How to read and write the same dataset in a transform? I have an input dataset (input_ds1) and another input dataset (input_ds2). When I output to one of these dataset's paths (ex.dataset2 in code below) the check fails, with a cyclical dependency error.
Below I attacked an example:
#transform(
input_ds1=Input('Other Namespace/Other/Foundry_support_test/dataset1'),
input_ds2=Input('/Other Namespace/Other/Foundry_support_test/dataset2'),
output=Output('/Other Namespace/Other/Foundry_support_test/dataset2'),
)
def compute(input_ds1, input_ds2, output):
This is possible to read and write to the content of the output dataset with the #incremental() decorator. With it you can read the previous version of any dataset and avoid the cyclical dependency error.
#transform(
input_ds1=Input('Other Namespace/Other/Foundry_support_test/dataset1'),
output=Output('/Other Namespace/Other/Foundry_support_test/dataset2'),
)
def compute(input_ds1, input_ds2, output):
input_ds2 = output.dataframe('previous')
Incremental transform is designed for other use cases but contains a lot of features. More details in the incremental documentation: https://www.palantir.com/docs/foundry/transforms-python/incremental-reference/
Related
I have a dataset which have an xml column and i am trying to export individual xmls as files with filename being in another column using codeworkbook
I filtered the rows i want using below code
def prepare_input(xml_with_debug):
from pyspark.sql import functions as F
filter_column = "key"
filter_value = "test_key"
df_filtered = xml_with_debug.filter(filter_value == F.col(filter_column))
approx_number_of_rows = 1
sample_percent = float(approx_number_of_rows) / df_filtered.count()
df_sampled = df_filtered.sample(False, sample_percent, seed=0)
important_columns = ["key", "xml"]
return df_sampled.select([F.col(c).cast(F.StringType()).alias(c) for c in important_columns])
It works till here. Now for the last part i tried this in a python task, but was complaining about the parameters (i should have set it up wrongly). But even if it works it will be as a single file i think.
from transforms.api import transform, Input, Output
#transform(
output=Output("/path/to/python_csv"),
my_input=Input("/path/to/input")
)
def my_compute_function(output, my_input):
output.write_dataframe(my_input.dataframe().coalesce(1), output_format="csv", options={"header": "true"})
I am trying to set it up in GUI like below
My question i guess is, what will be the code in the last Python task (write_file) after the prepare input so that i extract individual xmls (And if possible zip them into single file for download)
You can access the output dataset filesystem and write files into it in whatever format you want.
The documentation for that can be found here: https://www.palantir.com/docs/foundry/code-workbook/transforms-unstructured/#writing-files
(If you want to do it from a code repository it's very similar https://www.palantir.com/docs/foundry/transforms-python/unstructured-files/#writing-files)
By doing that you can create multiple different files or you can create a single zip file and write it into a dataset.
I have a folder where I will upload one file every month. The file will have the same format in every month.
First problem
The idea is to concatenate all the files in this folder into one file. Currently I am hardcoding the filenames (filename[0], filename[1], filename[2]..) but imagine later I will have 50 files, should I explicitly add them to the transform_df decorator? Is there any other method to handle this?
Second problem:
Currently I have let's say 4 files (2021_07, 2021_08, 2021_09, 2021_10) and I want whenever I add the file presenting 2021_12 data to avoid changing the code.
If I add input_5 = Input(path_to_2021_12_do_not_exists) the code will not be run and give an error.
How can I implement the code for future files and let the code ignore the input if it does not exist without manually each month add a new value to my code?
Thank you
# from pyspark.sql import functions as F
from transforms.api import transform_df, Input, Output
from pyspark.sql.functions import to_date, year, col
from pyspark.sql.types import StringType
from myproject.datasets import utils
from pyspark.sql import DataFrame
from functools import reduce
input_dir = '/Company/Project_name/'
prefix_filename = 'DataInput1_'
suffixes = ['2021_07', '2021_08', '2021_09', '2021_10', '2021_11', '2021_12']
filenames = [input_dir + prefix_filename + suffixe for suffixe in suffixes]
#transform_df(
Output("/Company/Project_name/Data/clean/File_concat"),
input_1=Input(filenames[0]),
input_2=Input(filenames[1]),
input_3=Input(filenames[2]),
input_4=Input(filenames[3]),
)
def compute(input_1, input_2, input_3, input_4):
input_dfs = [input_1, input_2, input_3, input_4]
dfs = []
def transformation_input(df):
# some transformation
return df
for input_df in input_dfs:
dfs.append(transformation_input(input_df))
dfs = reduce(DataFrame.unionByName, dfs)
return dfs
This question comes up a lot, the simple answer is that you don't. Defining datasets and executing a build on them are two different steps executed at different stages.
