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Spark NLP + Spark ML Transformer
Vivek Gupta Sep 2nd, 2020 at 10:02 AM
I am new to sparknlp. I am writing a custom transformer which will remove tokens from text whose length is <=2. Transformer is working and doing its job. But it is not giving proper structure as an output. Instead it is returning only Array of String. I am struggling to get output in following structure -
ArrayType(
StructType([
StructField("annotatorType", StringType(), False),
StructField("begin", IntegerType(), False),
StructField("end", IntegerType(), False),
StructField("result", StringType(), False),
StructField("metadata", MapType(StringType(), StringType()), True)
])
)
Currently I am getting following output -
--------------------------------------------------------------------------------+
| modified_text|
+--------------------------------------------------------------------------------+
|[person, agree, with, results, important, for, her|
|[pef, are, not, available, this, province, the, mainly...
Following is code for custom transformer -
from pyspark.ml import Pipeline, Transformer
from pyspark.ml.feature import Tokenizer, NGram
from typing import Iterable
from pyspark.sql.types import *
from pyspark.sql.functions import col, explode, count
from pyspark.sql import DataFrame
from pyspark.ml.param.shared import HasInputCol, HasOutputCol, Param
class ShortTokenRemover(Transformer, HasInputCol, HasOutputCol):
def __init__(self):
super(ShortTokenRemover, self).__init__()
def _transform(self, df: DataFrame) -> DataFrame:
def remove_token_short_length(inp):
inp = [token for token in inp if len(token) > 2]
return inp
udf_remove_token_short_length = udf(remove_token_short_length, ArrayType(StringType()))
out_col_name = self.getOutputCol()
in_col = df[self.getInputCol()]
df = df.withColumn(out_col_name, udf_remove_token_short_length(in_col.result))
return df
(edited)
24 replies
Maziyar 6 months ago
The Tokenizer in Spark NLP comes with minLengh and maxLength parameters, no need to create a transformer since it will be pure Spark ML and you need to integrate it within Spark NLP pipeline which is not required: https://nlp.johnsnowlabs.com/api/#com.johnsnowlabs.nlp.annotators.Tokenizer
nlp.johnsnowlabs.comnlp.johnsnowlabs.com
Spark NLP 2.5.5 ScalaDoc
Spark NLP 2.5.5 ScalaDoc
Vivek Gupta 6 months ago
I have created transformer, its doing the job. When I have integrated this transformer in pipeline its giving following error -
Py4JJavaError: An error occurred while calling o1359.transform.
: java.lang.IllegalArgumentException: requirement failed: Wrong or missing inputCols annotators in StopWordsCleaner_61f3ca02188e.
Current inputCols: short_token_filtered. Dataset's columns:
(column_name=Text_en,is_nlp_annotator=false)
(column_name=Text_en_proc,is_nlp_annotator=false)
(column_name=Text_en_junk,is_nlp_annotator=false)
(column_name=Text_en_New,is_nlp_annotator=false)
(column_name=document,is_nlp_annotator=true,type=document)
(column_name=tokenized,is_nlp_annotator=true,type=token)
(column_name=lemmatized,is_nlp_annotator=true,type=token)
(column_name=short_token_filtered,is_nlp_annotator=false).
Make sure such annotators exist in your pipeline, with the right output names and that they have following annotator types: token
at scala.Predef$.require(Predef.scala:224)
I have created following pipeline -
pipeline = Pipeline() \
.setStages([documentAssembler,
tokenizer,
lemmatizer,
short_token_filter,
stopwords_cleaner,
pos_tagger,
ngrammer,
finisher])
I checked the transformer, It has annotator types: token
+--------------------------------------------------------------------------------+
| short_token_filtered|
+--------------------------------------------------------------------------------+
|[[token, 0, 5, doctor, [sentence -> 0], []], [token, 7, 11, agree, [sentence ...|
|[[token, 0, 9, spirometer, [sentence -> 0], []], [token, 13, 15, pef, [senten...|
+--------------------------------------------------------------------------------+
I am not sure, why I am getting this error.
Maziyar 6 months ago
Could you please show your entire pipeline? Also, the schema of the dataframe? It may say token but it may not be AnnotatorType.TOKEN.
Vivek Gupta 6 months ago
Please find Df schema. Error was reported for transformer which produced 'short_token_filtered' field.
