Added file to execute the complete cleaning pipeline

This commit is contained in:
GassiGiuseppe 2025-09-29 15:21:26 +02:00
parent 6ddb7de9da
commit bd72ad3571
9 changed files with 596 additions and 0 deletions

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from Scripts.Libs.Utils.dataframe_interaction import get_raw_from_dataframe
from Scripts.Libs.CleaningPipeline.special_token import SpecialToken
import pandas as pd
class BPE_corpus():
def __init__(self, output_path :str):
self.output_handler = open(output_path, "w")
def close(self):
# add corpus end before closing
self.output_handler.write(SpecialToken.CORPUS_END.value)
self.output_handler.close()
def write_from_str(self, output: str):
if output == '':
return
self.output_handler.write(output)
def write_from_df(self, df: pd.DataFrame):
self.write_from_str(get_raw_from_dataframe(df))

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import pandas as pd
class RDF_completation_task_dataset():
"""
Write the CSV for the fourth task, which is "Predicting subsequent triples based on a given context".
Each RDF is saved as str
CSV Composition: ["MovieID","RDF"]
"""
def __init__(self, output_path:str):
self.output = open(output_path, "w")
# then the first row as header
header = ["MovieID","RDF"]
self.output.write(",".join(header) + "\n")
def close(self):
self.output.close()
def write(self, RDF: pd.DataFrame):
"""
Args:
RDF (pd.DataFrame): ["MovieID","RDF"]
"""
RDF.to_csv(self.output, index=False, header=False)

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import pandas as pd
# do not worry about circular dependencies, this class will never call something else
from Scripts.DataCleaning.filter import PipelineApplier
class RDF_mask_task_dataset():
"""
Write the CSV for the third task, which is "Predicting a masked component within an RDF triple".
The CSV is like: for each RDF there will be 3 rows, where every time one of the componments is missing.
CSV Composition: ["MovieID","IncompleteRDF","Missing","RDF"]
"""
def __init__(self, output_path:str):
# this methods will only be used by this class, but they belong in a lower level
self._build_triple = PipelineApplier.build_triple
self._build_incomplete_triple = PipelineApplier.build_incomplete_triple
self.output = open(output_path, "w")
# then the first row as header
header = ["MovieID","IncompleteRDF","Missing","RDF"]
self.output.write(",".join(header) + "\n")
def close(self):
self.output.close()
def write(self, RDF: pd.DataFrame):
rdf_complete = self._build_triple(RDF)
rdf_without_subject = self._build_incomplete_triple(RDF.drop(columns=["SubjectURI"]))
rdf_without_relationship = self._build_incomplete_triple(RDF.drop(columns=["RelationshipURI"]))
rdf_without_object = self._build_incomplete_triple(RDF.drop(columns=["ObjectURI"]))
####
df_subject = pd.DataFrame({
"MovieID": RDF["MovieID"],
"IncompleteRDF": rdf_without_subject,
"Missing": RDF["SubjectURI"],
"RDF": rdf_complete,
})
df_relationship = pd.DataFrame({
"MovieID": RDF["MovieID"],
"IncompleteRDF": rdf_without_relationship,
"Missing": RDF["RelationshipURI"],
"RDF": rdf_complete,
})
df_object = pd.DataFrame({
"MovieID": RDF["MovieID"],
"IncompleteRDF": rdf_without_object,
"Missing": RDF["ObjectURI"],
"RDF": rdf_complete,
})
output_df = pd.concat([df_subject, df_relationship, df_object], ignore_index=True)
output_df.to_csv(self.output, index=False, header=False)

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import pandas as pd
class RDF_text_task_dataset():
"""
Write the CSV for the firsts two tasks, which are "Generating structured RDF triples from natural language text" and reverse.
In the CVS the RDFs will be saved toghether as a string.