Whenever you commit your code and run the checks, your overall python code is executed during the renderSchrinkwrap stage, except for the compute part. This allows Foundry to discover what datasets exist and publish.
Publishing involves creating your dataset and putting whatever is inside your compute function is published into the jobspec of the dataset, so foundry knows what code to execute whenever you run a build.
Once you hit build on the dataset, Foundry will only pick up whatever is on the jobspec and execute it. Any other code has already run during your checks, and it has run just once.
So any dynamic input/output would require you to re-run checks on your repo, which means that some code change would have had to happen since the Checks is part of the CI process, not part of the build.
Taking a step back, assuming each of your input files has the same schema, Foundry would expect you to have all of those files in the same dataset as append transactions.
This might not be possible though, if for instance, the only indication of the "year" of the data is embedded in the filename, but your sample code would indicate that you expect all these datasets to have the same schema and easily union together.
You can do this manually through the Dataset Preview - just use the Upload File button or drag-and-drop the new file into the Preview window - or, if it's an "end user" workflow, with a File Upload Widget in a Workshop app. You may need to coordinate with your Foundry support team if this widget isn't available.
Bit late to the post although for anyone who is interested in an answer to most of the question. Dynamically determining file names from within a folder is not doable although having some level of dynamic input is possible as follows:
# from pyspark.sql import functions as F
from transforms.api import transform, Input, Output
from pyspark.sql.functions import to_date, year, col
from pyspark.sql.types import StringType
from myproject.datasets import utils
from pyspark.sql import DataFrame
# from functools import reduce
from transforms.verbs.dataframes import union_many # use this instead of reduce
input_dir = '/Company/Project_name/'
prefix_filename = 'DataInput1_'
suffixes = ['2021_07', '2021_08', '2021_09', '2021_10', '2021_11', '2021_12']
filenames = [input_dir + prefix_filename + suffixe for suffixe in suffixes]
inputs = {('input{}'.format(index)): Input(filename) for (index, filename) in enumerate(filenames))}
#transform(
output=Output("/Company/Project_name/Data/clean/File_concat"),
**inputs
)
def compute(output, **kwargs):
# Extract dataframes from input datasets
input_dfs = [dataset_df.dataframe() for dataset_name, dataset_df in kwargs.items()]
dfs = []
def transformation_input(df):
# some transformation
return df
for input_df in input_dfs:
dfs.append(transformation_input(input_df))
# dfs = reduce(DataFrame.unionByName, dfs)
unioned_dfs = union_many(*dfs)
return unioned_dfs
Couple points:
Created dynamic input dict.
That dict is read into the transform using **kwargs.
Using transform decorator not transform_df, we can extract the dataframes.
(not in question) Combine multiple dataframes using union_many function from transforms_verbs library.
I have a data feed that gives a large .txt file (50-75GB) every day. The file contains several different schemas within it, where each row corresponds to one schema. I would like to split this into partitioned datasets for each schema, how can I do this efficiently?
The largest problem you need to solve is the iteration speed to recover your schemas, which can be challenging for a file at this scale.
Your best tactic here will be to get an example 'notional' file with each of the schemas you want to recover as a line within it, and to add this as a file within your repository. When you add this file into your repo (alongside your transformation logic), you will then be able to push it into a dataframe, much as you would with the raw files in your dataset, for quick testing iteration.
First, make sure you specify txt files as a part of your package contents, this way your tests will discover them (this is covered in documentation under Read a file from a Python repository):
You can read other files from your repository into the transform context. This might be useful in setting parameters for your transform code to reference.
To start, In your python repository edit setup.py:
setup(
name=os.environ['PKG_NAME'],
# ...
package_data={
'': ['*.txt']
}
)
I am using a txt file with the following contents:
my_column, my_other_column
some_string,some_other_string
some_thing,some_other_thing,some_final_thing
This text file is at the following path in my repository: transforms-python/src/myproject/datasets/raw.txt
Once you have configured the text file to be shipped with your logic, and after you have included the file itself in your repository, you can then include the following code. This code has a couple of important functions:
It keeps raw file parsing logic completely separate from the stage of reading the file into a Spark DataFrame. This is so that the way this DataFrame is constructed can be left to the test infrastructure, or to the run time, depending on where you are running.
