Module Hierarchy

• Pyblio: A framework for manipulating bibliographic databases.
  • Adapter: Adapt a database schema to another one.
  • Adapters
    • PubMed2BibTeX
  • Arrays: Result sets and indexes implemented on top of numpy arrays.
  • Attribute: Basic data types that can be used as attributes for a Record.
  • Callback: A generic callback mechanism.
  • Cite
    • Citator: Defines the Citator, a class that glues together every aspect related to citations.
    • Style
      • Base: Generate citation keys.
      • BibTeX
    • WP: This module contains bindings for specific Word Processors.
      • File: A convenience object to write citations to a plain file.
      • LyX: Operations on a running LyX instance.
      • OpenOffice: A simple API to cite references in OpenOffice.org
  • Exceptions: This module defines some common exceptions
  • External: Support for queries on external services.
    • CrossRef: An asynchronous query module to get DOI numbers given publication information.
    • HTTP
    • PubMed: Programmatic access to the PubMed database
    • WOK: Interface to ISI Web of Knowledge.
  • Format: Citation formatting layer.
    • Base: (Base classes of the formatting code)
    • Date: Date formatting functions.
    • DSL: Basic syntactic elements used to format a citation.
    • Generator: A base generator, specialized for every output style.
    • HTML: Transformation of the formatted record into an HTML representation.
    • Misc: Miscellanous formatting helpers.
    • OpenOffice
    • Pages
    • Person
    • S2: (Data structures for stage 2 of the formatter)
    • S3: (Stage 3 objects, ie abstract representation of the actual layout)
    • Text: Transformation of the formatted record into a textual representation.
  • I18n: Useful tools related to internationalization issues.
  • Parsers: Bibliographic database parsers for foreign formats.
    • Protocol: Protocol definition for importing or exporting data from alien file formats.
    • Semantic: Parsers for bibliographic formats and specific schemas.
      • BibTeX
      • PubMed: Parser for the XML format returned by PubMed's Web API
      • WOK
    • Syntax: Syntactic parsers for bibliographic formats.
      • BibTeX: Extension module for BibTeX files
        • Coding: Handles coding and decoding of LaTeX-escaped characters.
        • Environ: Handles decoding of @string substitution and of LaTeX commands.
        • Parser: Stream oriented reading of a BibTeX file, with no actual semantic operation on the content.
      • ISI
      • RIS
      • Tagged
      • XMLEndNote
      • XMLMARC
  • Query: Definition of the query language.
  • Registry: Support for RIP files.
  • Schema: Schema definition for a pyblio database.
  • Sort: Definition of the sort language.
  • Store: Contains the base classes and interfaces used to define a database of records.
  • Stores: Available physical stores.
    • bsddbstore: Store implementation on top of Berkeley DB (>= 4.1)
    • filestore: Provides an in-memory store, which can read and save the database in Pyblio's XML format.
    • memorystore: Provides an UNSAVED in-memory store.
  • Tools