CSV Composition: ["MovieID","RDFs","Abstract"]
"""
def __init__(self, output_path:str):
self.output = open(output_path, "w")
# then the first row as header
header = ["MovieID","RDFs","Abstract"]
self.output.write(",".join(header) + "\n")
def close(self):
self.output.close()
def write(self, RDF: pd.DataFrame):
"""
Args:
RDF (pd.DataFrame): ["MovieID","Triple","Abstract"]
"""
RDF.to_csv(self.output, index=False, header=False)

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# This file deletes in the pipeline the unwanted relationship by different rules
import pandas as pd
import sqlite3
import numpy as np
from Scripts.Libs.CleaningPipeline.special_token import SpecialToken
from Scripts.Libs.CleaningPipeline.sql_endpoint import SqlEndpoint
class PipelineApplier():
def __init__(self):
self.MOVIE_FILTER = pd.DataFrame()
self.REL_FILTER = pd.DataFrame()
def delete_relationship_by_str(self, RDF: pd.DataFrame, uri: str) -> pd.DataFrame:
return RDF[RDF["RelationshipURI"]!= uri]
def generate_list_relationship_filter(self, filter_list: list[str]) -> None:
"""Store RelationshipURI filters as a set """
self.relationship_filter_list: set[str] = set(filter_list)
def delete_relationship_by_list_filter(self, RDF: pd.DataFrame) -> pd.DataFrame:
"""Remove rows whose RelationshipURI is in the stored filter. Generate it first callig the generate_list_relationship_filter"""
return RDF[~RDF["RelationshipURI"].isin(self.relationship_filter_list)]
def generate_frequency_movie_filter(self, MOVIE_COUNT: pd.DataFrame ,min_treshold: int, max_treshold: int):
"""
You MUST call this before filter the dataset by movie frequence [filter_by_frequence_movie_id()],
since this method creates such filter
Args:
MOVIE_COUNT (pd.DataFrame): ["MovieID","Count"]
min_treshold (int):
max_treshold (int):
"""
MOVIE_COUNT = MOVIE_COUNT[MOVIE_COUNT["Count"] >= min_treshold]
MOVIE_COUNT = MOVIE_COUNT[MOVIE_COUNT["Count"] < max_treshold]
self.MOVIE_FILTER = MOVIE_COUNT #["MovieID"]
def generate_frequency_relationship_filter(self, REL_COUNT: pd.DataFrame ,min_treshold: int, max_treshold: int):
REL_COUNT = REL_COUNT[REL_COUNT["Count"] >= min_treshold]
REL_COUNT = REL_COUNT[REL_COUNT["Count"] < max_treshold]
self.REL_FILTER = REL_COUNT #["RelationshipURI"]
def filter_by_frequency_movie_id(self, RDF: pd.DataFrame) -> pd.DataFrame:
RDF = RDF[RDF["MovieID"].isin(self.MOVIE_FILTER["MovieID"])]
return RDF
def filter_by_frequency_relationship(self, RDF: pd.DataFrame) -> pd.DataFrame:
RDF = RDF[RDF["RelationshipURI"].isin(self.REL_FILTER["RelationshipURI"])]
return RDF
def rdf_add_special_token(self, RDF: pd.DataFrame):
"""
Adds RDF special token to each element of the tuple. i.e: SUBJ to SubjectURI, OBJ to ObjectURI, REL to RelationshipURI.
Check Scrits/Libs/CleaningPipeline/special_token.py for the up-to-date special token.
It only adds the special token of the three element of the RDF, no other special token.
