Merge pull request 'v2.4' (#5) from v2.4 into main

Reviewed-on: #5

README.md

@@ -13,20 +13,28 @@ Data transport is a simple framework that:
 
 ## Installation
 
-Within the virtual environment perform the following :
+Within the virtual environment perform the following (the following will install everything):
 
-    pip install git+https://github.com/lnyemba/data-transport.git
+    pip install data-transport[all]@git+https://github.com/lnyemba/data-transport.git
 
-Options to install components in square brackets
+Options to install components in square brackets are **nosql**; **cloud**; **other** and **warehouse**
 
-    pip install data-transport[nosql,cloud,warehouse,all]@git+https://github.com/lnyemba/data-transport.git
+    pip install data-transport[nosql,cloud,other, warehouse,all]@git+https://github.com/lnyemba/data-transport.git
 
+The components available:
+
+    0. sql          by default netezza; mysql; postgresql; duckdb; sqlite3; sqlserver
+    1. nosql        mongodb/ferretdb; couchdb
+    2. cloud        s3; bigquery; databricks
+    3. other        files; http; rabbitmq
+    4. warehouse    apache drill; apache iceberg
 
 ## Additional features
 
-    - In addition to read/write, there is support for functions for pre/post processing
+    - Reads are separated from writes to avoid accidental writes.
+    - Streaming (for large volumes of data) by specifying chunksize
     - CLI interface to add to registry, run ETL
-    - scales and integrates into shared environments like apache zeppelin; jupyterhub; SageMaker; ...
+    - Implements best-pracices for collaborative environments like apache zeppelin; jupyterhub; SageMaker; ...
 
 
 ## Learn More

bin/transport

@@ -53,6 +53,8 @@ def wait(jobs):
     while jobs :
         jobs = [thread for thread in jobs if thread.is_alive()]
         time.sleep(1)
+def job (_args):
+    pass
 @app_e.command(name="run")
 def apply (path:Annotated[str,typer.Argument(help="path of the configuration file")],
         index:int = typer.Option(default= None, help="index of the item of interest, otherwise everything in the file will be processed"),
@@ -177,7 +179,25 @@ def register (label:Annotated[str,typer.Argument(help="unique label that will be
     except Exception as e:
         _msg = f"""{TIMES_MARK} {e}"""
     print (_msg)
-    
+@app_r.command(name="template")    
+def template(name:Annotated[str,typer.Argument(help="database technology provider" ) ]):
+    """
+    This function will generate a template entry for the registry (content of an auth file)
+    """
+    #
+    # retrieve the provider and display the template if it has one
+    for _module in  ['sql','cloud','warehouse','nosql','other'] :
+        ref = getattr(transport,_module) if hasattr(transport,_module) else None
+        _entry = {}
+        if ref :
+            if hasattr(ref,name) :
+                _pointer = getattr(ref,name)
+                _entry = dict({'provider':name},**_pointer.template()) if hasattr(_pointer,'template') else {}
+                break
+    #
+    #
+    print ( json.dumps(_entry))
+    pass    
 @app_r.command(name="list")
 def register_list ():
     """

notebooks/postgresql.ipynb

@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -58,7 +58,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -131,16 +131,28 @@
    ]
   },
   {
-   "cell_type": "code",
+   "cell_type": "markdown",
-   "execution_count": null,
+   "metadata": {},
+   "source": [
+    "#### Streaming Large Volumes of Data\n",
+    "\n",
+    "It is recommended for large volumes of data to stream the data using **chunksize** as a parameter \n",
+    "\n",
+    "1. in the **read** method \n",
+    "2. or **transport.get.reader(\\*\\*...,chunksize=1000)**\n",
+    "\n",
+    "Use streaming because with large volumes of data some databases limit the volume of data for a single transaction in order to efficiently guarantee maintain **data integrity**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "python (3.10.12)",
    "language": "python",
    "name": "python3"
   },
@@ -154,7 +166,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

