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9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /dataprep/connector/sql.py: -------------------------------------------------------------------------------- 1 | """ 2 | This module contains the method of read_sql. 3 | It is a wrapper on connectorx.read_sql function. 4 | """ 5 | 6 | from typing import Optional, Tuple, Union, List, Any 7 | 8 | try: 9 | import connectorx as cx 10 | 11 | _WITH_CX = True 12 | except ImportError: 13 | _WITH_CX = False 14 | 15 | 16 | def read_sql( 17 | conn: str, 18 | query: Union[List[str], str], 19 | *, 20 | return_type: str = "pandas", 21 | protocol: str = "binary", 22 | partition_on: Optional[str] = None, 23 | partition_range: Optional[Tuple[int, int]] = None, 24 | partition_num: Optional[int] = None, 25 | ) -> Any: 26 | """ 27 | Run the SQL query, download the data from database into a dataframe. 28 | Please check out https://github.com/sfu-db/connector-x for more details. 29 | 30 | Parameters 31 | ---------- 32 | conn 33 | the connection string. 34 | query 35 | a SQL query or a list of SQL query. 36 | return_type 37 | the return type of this function. It can be "arrow", "pandas", "modin", "dask" or "polars". 38 | protocol 39 | the protocol used to fetch data from source. Valid protocols are database dependent 40 | (https://github.com/sfu-db/connector-x/blob/main/Types.md). 41 | partition_on 42 | the column to partition the result. 43 | partition_range 44 | the value range of the partition column. 45 | partition_num 46 | how many partition to generate. 47 | 48 | Example 49 | -------- 50 | >>> db_url = "postgresql://username:password@server:port/database" 51 | >>> query = "SELECT * FROM lineitem" 52 | >>> read_sql(db_url, query, partition_on="partition_col", partition_num=10) 53 | """ 54 | if _WITH_CX: 55 | df = cx.read_sql( 56 | conn=conn, 57 | query=query, 58 | return_type=return_type, 59 | protocol=protocol, 60 | partition_on=partition_on, 61 | partition_range=partition_range, 62 | partition_num=partition_num, 63 | ) 64 | return df 65 | else: 66 | raise ImportError("connectorx is not installed." "Please run pip install connectorx") 67 | -------------------------------------------------------------------------------- /dataprep/datasets/__init__.py: -------------------------------------------------------------------------------- 1 | """This module implements load dataset related functions""" 2 | 3 | from ._base import load_dataset, _load_dataset_as_dask, load_db 4 | from ._base import get_dataset_names, get_db_names 5 | 6 | __all__ = ["load_dataset", "get_dataset_names", "_load_dataset_as_dask", "load_db", "get_db_names"] 7 | -------------------------------------------------------------------------------- /dataprep/datasets/database/sakila.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sfu-db/dataprep/be3f00c66f1248f05cc4f6007e84ac800f0700b5/dataprep/datasets/database/sakila.db -------------------------------------------------------------------------------- /dataprep/eda/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | dataprep.eda 3 | ============ 4 | """ 5 | 6 | from bokeh.io import output_notebook 7 | 8 | from ..utils import is_notebook 9 | from .correlation import compute_correlation, plot_correlation, render_correlation 10 | from .create_report import create_report 11 | from .create_db_report import create_db_report 12 | from .create_diff_report import create_diff_report 13 | from .distribution import compute, plot, render 14 | from .dtypes import ( 15 | Categorical, 16 | Continuous, 17 | GeoGraphy, 18 | GeoPoint, 19 | DateTime, 20 | Discrete, 21 | DType, 22 | Nominal, 23 | Numerical, 24 | Ordinal, 25 | Text, 26 | ) 27 | from .missing import compute_missing, plot_missing, render_missing 