Args:
RDF (pd.DataFrame):
Returns:
pd.DataFrame: ["MovieURI","SubjectURI","RelationshipURI","ObjectURI","Abstract"]
"""
# if the filter runned before sliced the RDF and created a View, here the problem is resolved
# for more context: SettingWithCopyWarning
RDF = RDF.copy()
# at the beginning of SubjectURI RelationshipURI ObjectURI, add their special token
RDF["SubjectURI"] = SpecialToken.SUBJECT.value + RDF["SubjectURI"]
RDF["ObjectURI"] = SpecialToken.OBJECT.value + RDF["ObjectURI"]
RDF["RelationshipURI"] = SpecialToken.RELATIONSHIP.value + RDF["RelationshipURI"]
return RDF
def drop_na_from_dataset(self, RDF: pd.DataFrame) -> pd.DataFrame:
# dataset has SubjectURI RelationshipURI ObjectURI
# want to drop the '' in them
# Replace empty strings with NaN
RDF = RDF.replace('', np.nan)
# Drop rows where any of the key columns are NaN
RDF = RDF.dropna(subset=["SubjectURI", "RelationshipURI", "ObjectURI"])
return RDF
def rebuild_by_movie(self, RDF: pd.DataFrame) -> pd.DataFrame:
"""_summary_
Args:
RDF (pd.DataFrame): ["MovieID","SubjectURI","RelationshipURI","ObjectURI","Abstract"]
Returns:
pd.DataFrame: ["MovieID","Triple","Abstract"]
"""
# to execute this method you have to have itereted by movie_id
# because as design we want at the end one row for each movie
# MovieID and abstract can be given as input for a more generic method
# movie_id = RDF["MovieID"].iloc(0)
# abstract = RDF["Abstract"].iloc(0)
# first let's combine each row creating column triple as join of rdf
RDF["Triple"] = RDF["SubjectURI"] + RDF["RelationshipURI"] + RDF["ObjectURI"]
# special token
RDF["Triple"] = SpecialToken.START_TRIPLE.value + RDF["Triple"] + SpecialToken.END_TRIPLE.value
# combine rows into one
# MovieID and Abstract are unique for each other 1 <-> 1
RDF = RDF.groupby(["MovieID", "Abstract"])["Triple"].apply("".join).reset_index()
# add special token for: start of triple, end of triple and start of abstract
RDF["Triple"] = SpecialToken.START_TRIPLE_LIST.value + RDF["Triple"]
RDF["Abstract"] = SpecialToken.ABSTRACT.value + RDF["Abstract"]
return RDF[["MovieID","Triple","Abstract"]]
def group_by_movie_from_triple(self, RDF: pd.DataFrame) -> pd.DataFrame:
"""
Args:
RDF (pd.DataFrame): ["MovieID","Triple","Abstract"]
Returns:
pd.DataFrame: ["MovieID","Triple","Abstract"]
"""
# combine rows into one
# MovieID and Abstract are unique for each other 1 <-> 1
RDF = RDF.groupby(["MovieID", "Abstract"])["Triple"].apply("".join).reset_index()
# add special token for: start of triple, end of triple and start of abstract
RDF["Triple"] = SpecialToken.START_TRIPLE_LIST.value + RDF["Triple"]
RDF["Abstract"] = SpecialToken.ABSTRACT.value + RDF["Abstract"]
return RDF[["MovieID","Triple","Abstract"]]
@staticmethod
def build_triple(RDF: pd.DataFrame):
"""
Obtains joined RDF triple in one element, togheter with START and END special token
Args:
RDF (pd.DataFrame): at least ["SubjectURI", "RelationshipURI", "ObjectURI"]
Returns:
pd.DataFrame: RDF["Triple"] (just this column)
"""
# let's combine each row creating column triple as join of rdf
RDF["Triple"] = RDF["SubjectURI"] + RDF["RelationshipURI"] + RDF["ObjectURI"]
# special token
RDF["Triple"] = SpecialToken.START_TRIPLE.value + RDF["Triple"] + SpecialToken.END_TRIPLE.value
return RDF["Triple"]
@staticmethod
def build_incomplete_triple(RDF: pd.DataFrame):
"""
Method helper used for the third task: "Predicting a masked component within an RDF triple".
Obtains joined RDF triple in one element, togheter with START and END special token.
The MISSING element will be replaced by the special token <MASK>
Args:
RDF (pd.DataFrame): 2 of the following ["SubjectURI", "RelationshipURI", "ObjectURI"]
Returns:
RDF["Triple"]: pd.Series (just this column, NOT A DATAFRAME)
"""
# let's create a new column "Triple" with the joined RDF
# the following creates a column of MASK token of the lenght of the dataframe,
# it is not needed since we expect to have a dataframe of just one column, but its more robust (AND SLOW)
MISSING = pd.Series([SpecialToken.MASK.value] * len(RDF), index=RDF.index)
RDF["Triple"] = (
RDF.get("SubjectURI", MISSING) +
RDF.get("RelationshipURI", MISSING) +
RDF.get("ObjectURI", MISSING))
# special token
RDF["Triple"] = SpecialToken.START_TRIPLE.value + RDF["Triple"] + SpecialToken.END_TRIPLE.value
return RDF["Triple"]
@staticmethod
def build_for_mask_task(RDF_incomplete: pd.DataFrame, MISSING: pd.DataFrame) -> pd.DataFrame:
# currently not used
"""
Method helper used for the third task: "Predicting a masked component within an RDF triple".