root
|-- Id: integer (nullable = true)
|-- Text_en: string (nullable = true)
|-- Text_en_proc: string (nullable = true)
|-- document: array (nullable = true)
| |-- element: struct (containsNull = true)
| | |-- annotatorType: string (nullable = true)
| | |-- begin: integer (nullable = false)
| | |-- end: integer (nullable = false)
| | |-- result: string (nullable = true)
| | |-- metadata: map (nullable = true)
| | | |-- key: string
| | | |-- value: string (valueContainsNull = true)
| | |-- embeddings: array (nullable = true)
| | | |-- element: float (containsNull = false)
|-- tokenized: array (nullable = true)
| |-- element: struct (containsNull = true)
| | |-- annotatorType: string (nullable = true)
| | |-- begin: integer (nullable = false)
| | |-- end: integer (nullable = false)
| | |-- result: string (nullable = true)
| | |-- metadata: map (nullable = true)
| | | |-- key: string
| | | |-- value: string (valueContainsNull = true)
| | |-- embeddings: array (nullable = true)
| | | |-- element: float (containsNull = false)
|-- short_token_filtered: array (nullable = true)
| |-- element: struct (containsNull = true)
| | |-- annotatorType: string (nullable = false)
| | |-- begin: integer (nullable = false)
| | |-- end: integer (nullable = false)
| | |-- result: string (nullable = false)
| | |-- metadata: map (nullable = true)
| | | |-- key: string
| | | |-- value: string (valueContainsNull = true)
| | |-- embeddings: array (nullable = true)
| | | |-- element: float (containsNull = true)
Vivek Gupta 6 months ago
To focus on specific issue, I have shortened pipeline, now pipeline is -
pipeline = Pipeline() \
.setStages([documentAssembler,
tokenizer,
short_token_filter,
lemmatizer,
finisher])
Maziyar 6 months ago
thanks, I meant the whole pipeline code not just the stages. I would like to see what are the inputs for each annotator
Vivek Gupta 6 months ago
from sparknlp.base import DocumentAssembler
text_col = 'Text_en_New'
documentAssembler = DocumentAssembler() \
.setInputCol(text_col) \
.setOutputCol('document') \
.setCleanupMode("shrink")
from sparknlp.annotator import Tokenizer
tokenizer = Tokenizer() \
.setInputCols(['document']) \
.setOutputCol('tokenized')
short_token_filter = ShortTokenFilter() \
.setInputCol('tokenized') \
.setOutputCol('short_token_filtered')
from sparknlp.annotator import LemmatizerModel
lemmatizer = LemmatizerModel.pretrained() \
.setInputCols(['short_token_filtered']) \
.setOutputCol('lemmatized')
from sparknlp.base import Finisher
finisher = Finisher() \
.setInputCols(['tokenized', 'lemmatized'])
from pyspark.ml import Pipeline
pipeline = Pipeline() \
.setStages([documentAssembler,
tokenizer,
short_token_filter,
lemmatizer,
finisher]) (edited)
Maziyar 6 months ago
Your error is talking about StopWordsCleaner, I don't see that in your pipeline:
Py4JJavaError: An error occurred while calling o1359.transform.
: java.lang.IllegalArgumentException: requirement failed: Wrong or missing inputCols annotators in StopWordsCleaner_61f3ca02188e.
If you have this all in a working notebook I can give it a shot, it requires a detail evaluation of all the code to see what goes wrong
Vivek Gupta 6 months ago
Sharing error details. I have reduced the pipeline so that I can focus on error. Below is error details -
Py4JJavaError: An error occurred while calling o828.transform.
: java.lang.IllegalArgumentException: requirement failed: Wrong or missing inputCols annotators in LEMMATIZER_c62ad8f355f9.
Current inputCols: short_token_filtered. Dataset's columns:
(column_name=Text_en,is_nlp_annotator=false)
(column_name=Text_en_proc,is_nlp_annotator=false)
(column_name=Text_en_junk,is_nlp_annotator=false)
(column_name=Text_en_New,is_nlp_annotator=false)
(column_name=document,is_nlp_annotator=true,type=document)
(column_name=tokenized,is_nlp_annotator=true,type=token)
(column_name=short_token_filtered,is_nlp_annotator=false).
Make sure such annotators exist in your pipeline, with the right output names and that they have following annotator types: token
at scala.Predef$.require(Predef.scala:224)
at com.johnsnowlabs.nlp.AnnotatorModel._transform(AnnotatorModel.scala:43)
at com.johnsnowlabs.nlp.AnnotatorModel.transform(AnnotatorModel.scala:79)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:380)
at py4j.Gateway.invoke(Gateway.java:295)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:251)
at java.lang.Thread.run(Thread.java:748)
During handling of the above exception, another exception occurred:
IllegalArgumentException Traceback (most recent call last)
<command-4262523904952880> in <module>
----> 1 processed_review = pipeline.fit(review_text).transform(review_text)
/databricks/spark/python/pyspark/ml/base.py in transform(self, dataset, params)
171 return self.copy(params)._transform(dataset)
172 else:
--> 173 return self._transform(dataset)
174 else:
175 raise ValueError("Params must be a param map but got %s." % type(params))
/databricks/spark/python/pyspark/ml/pipeline.py in _transform(self, dataset)
260 def _transform(self, dataset):
261 for t in self.stages:
--> 262 dataset = t.transform(dataset)
263 return dataset
Maziyar 6 months ago
Thanks, I think this requires debugging, it's hard to say what goes wrong since the code and the transformer looks ok. Could you please provide an end to end notebook that produces this error? We can take a closer look at it
Vivek Gupta 6 months ago
Please find notebook attached.