28 | from .diff import plot_diff, compute_diff, render_diff 29 | 30 | __all__ = [ 31 | "plot_correlation", 32 | "compute_correlation", 33 | "render_correlation", 34 | "compute_missing", 35 | "render_missing", 36 | "plot_missing", 37 | "plot", 38 | "compute", 39 | "render", 40 | "DType", 41 | "Categorical", 42 | "Nominal", 43 | "Ordinal", 44 | "Numerical", 45 | "Continuous", 46 | "Discrete", 47 | "DateTime", 48 | "Text", 49 | "create_report", 50 | "create_db_report", 51 | "create_diff_report", 52 | "plot_diff", 53 | "compute_diff", 54 | "render_diff", 55 | ] 56 | 57 | 58 | if is_notebook(): 59 | output_notebook(hide_banner=True) 60 | -------------------------------------------------------------------------------- /dataprep/eda/correlation/compute/common.py: -------------------------------------------------------------------------------- 1 | """Common components for compute correlation.""" 2 | 3 | from enum import Enum, auto 4 | 5 | import dask 6 | import numpy as np 7 | from scipy.stats.mstats import rankdata 8 | from scipy.stats import kendalltau as kendalltau_ 9 | 10 | 11 | class CorrelationMethod(Enum): 12 | """Supported correlation methods""" 13 | 14 | # pylint: disable=invalid-name 15 | Pearson = auto() 16 | Spearman = auto() 17 | KendallTau = auto() 18 | 19 | 20 | # @dask.delayed(name="rankdata-bottleneck", pure=True) # pylint: disable=no-value-for-parameter 21 | # def nanrankdata(data: np.ndarray, axis: int = 0) -> np.ndarray: 22 | # """delayed version of rankdata.""" 23 | # return nanrankdata_(data, axis=axis) 24 | 25 | 26 | @dask.delayed(name="nanrankdata", pure=True) # pylint: disable=no-value-for-parameter 27 | def nanrankdata(data: np.ndarray, axis: int = 0) -> np.ndarray: 28 | """delayed version of rankdata.""" 29 | ranks = rankdata(np.ma.masked_invalid(data), axis=axis) 30 | ranks[ranks == 0] = np.nan 31 | return ranks 32 | 33 | 34 | @dask.delayed(name="kendalltau-scipy", pure=True) # pylint: disable=no-value-for-parameter 35 | def kendalltau(a: np.ndarray, b: np.ndarray) -> np.ndarray: # pylint: disable=invalid-name 36 | """delayed version of kendalltau.""" 37 | corr = kendalltau_(a, b).correlation 38 | return np.float64(corr) # Sometimes corr is a float, causes dask error 39 | 40 | 41 | @dask.delayed(name="kendalltau-scipy", pure=True) # pylint: disable=no-value-for-parameter 42 | def corrcoef(arr: np.ndarray) -> np.ndarray: 43 | """delayed version of np.corrcoef.""" 44 | _, (corr, _) = np.corrcoef(arr, rowvar=False) 45 | return corr 46 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | This module implements the create_db_report(sql_engine) function. 3 | """ 4 | 5 | import warnings 6 | from sqlalchemy.engine.base import Engine 7 | from .run_function import generate_db_report 8 | from .report import Report 9 | 10 | __all__ = ["create_db_report"] 11 | 12 | 13 | def create_db_report( 14 | sql_engine: Engine, 15 | analyze: bool = False, 16 | ) -> Report: 17 | """ 18 | This function is to generate and render database report and show in browser. 19 | 20 | Parameters 21 | ---------- 22 | sql_engine 23 | SQL Alchemy Engine object returned from create_engine() with an url passed 24 | E.g. sql_engine = create_engine(url) 25 | analyze 26 | Whether to execute ANALYZE to write database statistics to the database 27 | 28 | Examples 29 | -------- 30 | >>> from dataprep.eda import create_db_report 31 | >>> from dataprep.datasets import load_db 32 | >>> db_engine = load_db('sakila.db') 33 | >>> create_db_report(db_engine) 34 | """ 35 | _suppress_warnings() 36 | return Report(*generate_db_report(sql_engine, analyze)) 37 | 38 | 39 | def _suppress_warnings() -> None: 40 | """ 41 | suppress warnings in create_db_report 42 | """ 43 | warnings.filterwarnings( 44 | "ignore", 45 | "The default value of regex will change from True to False in a future version", 46 | category=FutureWarning, 47 | ) 48 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sfu-db/dataprep/be3f00c66f1248f05cc4f6007e84ac800f0700b5/dataprep/eda/create_db_report/db_models/__init__.py -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/database.py: -------------------------------------------------------------------------------- 1 | from .db_meta import DbMeta 2 | 3 | 4 | class Database: 5 | def __init__(self, name: str, schema: str, stats: DbMeta) -> None: 6 | self.name = name.replace("'", "") 7 | self.schema = schema 8 | self.tables = {} 9 | self.views = {} 10 | for key, value in stats.__dict__.items(): 11 | if not hasattr(self, key): 12 | setattr(self, key, value) 13 | 14 | def add_table(self, table_name: str, table_object): 15 | self.tables[table_name] = table_object 16 | 17 | def add_view(self, view_name: str, view_object): 18 | self.views[view_name] = view_object 19 | 20 | def get_tables(self): 21 | return self.tables.values() 22 | 23 | def get_tables_dict(self): 24 | return self.tables 25 | 26 | def get_views(self): 27 | return self.views.values() 28 | 29 | def get_name(self): 30 | return self.name 31 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/db_meta.py: -------------------------------------------------------------------------------- 1 | class DbMeta: 2 | num_of_views = 0 3 | num_of_schemas = 0 4 | num_of_fk = 0 5 | num_of_uk = 0 6 | num_of_pk = 0 7 | num_of_tables = 0 8 | 9 | engine_name_dict = { 10 | "mysql": "MySQL", 11 | "postgresql": "PostgreSQL", 12 | "sqlite": "SQLite", 13 | } 14 | 15 | def __init__( 16 | self, 17 | engine_name: str, 18 | num_of_views: int, 19 | num_of_schemas: int, 20 | num_of_fk: int, 21 | num_of_uk: int, 22 | num_of_pk: int, 23 | num_of_tables: int, 24 | product_version: str, 25 | connection_url: str, 26 | ) -> None: 27 | self.num_of_views = num_of_views 28 | self.num_of_schemas = num_of_schemas 29 | self.num_of_fk = num_of_fk 30 | self.num_of_uk = num_of_uk 31 | self.num_of_pk = num_of_pk 32 | self.num_of_table = num_of_tables 33 | self.connection_url = connection_url 34 | self.database_product = self.engine_name_dict[engine_name] + " - " + product_version 35 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/table_column.py: -------------------------------------------------------------------------------- 1 | from .table import Table 2 | from .constraint import ForeignKeyConstraint 3 | 4 | 5 | class TableColumn: 6 | def __init__( 7 | self, 8 | table: Table, 9 | name: str, 10 | type_name: str, 11 | not_null: bool, 12 | default_value: str, 13 | is_auto_updated: bool, 14 | comments: str, 15 | ): 16 | self.table = table 17 | self.name = name.replace("'", "") 18 | self.type_name = type_name 19 | self.not_null = not_null 20 | self.default_value = default_value.replace("'", "") if default_value else "" 21 | self.comments = comments.replace("'", "") if comments else "" 22 | self.parents = {} 23 | self.children = {} 24 | self.type = 0 25 | self.decimal_digits = 0 26 | self.detailed_size = "" 27 | self.is_auto_updated = is_auto_updated 28 | self.index = False 29 | 30 | def set_index(self): 31 | self.index = True 32 | 33 | def is_primary(self): 34 | if self.table.primary_keys is not None: 35 | return self in self.table.primary_keys 36 | return False 37 | 38 | def is_foreign_key(self): 39 | return len(self.parents) != 0 40 | 41 | def get_default_value(self): 42 | return self.default_value 43 | 44 | def set_comments(self, comments: str): 45 | if comments is None or len(comments.strip()) == 0: 46 | self.comments = None 47 | else: 48 | self.comments = comments.strip() 49 | 50 | def add_parent(self, parent, constraint: ForeignKeyConstraint): 51 | self.parents[parent] = constraint 52 | self.table.add_max_parents() 53 | 54 | def add_child(self, child, constraint: ForeignKeyConstraint): 55 | self.children[child] = constraint 56 | self.table.add_max_children() 57 | 58 | def get_parents(self): 59 | return list(self.parents.values()) 60 | 61 | def get_children(self): 62 | return list(self.children.values()) 63 | 64 | def get_name(self): 65 | return self.name 66 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/table_index.py: -------------------------------------------------------------------------------- 1 | class TableIndex: 2 | def __init__(self, name: str, index_type: str) -> None: 3 | self.name = name.replace("'", "") 4 | self.is_unique = False 5 | self.is_primary = False 6 | self.columns = {} 7 | self.index_type = index_type 8 | 9 | def add_column(self, col_string: str, column): 10 | if column is not None: 11 | self.columns[col_string] = column 12 | 13 | def set_primary(self): 14 | self.is_primary = True 15 | 16 | def set_unique(self): 17 | self.is_unique = True 18 | 19 | def get_type(self): 20 | if self.is_primary: 21 | return "Primary key" 22 | if self.is_unique: 23 | return "Must be unique" 24 | return "Performance" 25 | 26 | def get_index_type(self): 27 | return self.index_type 28 | 29 | def columns_as_string(self): 30 | return "".join(self.columns.keys()) 31 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/db_models/view.py: -------------------------------------------------------------------------------- 1 | from .table import Table 2 | from .database import Database 3 | 4 | 5 | class View(Table): 6 | def __init__(self, db: Database, schema: str, name: str, view_def: str) -> None: 7 | self.view_definition = None 8 | super().__init__(db, schema, name) 9 | self.set_view_definition(view_def) 10 | 11 | def set_view_definition(self, view_definition: str): 12 | if view_definition is not None and len(view_definition.strip()) > 0: 13 | self.view_definition = view_definition 14 | 15 | def get_view_definition(self): 16 | return self.view_definition 17 | 18 | def is_view(self): 19 | return True 20 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/header/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sfu-db/dataprep/be3f00c66f1248f05cc4f6007e84ac800f0700b5/dataprep/eda/create_db_report/header/__init__.py -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/layout/anomalies.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sfu-db/dataprep/be3f00c66f1248f05cc4f6007e84ac800f0700b5/dataprep/eda/create_db_report/layout/anomalies.js -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | // This file is autogenerated via the `commonjs` Grunt task. You can require() this file in a CommonJS environment. 2 | require('../../js/transition.js') 3 | require('../../js/alert.js') 4 | require('../../js/button.js') 5 | require('../../js/carousel.js') 6 | require('../../js/collapse.js') 7 | require('../../js/dropdown.js') 8 | require('../../js/modal.js') 9 | require('../../js/tooltip.js') 10 | require('../../js/popover.js') 11 | require('../../js/scrollspy.js') 12 | require('../../js/tab.js') 13 | require('../../js/affix.js') -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/layout/bower/admin-lte/dist/css/alt/AdminLTE-fullcalendar.css: -------------------------------------------------------------------------------- 1 | /* 2 | * Plugin: Full Calendar 3 | * --------------------- 4 | */ 5 | .fc-button { 6 | background: #f4f4f4; 7 | background-image: none; 8 | color: #444; 9 | border-color: #ddd; 10 | border-bottom-color: #ddd; 11 | } 12 | .fc-button:hover, 13 | .fc-button:active, 14 | .fc-button.hover { 15 | background-color: #e9e9e9; 16 | } 17 | .fc-header-title h2 { 18 | font-size: 15px; 19 | line-height: 1.6em; 20 | color: #666; 