Given two Dataframe, the first containing the incompleted RDF and the other only the missing componment,
this methods applies the special token
Args:
RDF (pd.DataFrame): _description_
Returns:
pd.DataFrame: _description_
"""
# take an example dataframe as ["SubjectURI",""]
# as input two dataframe, one with 2 column
return None

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import re
from Scripts.Libs.CleaningPipeline.sql_endpoint import SqlEndpoint
from Scripts.DataCleaning.filter import PipelineApplier
# tasks dataset builder
from Scripts.DataCleaning.data_output_models.rdf_mask_task import RDF_mask_task_dataset
from Scripts.DataCleaning.data_output_models.bpe_corpus import BPE_corpus
from Scripts.DataCleaning.data_output_models.rdf_text_tasks import RDF_text_task_dataset
from Scripts.DataCleaning.data_output_models.rdf_completation_task import RDF_completation_task_dataset
import pandas as pd
class Pipeline():
def __init__(self, output):
self.sql_endpoint = SqlEndpoint()
# classes to manage taskes' datasets
self.task_rdf_mask = RDF_mask_task_dataset("./Assets/Dataset/Tmp/debug.csv")
self.task_bpe_corpus = BPE_corpus("./Assets/Dataset/Tmp/output.txt")
self.task_rdf_text = RDF_text_task_dataset("./Assets/Dataset/Tmp/rdf_text.csv")
self.task_rdf_completation = RDF_completation_task_dataset("./Assets/Dataset/Tmp/rdf_completation.csv")
# prepare the filter
# the filter applier needs to know thefrequence of Movies and Relationship among all the Dataset
self.filter_applier = PipelineApplier()
MOVIE_COUNT = self.sql_endpoint.get_movies_id_count()
REL_COUNT = self.sql_endpoint.get_relationship_count()
self.filter_applier.generate_frequency_movie_filter(MOVIE_COUNT,50,3000)
self.filter_applier.generate_frequency_relationship_filter(REL_COUNT, 50, 2395627)
# prepare the filter ot the relationshipURI you want to delete:
relationship_uri_banned_list = [
"dbp-dbp:wikiPageUsesTemplate","w3:2000/01/rdf-schema#label","dbp-dbo:abstract",
"dbp-dbo:wikiPageID","dbp-dbo:wikiPageRevisionID", "dbp-dbo:wikiPageDisambiguates",
"w3:2002/07/owl#sameAs","dbp-dbp:image","dbp-dbo:wikiPageLength", "w3:2000/01/rdf-schema#comment",
"dbp-dbo:thumbnail", "foaf:depiction", "w3:1999/02/22-rdf-syntax-ns#type"]
self.filter_applier.generate_list_relationship_filter(relationship_uri_banned_list)
def _end_file_handler(self):
self.task_bpe_corpus.close()
self.task_rdf_mask.close()
self.task_rdf_text.close()
self.task_rdf_completation.close()
def _get_cleaned_movie_rows(self):
for RDF in self.sql_endpoint.get_abbreviated_dataset_by_movie_id():
RDF = self.filter_applier.drop_na_from_dataset(RDF)
RDF = self.filter_applier.filter_by_frequency_movie_id(RDF)
RDF = self.filter_applier.filter_by_frequency_relationship(RDF)
# other filter
#
RDF = self.filter_applier.delete_relationship_by_list_filter(RDF)
if RDF.empty:
continue
RDF = self.filter_applier.rdf_add_special_token(RDF) # WARNING, THIS MUST BE DONE AFTER FILTER BY FREQUENCE
yield RDF
def execute_task_bpe_corpus(self):
for RDF in self._get_cleaned_movie_rows():
RDF = self.filter_applier.rebuild_by_movie(RDF)
RDF = RDF[["Triple","Abstract"]]
self.task_bpe_corpus.write_from_df(RDF)
self._end_file_handler()
def execute_task_rdf_mask(self):
for RDF in self._get_cleaned_movie_rows():
self.task_rdf_mask.write(RDF)
self._end_file_handler()