transport/cloud/bigquery.py

@@ -14,6 +14,9 @@ import numpy as np
 import time
 
 MAX_CHUNK = 2000000
+def template ():
+    return {'provider':'bigquery','private_key':'path-to-key','dataset':'name-of-dataset','table':'table','chunksize':MAX_CHUNK}
+
 class BigQuery:
     __template__= {"private_key":None,"dataset":None,"table":None}
     def __init__(self,**_args):
@@ -24,6 +27,7 @@ class BigQuery:
         self.dtypes = _args['dtypes'] if 'dtypes' in _args else None
         self.table = _args['table'] if 'table' in _args else None
         self.client = bq.Client.from_service_account_json(self.path)
+        self._chunksize = int(_args['chunksize']) if 'chunksize' in _args else None
     def meta(self,**_args):
         """
         This function returns meta data for a given table or query with dataset/table properly formatted
@@ -81,7 +85,14 @@ class Reader (BigQuery):
             SQL += " LIMIT "+str(_args['limit'])
         if (':dataset' in SQL or ':DATASET' in SQL)  and self.dataset:
             SQL = SQL.replace(':dataset',self.dataset).replace(':DATASET',self.dataset)
-        _info = {'credentials':self.credentials,'dialect':'standard'}       
+        _info = {'credentials':self.credentials,'dialect':'standard'}  
+        #
+        # @Ent-Feature : adding streaming capability here 
+        # 
+        if 'chunksize' in _args :
+            self._chunksize = int(_args['chunksize'])
+        if self._chunksize :
+            _info['chunksize'] = self._chunksize 
         return pd_gbq.read_gbq(SQL,**_info) if SQL else None  
         # return self.client.query(SQL).to_dataframe() if SQL else None
  

transport/cloud/databricks.py

@@ -17,6 +17,8 @@ import sqlalchemy
 # from transport.common import Reader,Writer
 import pandas as pd
 
+def template ():
+    return {'provider':'databricks','host':'fqn-host','token':'token','cluster_path':'path-of-cluster','catalog':'name-of-catalog','database':'schema-or-database','table':'table','chunksize':10000}
 
 class Bricks:
     """
@@ -42,6 +44,7 @@ class Bricks:
 
         _uri = f'''databricks+connector://token:{_token}@{_host}?http_path={_cluster_path}&catalog={_catalog}&schema={self._schema}'''
         self._engine = sqlalchemy.create_engine (_uri)
+        self._chunksize = int(_args['chunksize']) if 'chunksize' in _args else None
         pass
     def meta(self,**_args):
         table = _args['table'] if 'table' in _args else self._table
@@ -64,7 +67,14 @@ class Bricks:
     def apply(self,_sql):
         try:
             if _sql.lower().startswith('select') :
-                return pd.read_sql(_sql,self._engine)
+                #
+                # @ENT-Feature:  adding streaming functions/variables
+
+                if not self._chunksize :
+                    return pd.read_sql(_sql,self._engine)
+                else:
+                    return pd.read_sql(_sql,self._engine,chunksize=self._chunksize)
+
         except Exception as e:
             pass
 
@@ -84,7 +94,10 @@ class Reader(Bricks):
             sql = f'SELECT * FROM {table}'
         if limit :
             sql = sql + f' LIMIT {limit}'
-
+        #
+        # @ENT-Feature:  adding streaming functions/variables
+        if 'chunksize' in _args :
+            self._chunksize = int(_args['chunksize'])
         if 'sql' in _args or 'table' in _args :            
             return self.apply(sql)
         else:

transport/cloud/nextcloud.py

@@ -8,7 +8,8 @@ import pandas as pd
 from io import StringIO
 import json
 import nextcloud_client as nextcloud
-
+def template():
+    return {"url":None,"token":None,"uid":None,"file":None}
 class Nextcloud :
     __template__={"url":None,"token":None,"uid":None,"file":None}
     def __init__(self,**_args):