Binary
jsl_poc-5.ipynb
23 kB Binary23 kB — Click to download
:+1:
1
Maziyar 6 months ago
@Vivek Gupta We are workin on it, it's actually a missing annotatorType in the metadata which should be added by PySpark itself and the error also indicates that. I'll let you know once we found the line to be added to your schema in the transformer
:+1:
1
Vivek Gupta 6 months ago
Thanks. Looking forward for a solution.
Vivek Gupta 5 months ago
Hi @Maziyar,
can you help to resolve this issue?
Maziyar 5 months ago
Yes, sorry for the delay. Right after today's release I will sit and see what is that metadata schema from Spark ML
:question:
1
Vivek Gupta 5 months ago
Hi @Maziyar,
can you help to resolve this issue? (edited)
Andres Fernandez 5 months ago
hi @Vivek Gupta, @Maziyar, @Jiri Dobes please find the way to make a transformer compatible with SparkNLP. Please pay attention to the withMeta free function and the meta variable (you would need to use valid SparkNLP column metatypes https://github.com/JohnSnowLabs/spark-nlp/blob/master/src/main/scala/com/johnsnowlabs/nlp/AnnotatorType.scala)
src/main/scala/com/johnsnowlabs/nlp/AnnotatorType.scala
package com.johnsnowlabs.nlp
object AnnotatorType {
val DOCUMENT = "document"
val TOKEN = "token"
Show more
<https://github.com/JohnSnowLabs/spark-nlp|JohnSnowLabs/spark-nlp>JohnSnowLabs/spark-nlp | Added by GitHub
Added to your saved items
Andres Fernandez 5 months ago
from pyspark.ml import Pipeline, Transformer
from pyspark.ml.feature import Tokenizer, NGram
from typing import Iterable
from pyspark.sql.types import *
from pyspark.sql.functions import col, explode, count, udf
from pyspark.sql import DataFrame, Column
from pyspark.ml.param.shared import HasInputCol, HasOutputCol, Param
from pyspark.ml import PipelineModel
import json
from sparknlp.annotator import *
def withMeta(self, alias, meta):
sc = SparkContext._active_spark_context
jmeta = sc._gateway.jvm.org.apache.spark.sql.types.Metadata
return Column(getattr(self._jc, "as")(alias, jmeta.fromJson(json.dumps(meta))))
dataType = StructType([
StructField('annotatorType', StringType(), False),
StructField('begin', IntegerType(), False),
StructField('end', IntegerType(), False),
StructField('result', StringType(), False),
StructField('metadata', MapType(StringType(), StringType()), False),
StructField('embeddings', ArrayType(FloatType()), False)
])
class ShortTokenRemover(Transformer, HasInputCol, HasOutputCol):
def __init__(self):
super(ShortTokenRemover, self).__init__()
def _transform(self, df: DataFrame) -> DataFrame:
def remove_token_short_length(inp):
inp = [token for token in inp if len(token.result) > 4]
return inp
udf_remove_token_short_length = udf(remove_token_short_length, ArrayType(dataType))
out_col_name = self.getOutputCol()
in_col = df[self.getInputCol()]
Column.withMeta = withMeta
meta = {"annotatorType": "token"}
df = df.withColumn(out_col_name, udf_remove_token_short_length(in_col).withMeta("", meta))
return df
(edited)
:+1:
1
Vivek Gupta 5 months ago
@Andres Fernandez Thanks for providing solution. (edited)
Vivek Gupta 5 months ago
@Andres Fernandez
sc = SparkContext._active_spark_context
In above statement, from where I can get SparkContext?
Andres Fernandez 5 months ago
depends on how you start the session, is basically what you get returned when you start it
Andres Fernandez 5 months ago
spark = SparkSession.builder \
.appName("Spark NLP Licensed") \
.master("local[*]") \
. . .
.getOrCreate()
(edited)
:+1:
1
Added to your saved items
Vivek Gupta 5 months ago
@Andres Fernandez
Transformer is working as expected now, Pipeline looks like as below -
pipeline = Pipeline() \
.setStages([documentAssembler,
tokenizer,
short_token_remover,
lemmatizer,
finisher])
Output of 'short_token_filtered' is not tokens, rather its object.
Please let me know, how to get tokens rather object?
+--------------------+--------------------+--------------------+-----------------------------+--------------------+
| Text|short_token_filtered| finished_tokenized|finished_short_token_filtered| finished_lemmatized|
+--------------------+--------------------+--------------------+-----------------------------+--------------------+
|The smartphone in...|[[token, 4, 13, s...|[The, smartphone,...| [smartphone, indu...|[smartphone, indu...|
|The market has be...|[[token, 4, 9, ma...|[The, market, has...| [market, rumours,...|[market, rumour, ...|
|With the M-series...|[[token, 9, 16, M...|[With, the, M-ser...| [M-series, Samsun...|[M-series, Samsun...|
|Word on the stree...|[[token, 12, 17, ...|[Word, on, the, s...| [street, #Meanest...|[street, #Meanest...|
+--------------------+--------------------+--------------------+-----------------------------+--------------------+
Andres Fernandez 5 months ago
yeah just using spark sql like
df.selectExpr("finished_lemmatized.result").show()
:+1:
1
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