: ABC
Open Targets Gentropy Dataset.
Dataset
is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the schemas
module.
Source code in src/gentropy/dataset/dataset.py
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|
df: DataFrame
property
writable
¶
Dataframe included in the Dataset.
Returns:
Name | Type | Description |
---|---|---|
DataFrame |
DataFrame
|
Dataframe included in the Dataset |
schema: StructType
property
¶
Dataframe expected schema.
Returns:
Name | Type | Description |
---|---|---|
StructType |
StructType
|
Dataframe expected schema |
coalesce(num_partitions: int, **kwargs: Any) -> Self
¶
Coalesce the DataFrame included in the Dataset.
Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
num_partitions
|
int
|
Number of partitions to coalesce to |
required |
**kwargs
|
Any
|
Arguments to pass to the coalesce method |
{}
|
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Coalesced Dataset |
Source code in src/gentropy/dataset/dataset.py
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|
drop_infinity_values(*cols: str) -> Self
¶
Drop infinity values from Double typed column.
Infinity type reference - https://spark.apache.org/docs/latest/sql-ref-datatypes.html#floating-point-special-values The implementation comes from https://stackoverflow.com/questions/34432998/how-to-replace-infinity-in-pyspark-dataframe
Parameters:
Name | Type | Description | Default |
---|---|---|---|
*cols
|
str
|
names of the columns to check for infinite values, these should be of DoubleType only! |
()
|
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Dataset after removing infinite values |
Source code in src/gentropy/dataset/dataset.py
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|
filter(condition: Column) -> Self
¶
Creates a new instance of a Dataset with the DataFrame filtered by the condition.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
condition
|
Column
|
Condition to filter the DataFrame |
required |
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Filtered Dataset |
Source code in src/gentropy/dataset/dataset.py
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|
flag_duplicates(test_column: Column) -> Column
staticmethod
¶
Return True for rows, where the value was already seen in column.
This implementation allows keeping the first occurrence of the value.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
test_column
|
Column
|
Column to check for duplicates |
required |
Returns:
Name | Type | Description |
---|---|---|
Column |
Column
|
Column with a boolean flag for duplicates |
Source code in src/gentropy/dataset/dataset.py
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|
from_parquet(session: Session, path: str | list[str], **kwargs: bool | float | int | str | None) -> Self
classmethod
¶
Reads parquet into a Dataset with a given schema.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
session
|
Session
|
Spark session |
required |
path
|
str | list[str]
|
Path to the parquet dataset |
required |
**kwargs
|
bool | float | int | str | None
|
Additional arguments to pass to spark.read.parquet |
{}
|
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Dataset with the parquet file contents |
Raises:
Type | Description |
---|---|
ValueError
|
Parquet file is empty |
Source code in src/gentropy/dataset/dataset.py
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|
generate_identifier(uniqueness_defining_columns: list[str]) -> Column
staticmethod
¶
Hashes the provided columns to generate a unique identifier.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
uniqueness_defining_columns
|
list[str]
|
list of columns defining uniqueness |
required |
Returns:
Name | Type | Description |
---|---|---|
Column |
Column
|
column with a unique identifier |
Source code in src/gentropy/dataset/dataset.py
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|
get_QC_column_name() -> str | None
classmethod
¶
Abstract method to get the QC column name. Assumes None unless overriden by child classes.
Returns:
Type | Description |
---|---|
str | None
|
str | None: Column name |
Source code in src/gentropy/dataset/dataset.py
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|
get_QC_mappings() -> dict[str, str]
classmethod
¶
Method to get the mapping between QC flag and corresponding QC category value.
Returns empty dict unless overriden by child classes.
Returns:
Type | Description |
---|---|
dict[str, str]
|
dict[str, str]: Mapping between flag name and QC column category value. |
Source code in src/gentropy/dataset/dataset.py
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|
get_schema() -> StructType
abstractmethod
classmethod
¶
Abstract method to get the schema. Must be implemented by child classes.
Returns:
Name | Type | Description |
---|---|---|
StructType |
StructType
|
Schema for the Dataset |
Raises:
Type | Description |
---|---|
NotImplementedError
|
Must be implemented in the child classes |
Source code in src/gentropy/dataset/dataset.py
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|
persist() -> Self
¶
Persist in memory the DataFrame included in the Dataset.
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Persisted Dataset |
Source code in src/gentropy/dataset/dataset.py
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|
repartition(num_partitions: int, **kwargs: Any) -> Self
¶
Repartition the DataFrame included in the Dataset.
Repartitioning creates new partitions with data that is distributed evenly.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
num_partitions
|
int
|
Number of partitions to repartition to |
required |
**kwargs
|
Any
|
Arguments to pass to the repartition method |
{}
|
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Repartitioned Dataset |
Source code in src/gentropy/dataset/dataset.py
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|
unpersist() -> Self
¶
Remove the persisted DataFrame from memory.
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
Unpersisted Dataset |
Source code in src/gentropy/dataset/dataset.py
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|
update_quality_flag(qc: Column, flag_condition: Column, flag_text: Enum) -> Column
staticmethod
¶
Update the provided quality control list with a new flag if condition is met.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
qc
|
Column
|
Array column with the current list of qc flags. |
required |
flag_condition
|
Column
|
This is a column of booleans, signing which row should be flagged |
required |
flag_text
|
Enum
|
Text for the new quality control flag |
required |
Returns:
Name | Type | Description |
---|---|---|
Column |
Column
|
Array column with the updated list of qc flags. |
Source code in src/gentropy/dataset/dataset.py
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|
valid_rows(invalid_flags: list[str], invalid: bool = False) -> Self
¶
Filters Dataset
according to a list of quality control flags. Only Dataset
classes with a QC column can be validated.
This method checks do following steps: - Check if the Dataset contains a QC column. - Check if the invalid_flags exist in the QC mappings flags. - Filter the Dataset according to the invalid_flags and invalid parameters.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
invalid_flags
|
list[str]
|
List of quality control flags to be excluded. |
required |
invalid
|
bool
|
If True returns the invalid rows, instead of the valid. Defaults to False. |
False
|
Returns:
Name | Type | Description |
---|---|---|
Self |
Self
|
filtered dataset. |
Raises:
Type | Description |
---|---|
ValueError
|
If the Dataset does not contain a QC column or if the invalid_flags elements do not exist in QC mappings flags. |
Source code in src/gentropy/dataset/dataset.py
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|
validate_schema() -> None
¶
Validate DataFrame schema against expected class schema.
Raises:
Type | Description |
---|---|
SchemaValidationError
|
If the DataFrame schema does not match the expected schema |
Source code in src/gentropy/dataset/dataset.py
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|