def execute_tasks_rdf_text(self):
for RDF in self._get_cleaned_movie_rows():
RDF = self.filter_applier.rebuild_by_movie(RDF)
self.task_rdf_text.write(RDF)
self._end_file_handler()
def execute_task_rdf_completation(self):
for RDF in self._get_cleaned_movie_rows():
RDF["Triple"] = self.filter_applier.build_triple(RDF)
self.task_rdf_completation.write(RDF[["MovieID","Triple"]])
self._end_file_handler()
def execute_all_task(self):
for RDF in self._get_cleaned_movie_rows():
self.task_rdf_mask.write(RDF)
RDF["Triple"] = self.filter_applier.build_triple(RDF)
self.task_rdf_completation.write(RDF[["MovieID","Triple"]])
RDF = self.filter_applier.group_by_movie_from_triple(RDF[["MovieID","Triple","Abstract"]])
self.task_rdf_text.write(RDF)
self.task_bpe_corpus.write_from_df(RDF[["Triple","Abstract"]])
self._end_file_handler()
pipeline = Pipeline("./Assets/Dataset/Tmp/output.txt")
# pipeline.execute_task_bpe_corpus()
# pipeline.execute_task_rdf_mask()
# pipeline.execute_tasks_rdf_text()
# pipeline.execute_task_rdf_completation()
pipeline.execute_all_task()

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from enum import Enum
class SpecialToken(str, Enum):
# (Enum, str) -> throws an error
START_TRIPLE_LIST = "<SOTL>"
START_TRIPLE = "<SOT>"
END_TRIPLE = "<EOT>"
SUBJECT = "<SUBJ>"
RELATIONSHIP = "<PRED>"
OBJECT = "<OBJ>"
ABSTRACT = "<ABS>"
CORPUS_END = "<END>"
## Tasks' Token
RDF_TO_TEXT = "<RDF2TXT>"
TEXT_TO_RDF = "<TEXT2RDF>"
CONTINUE_RDF = "<CONTINUERDF>"
MASK = "<MASK>"
#BPE Training:

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#######################################################
# This file stand as endpoint to interact with DB #
#######################################################
# import sqlite3
import pandas as pd
from sqlalchemy import create_engine
from Scripts.Libs.CleaningPipeline.special_token import SpecialToken
class SqlEndpoint():
def __init__(self, DB_PATH = "./Assets/Dataset/DatawareHouse/dataset.db", chunk_size_row = 500):
# self.CONN = sqlite3.connect(DB_PATH) # DEPRECATED
self.sql_engine = create_engine(f"sqlite:///{DB_PATH}")
# /// 3 slash -> relative path
# //// 4 slash -> absolute
# self.conn = self.sql_engine.connect().execution_options(stream_results=True)
# it seems that sqlite doenst support streamer cursor
# PRAGMA exeutes better in writing not reading
self.chunk_size_row = chunk_size_row
pass
def get_RDF(self) -> pd.DataFrame :
QUERY = """
SELECT MovieID, SubjectURI, RelationshipURI, ObjectURI
FROM RDFs
INNER JOIN Subjects USING (SubjectID)
INNER JOIN Relationships USING (RelationshipID)
INNER JOIN Objects USING (ObjectID);
"""
return pd.read_sql_query(QUERY, self.CONN)
def get_chunked_abbreviated_dataset(self) -> pd.DataFrame :
"""
Returns:
pd.DataFrame: MovieID, SubjectURI, RelationshipURI, ObjectURI, Abstract
"""
QUERY = """
SELECT MovieID, SubjectURI, RelationshipURI, ObjectURI, Abstract
FROM RDFs
INNER JOIN ParsedSubjects USING (SubjectID)
INNER JOIN ParsedRelationships USING (RelationshipID)
INNER JOIN ParsedObjects USING (ObjectID)
INNER JOIN WikipediaAbstracts USING (MovieID);
"""
# return pd.read_sql_query(QUERY, self.CONN, chunksize=500)
# sqlite3
return pd.read_sql_query(QUERY, self.sql_engine, chunksize=self.chunk_size_row)
def get_chunked_abbreviated_dataset_with_start_token(self)-> pd.DataFrame:
# DEPRECATED !
start_token = SpecialToken()
QUERY = """
SELECT
MovieID,
? || SubjectURI AS SubjectURI,
? || RelationshipURI AS RelationshipURI,
? || ObjectURI AS ObjectURI,
Abstract
FROM RDFs
INNER JOIN ParsedSubjects USING (SubjectID)
INNER JOIN ParsedRelationships USING (RelationshipID)
INNER JOIN ParsedObjects USING (ObjectID)
INNER JOIN WikipediaAbstracts USING (MovieID);
"""
return pd.read_sql_query(QUERY, self.sql_engine, chunksize=self.chunk_size_row)
def get_abbreviated_dataset_by_movie_id(self):# -> iter[pd.DataFrame]:
"""
Gets each time a DataFrame per movie ( with all its rows in the dataset).
The retrieved RDFs are already abbrevieted by the sql parser
Yields:
Pandas.DataFrame: [MovieID, SubjectURI, RelationshipURI, ObjectURI, Abstract]
"""
# chunk by movieId, abstract is the same and some intersting logic are appliable
movie_ids = pd.read_sql_query("SELECT MovieID FROM Movies;", self.sql_engine)["MovieID"]
# CHOOSEN MOVIE:
# The Dark Knight : 117248
# Inception : 147074
# The Avengers : 113621
# Cast Away : 1123
# The Departed : 117586
# American Psycho : 90177
# Avatar : 71587
# Django Unchained : 138952
# Spirited Away : 144137
# Knives Out : 148025
movie_list = [117248, 147074, 113621, 1123, 117586, 90177, 71587, 138952, 144137, 148025]
movie_ids = movie_list
QUERY = """
SELECT MovieID, SubjectURI, RelationshipURI, ObjectURI, Abstract
FROM RDFs
INNER JOIN ParsedSubjects USING (SubjectID)
INNER JOIN ParsedRelationships USING (RelationshipID)
INNER JOIN ParsedObjects USING (ObjectID)
INNER JOIN WikipediaAbstracts USING (MovieID)
WHERE MovieID = (?);
"""
for movie_id in movie_ids:
yield pd.read_sql_query(QUERY, self.sql_engine, params=(movie_id,))
def get_movies_id_count(self) -> pd.DataFrame:
"""
Gets the count of each Movie in the Dataset
Returns:
Pandas.DataFrame: [MovieID, Count]
"""
QUERY = """
SELECT MovieID, COUNT(*) AS Count
FROM RDFs
GROUP BY MovieID;
"""
return pd.read_sql_query(QUERY, self.sql_engine)
def get_relationship_count(self) -> pd.DataFrame:
"""
Gets the count of each Relationship in the Dataset
Returns:
Pandas.DataFrame: [RelationshipURI, Count]
"""
QUERY = """
SELECT RelationshipURI, COUNT(*) AS Count
FROM RDFs
INNER JOIN ParsedRelationships USING (RelationshipID)
GROUP BY RelationshipURI;
"""
return pd.read_sql_query(QUERY, self.sql_engine)
if __name__ == "__main__" :
sql_endpoint = SqlEndpoint()
for pandas_row in sql_endpoint.get_abbreviated_dataset_by_movie_id():
print(pandas_row)
# sql_endpoint.get_RDF()
print("done")

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import pandas as pd
def get_raw_from_dataframe(DF: pd.DataFrame) -> str:
output = ''
for row in DF.itertuples(index=False, name=None):
output += "".join(map(str, row))
return output