rabaDB2 2.0__tar.gz

rabadb2-2.0/CHANGELOG.rst

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+2.1.0
+=====
+
+* Python 3 migration: fixed 25+ bugs blocking test coverage
+* Fixed circular imports in fields.py
+* Fixed recursion in Raba.__getattr__
+* Fixed RabaList metaclass reference (RabaList_Metaclass -> _RabaListSingleton_Metaclass)
+* Fixed RabaListPupa.insert signature (k,i,v -> i,v)
+* Fixed RabaQuery.run() returning only first element (return inside for loop)
+* Fixed RabaQuery._parseJoint() called with wrong number of args
+* Fixed pickle.loads(str(...)) -> pickle.loads(bytes(...))
+* Fixed hashlib.md5(str) -> hashlib.md5(str.encode('utf-8'))
+* Fixed SQLite partial index parameter prohibition (inline values)
+* Fixed dictionary changed size during iteration in metaclass __call__
+* Fixed _mutateNotifyAnchor crash on free RabaList (anchorObj is None)
+* Fixed RabaList.extend calling non-existent _checkRabaList
+* Fixed RabaList.__setitem__/_checkElmt extra argument
+* Fixed Raba.unreference referencing non-existent makeRabaObjectSingletonKey
+* Added no-op unregisterRabalist and updateRabaListLength for backward compat
+* Added test_rabadb_extended.py (184 new tests) -> 99% coverage
+
+1.0.5
+=====
+
+* fixed Rlists
+
+1.0.4
+=====
+
+* Minor bug fixes
+* Typos
+* More explicit error messages
+
+1.0.3:
+=======
+
+* Will print a more meaningfull error if the database file could not be opened
+
+1.0.1:
+=======
+* Added functions to free object registeries
+
+1.0.0:
+=======
+The begining of a new era

rabadb2-2.0/DESCRIPTION.rst

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+rabaDB:
+=======
+rabaDB is a Lightweight Uncomplicated Borderline NoSQL and Schemaless ORM on top of sqlite3.
+All that so you can Store, Search and Modify your objects easily. You're welcome.

rabadb2-2.0/LICENCE

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rabadb2-2.0/MANIFEST.in

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+include *.rst
+include LICENCE

rabadb2-2.0/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: rabaDB2
+Version: 2.0
+Summary: Store, Search, Modify your objects easily. You're welcome.
+Home-page: https://github.com/tariqdaouda/rabaDB
+Author: Tariq Daouda
+Author-email: tariq.daouda@umontreal.ca
+License: ApacheV2.0
+Keywords: NoSQL database ORM sqlite3
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: System Administrators
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Database
+Classifier: Topic :: Database :: Database Engines/Servers
+Classifier: Topic :: Database :: Front-Ends
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.7
+License-File: LICENCE
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: summary
+
+rabaDB:
+=======
+rabaDB is a Lightweight Uncomplicated Borderline NoSQL and Schemaless ORM on top of sqlite3.
+All that so you can Store, Search and Modify your objects easily. You're welcome.