transport/cloud/s3.py

@@ -20,6 +20,9 @@ from io import StringIO
 import pandas as pd
 import json
 
+def template():
+	return {'access_key':'access-key','secret_key':'secret-key','region':'region','bucket':'name-of-bucket','file':'file-name','chunksize':10000}
+
 class s3 :
 	"""
 		@TODO: Implement a search function for a file given a bucket??
@@ -38,6 +41,7 @@ class s3 :
 			self._bucket_name = args['bucket']	
 			self._file_name = args['file']
 			self._region = args['region']
+			self._chunksize = int(args['chunksize']) if 'chunksize' in args else None
 		except Exception as e :
 			print (e)
 			pass
@@ -89,7 +93,10 @@ class Reader(s3) :
 		if not _stream :
 			return None
 		if _object['ContentType'] in ['text/csv'] :
-			return pd.read_csv(StringIO(str(_stream).replace("\\n","\n").replace("\\r","").replace("\'","")))
+			if not self._chunksize :
+				return pd.read_csv(StringIO(str(_stream).replace("\\n","\n").replace("\\r","").replace("\'","")))
+			else:
+				return pd.read_csv(StringIO(str(_stream).replace("\\n","\n").replace("\\r","").replace("\'","")),chunksize=self._chunksize)
 		else:
 			return _stream
 		

transport/info.py

@@ -1,6 +1,6 @@
 __app_name__  = 'data-transport'
 __author__ = 'Steve L. Nyemba'
-__version__= '2.4.32'
+__version__= '2.4.34'
 __edition__= 'enterprise'
 __email__  = "info@the-phi.com"
 __license__=f"""

transport/iowrapper.py

@@ -163,6 +163,7 @@ class IReader(IO):
         
         _objectName = '.'.join([self._agent.__class__.__module__,self._agent.__class__.__name__])
         if types.GeneratorType == type(_data):
+            
             return self._stream(_data)
             # if self._plugins :
             #     return self._stream(_data) 
@@ -278,7 +279,7 @@ class IETL(BaseIO) :
                 if _item['type'] in ['INTEGER','BIGINT','INT'] :
                     _column  = _item['name']
                     _data[_column] = _data[_column].copy().fillna(0).astype(np.int64)
-            writer.write(_data,schema=_schema)
+            writer.write(_data)
         except Exception as e:
             _action = 'post-error'
             _input['error'] = str(e)

transport/nosql/couchdb.py

@@ -11,7 +11,8 @@ import sys
 # from transport.common import Reader, Writer
 from datetime import datetime
 
-
+def template():
+	return {'dbname':'database','doc':'document','username':'username','password':'password','url':'url-with-port'}
 class Couch:
 	"""
 	This class is a wrapper for read/write against couchdb. The class captures common operations for read/write.

transport/nosql/mongodb.py

@@ -20,6 +20,9 @@ import re
 from multiprocessing import Lock, RLock
 from transport.common import IEncoder
 
+def template():
+    return {'provider':'mongodb','host':'localhost','port':27017,'db':'db-name','collection':'collection-name','username':'username','password':'password','mechanism':'SCRAM-SHA-256'}
+
 class Mongo :
     lock = RLock()
     """

transport/other/files.py

@@ -4,6 +4,10 @@ This file is a wrapper around pandas built-in functionalities to handle characte
 import pandas as pd
 import numpy as np
 import os
+
+def template():
+	return {'path':None,'delimiter':None}
+
 class File :	
 	def __init__(self,**params):
 		"""

transport/other/http.py

@@ -7,6 +7,8 @@ import requests
 from io import StringIO
 import pandas as pd
 
+def template():
+	return {'url':None,'headers':{'key':'value'}}
 
 class Reader:
 	"""

transport/other/rabbitmq.py

@@ -17,6 +17,10 @@ import sys
 # 	from common import Reader, Writer
 import json
 from multiprocessing import RLock
+
+def template():
+	return {'port':5672,'host':'localhost','queue':None,'vhost':None,'username':None,'password':None}
+
 class MessageQueue:
 	"""
 		This class hierarchy is designed to handle interactions with a queue server using pika framework (our tests are based on rabbitmq)

transport/sql/common.py

@@ -1,11 +1,14 @@
 """
 This file encapsulates common operations associated with SQL databases via SQLAlchemy
-
+@ENT:
+    - To support streaming (with generators) we the parameter chunksize which essentially enables streaming
 """
 import sqlalchemy as sqa
 from sqlalchemy import text , MetaData, inspect
 
 import pandas as pd
+def template():
+    return {'host':'localhost','database':'database','table':'table'}
 
 class Base:
     def __init__(self,**_args):
@@ -20,6 +23,7 @@ class Base:
             