This keeping of the logic separate lets you ensure the actual row-by-row parsing you want to do is its own testable function, instead of having it live purely within your my_compute_function
This code uses the Spark-native spark_session.read.text method, which will be orders of magnitude faster than row-by-row parsing of a raw txt file. This will ensure the parallelized DataFrame is what you operate on, not a single file, line by line, inside your executors (or worse, your driver).
from transforms.api import transform, Input, Output
from pkg_resources import resource_filename
def raw_parsing_logic(raw_df):
return raw_df
#transform(
my_output=Output("/txt_tests/parsed_files"),
my_input=Input("/txt_tests/dataset_of_files"),
)
def my_compute_function(my_input, my_output, ctx):
all_files_df = None
for file_status in my_input.filesystem().ls('**/**'):
raw_df = ctx.spark_session.read.text(my_input.filesystem().hadoop_path + "/" + file_status.path)
parsed_df = raw_parsing_logic(raw_df)
all_files_df = parsed_df if all_files_df is None else all_files_df.unionByName(parsed_df)
my_output.write_dataframe(all_files_df)
def test_my_compute_function(spark_session):
file_path = resource_filename(__name__, "raw.txt")
raw_df = raw_parsing_logic(
spark_session.read.text(file_path)
)
assert raw_df.count() > 0
raw_columns_set = set(raw_df.columns)
expected_columns_set = {"value"}
assert len(raw_columns_set.intersection(expected_columns_set)) == 1
Once you have this code up and running, your test_my_compute_function method will be very fast to iterate on, so that you can perfect your schema recovery logic. This will make it substantially easier to get your dataset building at the very end, but without any of the overhead of a full build.
How to use the data set without my_compute_function. From file1 in repository, I want to call a function which is defined in another file. In the second file, I want to make use of the data set, my_input_integration, may be without my_compute_function. How to combine the datasets from two different repository files. I do not want to combine in one file because I want to use 2nd file as utility file. It would be great if anyone can answer this.
Repository File 1
from transforms.api import transform, Input, Output
#transform(
my_output=Output("/my/output"),
my_input=Input("/my/input"),
)
def my_compute_function(my_input, my_output):
return calling_function(my_input, my_output)
Repository File 2
from transforms.api import transform, Input, Output
#transform(
my_input_integration =Input("/my/input"),
)
def calling_function(my_input, my_output, my_input_integration??)
return my_output.write_dataframe(
my_input.dataframe(),
column_descriptions=my_dictionary
)
If I understand correctly what you're trying to achieve, you can't directly do that -- any input to a transform has to be defined in that transform, and then passed into the utility function, you can't "inject" inputs.
So the most straightforward way to achieve what you want would be to do something like this:
file 1:
#transform(
my_output=Output("/my/output"),
my_input=Input("/my/input"),
my_input_integration=Input("/my/input_integration"),
)
def my_compute_function(my_input, my_output, my_input_integration):
return calling_function(my_input, my_output, my_input_integration)
file 2:
def calling_function(my_input, my_output, my_input_integration)
return my_output.write_dataframe(
my_input.dataframe(),
column_descriptions=my_dictionary
)
If you really think you need the ability to automatically "inject" datasets, and adding them as parameters to your transform would be too cumbersome, it would be possible to take a more sophisticated approach where you define a custom wrapper that you apply to the transform function that makes the input datasets automatically available. I would really avoid this though, as it adds a lot of complexity and "magic" to the code that will be hard to understand for a newcomer and casual reader.
I have image save in 0.csv files.
The format is as picture below.
How can I read it to tensorflow?
Thanks!
You should use the Dataset input pipeline introduced in tensorflow 1.4:
https://www.tensorflow.org/programmers_guide/datasets#consuming_text_data
Here's the example from the developers guide (though you'll want to read through that guide, it's quite well written):
filenames = ["/var/data/file1.txt", "/var/data/file2.txt"]
dataset = tf.data.Dataset.from_tensor_slices(filenames)
# Use `Dataset.flat_map()` to transform each file as a separate nested dataset,
# and then concatenate their contents sequentially into a single "flat" dataset.
# * Skip the first line (header row).
# * Filter out lines beginning with "#" (comments).
dataset = dataset.flat_map(
lambda filename: (
tf.data.TextLineDataset(filename)
.skip(1)
.filter(lambda line: tf.not_equal(tf.substr(line, 0, 1), "#"))))
The Dataset preprocessing pipeline has a few nice advantages. Most of the functionality you'll need such as reading text records, shuffling, batching, etc. are reduced to one-liners. More importantly though, it forces you into writing your preprocessing pipeline in a good, modular, testable way. It takes a little bit to get used to the API, but it's time well spent.