rabadb2-2.0/README.rst

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+.. image:: http://depsy.org/api/package/pypi/rabaDB/badge.svg
+   :alt: depsy
+   :target: http://depsy.org/package/python/rabaDB
+ 
+Lightweight Object Persistency for python.
+=========================================================
+
+Installation
+-------------
+
+.. code:: python
+	
+	pip install rabaDB #for the latest stable version
+
+That's it, no need for anything else.
+
+What's rabaDB?
+--------------
+
+rabaDB is a lightweight, borderline NoSQL, uncomplicated, ORM on top of sqlite3.
+
+Basically it means:
+
+* *Uncomplicated syntax*
+* *No SQL knowledge needed*: supports queries by example
+* *You can still use SQL* if you want
+* *Lazy and Optimized*: objects are only fully loaded if you need them to be
+* *No dependencies*: super easy installation 
+* *Somewhat Schemaless*: you can modify field definitions whenever you want and it will automatically adapt to the new schema
+
+Can it be used for "big projects"?
+----------------------------------
+
+rabaDB is the backend behind pyGeno_, a python package for genomics and proteomics where it is typically used to store
+whole genomes annonations, along with huge sets of polymorphisms: millions of entries. and it's performing really well.
+
+.. _pyGeno: https://github.com/tariqdaouda/pyGeno
+
+99% of what you need to know in one Example
+--------------------------------------------
+
+.. code:: python
+	
+	#The initialisation
+	from rabaDB.rabaSetup import *
+	RabaConfiguration('test_namespace', './dbTest_BasicExample.db')
+	import rabaDB.Raba as R
+	import rabaDB.fields as rf
+	
+	class Human(R.Raba) :
+		_raba_namespace = 'test_namespace'
+		
+		#Everything that is not a raba object is primitive
+		name = rf.Primitive()
+		age = rf.Primitive()
+		city = rf.Primitive()
+		
+		#Only Cars can fit into this relation
+		cars = rf.Relation('Car')
+		
+		#best friend can only be a human
+		bestFriend = rf.RabaObject('Human')
+		
+		def __init__(self) :
+			pass
+	
+	class Car(R.Raba) :
+		_raba_namespace = 'test_namespace'
+	
+		number = rf.Primitive()
+		def __init__(self) :
+			pass
+	
+	if __name__ == '__main__':
+		georges = Human()
+		georges.name = 'Georges'
+		for i in range(10) :
+			car = Car()
+			car.number = i
+			georges.cars.append(car)
+	
+		#saving georges also saves all his cars to the db
+		georges.save()
+
+
+
+What's a namespace?
+-------------------
+
+You can think of rabaDB's namespace as independent databases. Each namespace has a name and a file where all the data
+will be saved. Here's how you initialise rabaDb:
+
+.. code:: python
+	
+	#The initialisation
+	from rabaDB.rabaSetup import *
+	RabaConfiguration('test', './dbTest_BasicExample.db')
+
+Once you've done that, the configuration is a singleton attached to the namespace. If the filename does not exist
+it will be created for you.
+
+You can access it everywhere in you script by simply doing
+
+.. code:: python
+	
+	myConf = RabaConfiguration('test')
+
+There's also a connection object associated to the namespace
+
+.. code:: python
+	
+	myConn = RabaConnnection('test')
+
+To know what you can do with that, have a look at the debugging part.
+
+Field types
+-----------
+
+RabaDB has only **four** variable types:
+
+*Primitive:
+	- Numbers
+	- Strings
+	- Serialized objects
+*RabaObject
+	- An object whose class derives from Raba.Raba
+*Relation:
+	- A list of only a certain type of RabaObject 
+*RList:
+	- A list of anything
+
+Schemaless?
+-----------
+
+rabaDB allows you to change the schemas of your classes on the fly. That means that you can add and remove fields
+from your class definitions at any moment during the developement and rabaDB will take care of composing with the
+SQL backend. However keep in mind that whenever you remove a field, all the information relative to that field
+are lost forever.
+
+You can even erase whole class definitions from you code, and rabaDB will automatically update the database.
+
+Indexation
+-----------
+No problem:
+
+.. code:: python
+	
+	Human.ensureIndex('name')
+	#even on several fields
+	Human.ensureIndex(('name', 'age', 'city'))
+	
+	#To drop an index
+	Human.dropIndex('name')
+
+Brutal Querying 
+---------------
+
+You can do things like:
+
+.. code:: python
+
+	georges = Human(name = 'Georges')
+
+And rabaDB will try to find a match for you.
+
+Querying by example
+-------------------
+Querying by example is done by creating filters, all the conditions inside the same filter are merged by **And**
+and filters between them are merged by **Or**.
+
+.. code::
+
+	f = RabaQuery(SomeClass)
+	
+	f.addFilter(A1, A2, A3)
+	f.addFilter(B1, B2)
+	
+	Means: (A1 AND A2 AND A3) OR (B1 AND B2)
+
+There are several syntaxes that you can use.
+
+.. code:: python
+
+	from rabaDB.filters import *
+	
+	f = RabaQuery(Human)
+	#Or
+	f = RabaQuery('Human')
+	
+	f.addFilter(name = "Fela", age = "22")
+	#Or the fancier
+	f.addFilter({"age >=" : 22, "name like": "fel%"})
+	#Or
+	f.addFilter(['age = "22"', 'name = Fela'])
+
+And then here's how you get your results:
+
+.. code:: python
+
+	for r in f.run() :
+		print r
+	
+You can add an SQL statement at the end
+
+.. code:: python
+	
+	for r in f.run(sqlTail = "ORDER By age") :
+		print r
+	
+
+Querying SQL style
+------------------
+
+You can also write your own SQL *WHERE* conditions
+
+.. code:: python
+
+	from rabaDB.filters import *
+	
+	f = RabaQuery(Human)
+	
+	for r in f.runWhere("age = ?, name = ?" , (22, "fela")) :
+		print r
+
+
+Getting raw SQL 
+----------------
+
+By default all querying functions return raba Object, but you can always ask for the raw **SQL** tuple:
+
+.. code:: python
+	
+	f.run(raw = True)
+	f.runWere(("age = ?, name = ?" , (22, "fela"), raw = True)
+
+Supported operators for queries
+--------------------------------
+
+The supported operators are: 'LIKE', '=', '<', '>', '=', '>=', '<=', '<>', '!=', 'IS'
+
+Yes, but I just want to loop through the results  
+------------------------------------------------
+
+There are also iterative versions. They have the same interface but they are faster and less memory consuming
+	
+	* f.iterRun
+	* f.iterRunWhere
+
+And counts?
+----------
+
+Here's how you do counts
+
+.. code:: python
+
+	from rabaDB.filters import *
+	
+	f = RabaQuery(Human)
+	f.addFilter(age = "22")
+	print f.count()
+
+Registry
+---------
+
+rabaDB keeps an internal registry to ensure a strong object consistency. If you do:
+
+.. code:: python
+	
+	georges = Human(name = 'Georges')
+	sameGeorges = Human(name = 'Georges')
+
+You get two times the same object, every modification you do to georges is also applied to sameGeorges,
+because georges **is** sameGeorges. This rules applies to any form of queries.
+
+However keep in mind that the registery will also prevent the garbage collector from erasing raba objects, and
+that can lead to "memory leak"-like situations. The way that is by telling raba that you
+no longer need some objects to be registered:
+
+.. code:: python
+
+	form rabaDB.Raba import *
+	
+	_unregisterRabaObjectInstance(georges)
+
+
+Debugging
+---------
+
+RabaDB has debugging tools that you can access through the namespace's connection.
+ 
+ .. code:: python
+ 
+ 	import rabaDB.rabaSetup
+ 	conn = rabaDB.rabaSetup.RabaConnection("mynamespace")
+	
+	#printing the SQL queries
+	conn.enableQueryPrint(True)
+	#the part you want to debug
+	conn.enableQueryPrint(False)
+	#debug: print each SQL querie and asks the permition to continue
+	conn.enableDebug(True)
+	#the part you want to debug
+	conn.enableDebug(False)
+	
+	#record all the queries performed
+	conn.enableStats(True, logQueries = True)
+	#the part you want to debug
+	conn.enableStats(False)
+	#a pretty print
+	conn.printStats()
+	
+	#when you're done
+	conn.eraseStats()
+	
+Transactions
+------------
+
+You can group several queries into one single transaction
+
+ .. code:: python
+ 
+ 	conn.beginTransaction()
+ 	#a lot of object saving
+ 	conn.endTransaction()
+
+Inheritence
+-----------
+
+rabaDB fully supports inheritence. Children classes automatically inherit the fields of their parents.
+rabaDB also supports abstract classes, that is to say classes that are never meant to be instanciated and that only
+serve as templates for other classes. Abstract classes have no effect on the database
+
+Here's how you declare an abstract class:
+
+.. code:: python
+	
+	class pyGenoRabaObject(Raba) :
+
+		_raba_namespace = "pyGeno"
+		_raba_abstract = True # abstractness
+		
+		name = rf.Primitive()
+