Copyright (C) 2008 Eithon Cadag
 
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
 
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 
srccat.py - source catalog
 
Eithon Cadag
 
Example usage:
   
   import sexpparse
   reader = sexpparse.SexpSchemaSourceLinkReader('myschema.txt')
   srccat = SourceCatalog(reader.get_schema(),reader.get_sources(),reader.get_links())
   srccat.get_mappings_by_srcname_clsname("NCBI","Gene")

Modules
		pydi.decorators pydi.schema warnings

Classes
		exceptions.Exception(exceptions.BaseException) InvalidLinkException InvalidMappableException InvalidMappingException InvalidPropertyException InvalidQueryException InvalidSourcePropertyException NoLinkException NoSourceException NoSourcedClassException Source SourceCatalog SourceLink SourceLinkHead SourceLinkReader SourceLinkTail SourceMapping SourceQueryable SourceReader SourcedCls SrcClsInterface   class InvalidLinkException(exceptions.Exception)       Method resolution order: InvalidLinkException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class InvalidMappableException(exceptions.Exception)       Method resolution order: InvalidMappableException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class InvalidMappingException(exceptions.Exception)       Method resolution order: InvalidMappingException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class InvalidPropertyException(exceptions.Exception)       Method resolution order: InvalidPropertyException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class InvalidQueryException(exceptions.Exception)       Method resolution order: InvalidQueryException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class InvalidSourcePropertyException(exceptions.Exception)       Method resolution order: InvalidSourcePropertyException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class NoLinkException(exceptions.Exception)       Method resolution order: NoLinkException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class NoSourceException(exceptions.Exception)       Method resolution order: NoSourceException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class NoSourcedClassException(exceptions.Exception)       Method resolution order: NoSourcedClassException exceptions.Exception exceptions.BaseException __builtin__.object Methods defined here: __init__(self, msg) Data descriptors defined here: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x6cb87ab0> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) __str__(...) x.__str__() <==> str(x) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class Source       Methods defined here: __init__(self, name, srcd_clses=None) Sources need: - Classes defined (generate SourcedCls) - Per class, per source specific properties (e.g., foreign keys) (done per class) - Knowledge of how it can be queried (consider defining the query within the   source, then allow link-mappings to cite the query within the source as a way of    linking. - Queries defined in the source need to know what parameters they may pass (handled in SourceQueryable) - Each source should have mappings (src->schema) defined (done per class) __repr__(self) cls_by_name(self, str_clsname) cls_to_query_hash(self) get_classes(self) These are SOURCED classes. get_name(self) query_by_cls(self, src_cls) Data descriptors defined here: classes These are SOURCED classes. name   class SourceCatalog     TODO: This class needs cleaning up...     Methods defined here: __init__(self, schema, sources, links) Source catalog needs: - References to Source objs - Access to Source queryables - Knowledge of how the sources interconnect - Schema activate_source(self, src) get_generator_by_link(self, linkname) Note -- generators are not generators in the strict Python sense -- they are DataSetGenerators. get_link_by_name(self, linkname) get_links_by_clsname(self, str_cls) Return the links that are pointed to by specific clsname. get_links_by_srcname_clsname(self, str_src, str_cls) Returns only links from active sources. get_links_from_head_srcname_clsname(self, str_src, str_cls) Return the sources that are pointed to from a specified source and class. get_mappings_by_srcname_clsname(self, str_src, str_cls) get_properties_by_srcname_clsname_propname(self, str_src, str_cls, str_prop) get_queries_by_srcname_clsname(self, str_src, str_cls) get_queries_by_srcname_clsname_queryname(self, str_src, str_cls, str_qry) get_source_names(self) get_src_by_srcname(self, str_src) Return the source by source name get_tail_clses_from_head_clsname(self, str_cls) Return the classes that are pointed to from a given class(str), regardless of source. get_tail_clses_from_head_srcname_clsname(self, str_src, str_cls) Return the classes that are pointed to from a given source, regardless of class. get_trigger_by_srcname_clsname(self, str_src, str_cls) inactivate_source(self, src_str) valid_clses_for_src_str(self, str_src) Data descriptors defined here: active_sources links schema sources   class SourceLink       Methods defined here: __init__(self, name, head, tail, gen=None) __repr__(self) __str__(self) get_generator_str(self) get_head(self) get_name(self) get_tail(self) Data descriptors defined here: gen_str head name tail   class SourceLinkHead       Methods defined here: __init__(self, src, src_cls, prp) __repr__(self) __str__(self) get_property(self) get_source(self) get_sourced_cls(self) Data descriptors defined here: prop source sourced_cls   class SourceLinkReader       Methods defined here: serialize_links(self)   class SourceLinkTail       Methods defined here: __init__(self, src, src_cls, qry, mappings) __repr__(self) __str__(self) get_mappings(self) get_query(self) get_source(self) get_sourced_cls(self) label2mapto(self, label) Data descriptors defined here: mappings query source sourced_cls   class SourceMapping       Methods defined here: __init__(self, lbl, mapto) lbl|->mapsto __repr__(self) __str__(self) get_label(self) get_mapsto(self) Data descriptors defined here: label mapsto   class SourceQueryable       Methods defined here: __init__(self, name, prps=None, params=None) __repr__(self) __str__(self) get_name(self) get_param(self, p) get_params(self) get_properties(self) Data descriptors defined here: name parameters properties   class SourceReader       Methods defined here: serialize_sources(self)   class SourcedCls     Essentially a decorator around ClsTemplate objs; adds property fields and storage for source-class-specific mappings.     Methods defined here: __init__(self, cls, trigger, mappings, queries, props=None) get_all_attributes(self) get_attr_prop(self, ap) get_cls(self) get_mappings(self) get_properties(self) get_queries(self) get_query_by_name(self, qname) get_trigger(self) is_valid_attr_prop(self, ap) label2mapto(self, label) Data descriptors defined here: attributes cls mappings properties queries trigger   class SrcClsInterface       Methods defined here: cls_name(self) get_value(self, lbl) set_value(self, lvl, val) source_name(self)