             _uri,_kwargs = _uri
             self._engine= sqa.create_engine(_uri,**_kwargs,future=True)
+        self._chunksize = int(_args['chunksize']) if 'chunksize' in _args else None
     def _set_uri(self,**_args) :
         """
         :provider   provider
@@ -78,7 +82,12 @@ class Base:
         @TODO: Execution of stored procedures
         """
         if sql.strip().lower().startswith('select') or sql.strip().lower().startswith('with') or sql.strip().startswith('show'):
-            return pd.read_sql(sql,self._engine) 
+            
+            if not self._chunksize:
+                return pd.read_sql(sql,self._engine) 
+            else:
+                return pd.read_sql(sql,self._engine,chunksize=self._chunksize) 
+
         else:
             _handler = self._engine.connect()
             _handler.execute(text(sql.strip()))
@@ -132,7 +141,12 @@ class BaseReader(SQLBase):
             if self._schema and type(self._schema) == str :
                 _table = f'{self._schema}.{_table}'
             sql = f'SELECT * FROM {_table}'
+        if 'chunksize' in _args :
+            self._chunksize = int(_args['chunksize'])
+        
+        
         return self.apply(sql)
+        
     
 
 class BaseWriter (SQLBase):

transport/sql/duckdb.py

@@ -3,6 +3,9 @@ This module implements the handler for duckdb (in memory or not)
 """
 from transport.sql.common import Base, BaseReader, BaseWriter
 
+def template ():
+    return {'database':'path-to-database','table':'table'}
+
 class Duck :
     def __init__(self,**_args):
         #

transport/sql/mysql.py

@@ -1,8 +1,11 @@
 """
 This file implements support for mysql and maria db (with drivers mysql+mysql)
 """
-from transport.sql.common import BaseReader, BaseWriter
+from transport.sql.common import BaseReader, BaseWriter, template as _template
 # import mysql.connector as my
+def template ():
+    return dict(_template(),**{'port':3306})
+
 class MYSQL:
     
     def get_provider(self):

transport/sql/netezza.py

@@ -1,5 +1,8 @@
 import nzpy as nz   
-from transport.sql.common import BaseReader, BaseWriter
+from transport.sql.common import BaseReader, BaseWriter , template as _template
+
+def template ():
+    return dict(_template(),**{'port':5480,'chunksize':10000})
 
 class Netezza:
     def get_provider(self):

transport/sql/postgresql.py

@@ -1,7 +1,10 @@
 
-from transport.sql.common import BaseReader , BaseWriter
+from transport.sql.common import BaseReader , BaseWriter, template as _template
+
 from psycopg2.extensions import register_adapter, AsIs
 import numpy as np
+def template ():
+    return dict(_template(),**{'port':5432,'chunksize':10000})
 
 register_adapter(np.int64, AsIs)
 

transport/sql/sqlite3.py

@@ -2,6 +2,8 @@ import sqlalchemy
 import pandas as pd
 from transport.sql.common import Base, BaseReader, BaseWriter
 from multiprocessing import RLock
+def template():
+    return {'database':'path-to-database','table':'table'}
 class SQLite3 :
     lock = RLock()
     def __init__(self,**_args):

transport/sql/sqlserver.py

@@ -3,7 +3,11 @@ Handling Microsoft SQL Server via pymssql driver/connector
 """
 import sqlalchemy
 import pandas as pd
-from transport.sql.common import Base, BaseReader, BaseWriter
+from transport.sql.common import Base, BaseReader, BaseWriter, template as _template
+
+def template ():
+    return dict(_template(),**{'port':1433})
+
 
 
 class MsSQLServer:

transport/warehouse/drill.py

@@ -3,6 +3,8 @@ import pandas as pd
 from .. sql.common import BaseReader , BaseWriter
 import sqlalchemy as sqa
 
+def template():
+    return {'host':'localhost','port':8047,'ssl':False,'table':None,'database':None}
 class Drill :
     __template = {'host':None,'port':None,'ssl':None,'table':None,'database':None}
     def __init__(self,**_args):

transport/warehouse/iceberg.py

@@ -11,6 +11,10 @@ from pyspark.sql.types import *
 from pyspark.sql.functions import col, to_date, to_timestamp
 import copy
 
+
+def template():
+    return {'catalog':None,'database':None,'table':None}
+
 class Iceberg :
     def __init__(self,**_args):
         """