--- a +++ b/docs/data/spark.md @@ -0,0 +1,66 @@ +# Spark + +??? abstract "TLDR" + + ```{ .python .no-check } + import edsnlp + + stream = edsnlp.data.from_spark(df, converter="omop") + stream = stream.map_pipeline(nlp) + res = stream.to_spark(converter="omop") + # or equivalently + edsnlp.data.to_spark(stream, converter="omop") + ``` + +We provide methods to read and write documents (raw or annotated) from and to Spark DataFrames. + +As an example, imagine that we have the following OMOP dataframe (we'll name it `note_df`) + +| note_id | note_text | note_datetime | +|--------:|:----------------------------------------------|:--------------| +| 0 | Le patient est admis pour une pneumopathie... | 2021-10-23 | + +## Reading from a Spark Dataframe {: #edsnlp.data.spark.from_spark } + +::: edsnlp.data.spark.from_spark + options: + heading_level: 3 + show_source: false + show_toc: false + show_bases: false + +## Writing to a Spark DataFrame {: #edsnlp.data.spark.to_spark } + +::: edsnlp.data.spark.to_spark + options: + heading_level: 3 + show_source: false + show_toc: false + show_bases: false + +## Importing entities from a Spark DataFrame + +If you have a dataframe with entities (e.g., `note_nlp` in OMOP), you must join it with the dataframe containing the raw text (e.g., `note` in OMOP) to obtain a single dataframe with the entities next to the raw text. For instance, the second `note_nlp` dataframe that we will name `note_nlp`. + +| note_nlp_id | note_id | start_char | end_char | note_nlp_source_value | lexical_variant | +|------------:|--------:|-----------:|---------:|:----------------------|:----------------| +| 0 | 0 | 46 | 57 | disease | coronavirus | +| 1 | 0 | 77 | 88 | drug | paracétamol | + +```{ .python .no-check } +import pyspark.sql.functions as F + +df = note_df.join( + note_nlp_df + .groupBy("note_id") + .agg( + F.collect_list( + F.struct( + F.col("note_nlp_id"), + F.col("start_char"), + F.col("end_char"), + F.col("note_nlp_source_value") + ) + ).alias("entities") + ), "note_id", "left") +```