21 | margin-left: 10px; 22 | } 23 | .fc-header-right { 24 | padding-right: 10px; 25 | } 26 | .fc-header-left { 27 | padding-left: 10px; 28 | } 29 | .fc-widget-header { 30 | background: #fafafa; 31 | } 32 | .fc-grid { 33 | width: 100%; 34 | border: 0; 35 | } 36 | .fc-widget-header:first-of-type, 37 | .fc-widget-content:first-of-type { 38 | border-left: 0; 39 | border-right: 0; 40 | } 41 | .fc-widget-header:last-of-type, 42 | .fc-widget-content:last-of-type { 43 | border-right: 0; 44 | } 45 | .fc-toolbar { 46 | padding: 10px; 47 | margin: 0; 48 | } 49 | .fc-day-number { 50 | font-size: 20px; 51 | font-weight: 300; 52 | padding-right: 10px; 53 | } 54 | .fc-color-picker { 55 | list-style: none; 56 | margin: 0; 57 | padding: 0; 58 | } 59 | .fc-color-picker > li { 60 | float: left; 61 | font-size: 30px; 62 | margin-right: 5px; 63 | line-height: 30px; 64 | } 65 | .fc-color-picker > li .fa { 66 | -webkit-transition: -webkit-transform linear 0.3s; 67 | -moz-transition: -moz-transform linear 0.3s; 68 | -o-transition: -o-transform linear 0.3s; 69 | transition: transform linear 0.3s; 70 | } 71 | .fc-color-picker > li .fa:hover { 72 | -webkit-transform: rotate(30deg); 73 | -ms-transform: rotate(30deg); 74 | -o-transform: rotate(30deg); 75 | transform: rotate(30deg); 76 | } 77 | #add-new-event { 78 | -webkit-transition: all linear 0.3s; 79 | -o-transition: all linear 0.3s; 80 | transition: all linear 0.3s; 81 | } 82 | .external-event { 83 | padding: 5px 10px; 84 | font-weight: bold; 85 | margin-bottom: 4px; 86 | box-shadow: 0 1px 1px rgba(0, 0, 0, 0.1); 87 | text-shadow: 0 1px 1px rgba(0, 0, 0, 0.1); 88 | border-radius: 3px; 89 | cursor: move; 90 | } 91 | .external-event:hover { 92 | box-shadow: inset 0 0 90px rgba(0, 0, 0, 0.2); 93 | } 94 | -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/layout/bower/admin-lte/dist/css/alt/AdminLTE-fullcalendar.min.css: -------------------------------------------------------------------------------- 1 | .fc-button{background:#f4f4f4;background-image:none;color:#444;border-color:#ddd;border-bottom-color:#ddd}.fc-button:hover,.fc-button:active,.fc-button.hover{background-color:#e9e9e9}.fc-header-title h2{font-size:15px;line-height:1.6em;color:#666;margin-left:10px}.fc-header-right{padding-right:10px}.fc-header-left{padding-left:10px}.fc-widget-header{background:#fafafa}.fc-grid{width:100%;border:0}.fc-widget-header:first-of-type,.fc-widget-content:first-of-type{border-left:0;border-right:0}.fc-widget-header:last-of-type,.fc-widget-content:last-of-type{border-right:0}.fc-toolbar{padding:10px;margin:0}.fc-day-number{font-size:20px;font-weight:300;padding-right:10px}.fc-color-picker{list-style:none;margin:0;padding:0}.fc-color-picker>li{float:left;font-size:30px;margin-right:5px;line-height:30px}.fc-color-picker>li .fa{-webkit-transition:-webkit-transform linear .3s;-moz-transition:-moz-transform linear .3s;-o-transition:-o-transform linear .3s;transition:transform linear .3s}.fc-color-picker>li .fa:hover{-webkit-transform:rotate(30deg);-ms-transform:rotate(30deg);-o-transform:rotate(30deg);transform:rotate(30deg)}#add-new-event{-webkit-transition:all linear .3s;-o-transition:all linear .3s;transition:all linear .3s}.external-event{padding:5px 10px;font-weight:bold;margin-bottom:4px;box-shadow:0 1px 1px rgba(0,0,0,0.1);text-shadow:0 1px 1px rgba(0,0,0,0.1);border-radius:3px;cursor:move}.external-event:hover{box-shadow:inset 0 0 90px rgba(0,0,0,0.2)} -------------------------------------------------------------------------------- /dataprep/eda/create_db_report/layout/bower/datatables.net-bs/js/dataTables.bootstrap.min.js: -------------------------------------------------------------------------------- 1 | /*! 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