Class Hierarchy

• Pyblio.Callback.WeakMethodBound: A weak reference on a bound method
• Pyblio.Callback.WeakMethodFree: A weak reference on an unbound method
• Pyblio.Cite.WP.IWordProcessor: Interface a WordProcessor object should provide
• Pyblio.Parsers.Syntax.BibTeX.Parser.IBibTeX
• __builtin__.object: The most base type
  • Pyblio.Schema.Attribute
    • Pyblio.Schema.TxoAttribute
  • __builtin__.basestring: Type basestring cannot be instantiated; it is the base for str and unicode.
    • __builtin__.str: str(object) -> string
      • Pyblio.Attribute.URL: An URL
    • __builtin__.unicode: unicode(string [, encoding[, errors]]) -> object
      • Pyblio.Parsers.Syntax.BibTeX.Parser.Comment: A bibtex file comment
        • Pyblio.Parsers.Syntax.BibTeX.Parser.ATComment
      • Pyblio.Attribute.ID: An external identifier
      • Pyblio.Attribute.Text: Textual data
      • Pyblio.Parsers.Syntax.BibTeX.Parser.Text
  • Pyblio.Parsers.Syntax.BibTeX.Parser.Block: A textual block, as a sequence of text and commands
  • Pyblio.Parsers.Syntax.BibTeX.Parser.Cache
  • Pyblio.Cite.Citator.Citator
  • Pyblio.Parsers.Syntax.BibTeX.Parser.Cmd: A LaTeX \-command
  • Pyblio.Parsers.Syntax.BibTeX.Parser.Context
  • Pyblio.Store.Database: A bibliographic database.
    • Pyblio.Adapter.Adapter: This class is a db built on top of another db, which behaves as if it were of a different schema.
      • Pyblio.Adapter.OneToOneAdapter: This adapter assumes a one-to-one mapping between the source and the target databases.
        • Pyblio.Adapters.PubMed2BibTeX.PubMed2BibTeX
    • Pyblio.Stores.bsddbstore.Database: A Pyblio database stored in a Berkeley DB engine
    • Pyblio.Stores.filestore.Database
  • __builtin__.dict: dict() -> new empty dictionary.
    • Pyblio.Store.Record: A database record.
    • Pyblio.Stores.filestore.ResultSet
    • Pyblio.Stores.bsddbstore.ResultSetStore
    • Pyblio.Stores.filestore.ResultSetStore
    • Pyblio.Schema.Schema
    • Pyblio.Schema.TxoGroup
  • Pyblio.External.CrossRef.DOIQuery: Query DOI numbers.
  • Pyblio.Parsers.Syntax.BibTeX.Environ.Environ
    • Pyblio.Parsers.Syntax.BibTeX.Environ
  • Pyblio.Cite.WP.File.File
  • Pyblio.Format.Generator.Generator
    • Pyblio.Format.HTML.Generator
    • Pyblio.Format.OpenOffice.Generator: Returns an object capable of transforming an abstract representation of text into actual text in OpenOffice.
    • Pyblio.Format.Text.Generator
  • Pyblio.Format.DSL.Glue: A base class that known how to join together multiple fragments of DSL code.
    • Pyblio.Format.DSL.i18n: Translatable content.
    • Pyblio.Format.DSL.switch: The switch operator helps in bringing together multiple citation parts, according to the value of a Txo.
  • __builtin__.int: int(x[, base]) -> integer
    • Pyblio.Store.Key: A key that uniquely identifies a record in a database.
  • protocols.interfaces.Interface
    • Pyblio.Parsers.Protocol.IReader
    • Pyblio.Parsers.Protocol.IWriter
  • Pyblio.Format.S2.Join
  • Pyblio.Arrays.KeyArray: A growing array of Pyblio keys.
  • __builtin__.list: list() -> new list list(sequence) -> new list initialized from sequence's items
    • Pyblio.Parsers.Syntax.BibTeX.Parser.Join: A value, as a concatenation of blocks
  • Pyblio.I18n.Localize: Select a translation among a set of possible values
  • Pyblio.Cite.WP.LyX.LyX
  • Pyblio.Cite.WP.OpenOffice.OOo
  • Pyblio.Format.S2.Or
  • Pyblio.Parsers.Syntax.Tagged.Parser: Generic Parser for 'tagged' records, to be derived by actual parsers.
    • Pyblio.Parsers.Syntax.ISI.ISIParser: This parser knows how to split ISI records in fields
    • Pyblio.Parsers.Syntax.RIS.RISParser: This parser knows how to split RIS records in fields
  • Pyblio.Callback.Publisher: Base class for objects that wish to emit signals to registered clients.
    • Pyblio.Stores.bsddbstore.Database: A Pyblio database stored in a Berkeley DB engine
    • Pyblio.Stores.filestore.Database
    • Pyblio.Parsers.Syntax.Tagged.Reader
      • Pyblio.Parsers.Syntax.ISI.Reader: The importer knows how to map the RIS fields to the 'standard' pyblio model.
      • Pyblio.Parsers.Syntax.RIS.Reader: The importer knows how to map the RIS fields to the 'standard' pyblio model.
    • Pyblio.Stores.bsddbstore.ResultSet
    • Pyblio.Stores.filestore.ResultSet
    • Pyblio.Stores.bsddbstore.ResultSetStore
    • Pyblio.Stores.filestore.RODict: Read-only dictionnary
    • Pyblio.Stores.bsddbstore.RSDB: Virtual result set that loops over the full database
    • Pyblio.Stores.bsddbstore.View
    • Pyblio.Stores.filestore.View
  • Pyblio.External.PubMed.PubMed: A connection to the PubMed database
  • Pyblio.Query.Queryable: A mixin that provides an (one day optimized) query engine to a store
    • Pyblio.Stores.bsddbstore.Database: A Pyblio database stored in a Berkeley DB engine
    • Pyblio.Stores.filestore.Database
  • Pyblio.Parsers.Semantic.PubMed.Reader: Parse records as returned by PubMed's web service.
  • Pyblio.Parsers.Semantic.WOK.Reader: Parse records as returned by Web of Science's web service.
  • Pyblio.Parsers.Syntax.BibTeX.Reader
    • Pyblio.Parsers.Semantic.BibTeX.Reader: Default BibTeX parser.
  • Pyblio.Parsers.Syntax.XMLEndNote.Reader
  • Pyblio.Parsers.Syntax.XMLMARC.Reader
    • Pyblio.Parsers.Syntax.XMLMARC.SimpleReader
  • Pyblio.Parsers.Syntax.BibTeX.Parser.Record
  • Pyblio.Store.ResultSet: A set of keys from the database.
    • Pyblio.Stores.bsddbstore.ResultSet
    • Pyblio.Stores.filestore.ResultSet
  • Pyblio.Store.ResultSetStore: Interface to the stored result sets.
    • Pyblio.Stores.bsddbstore.ResultSetStore
    • Pyblio.Stores.filestore.ResultSetStore
  • Pyblio.Registry.RIP: A RIP object represents a dynamic class that can be loaded on demand, and that has been registered via the Registry system.
    • Pyblio.Registry.AdapterRIP: A special RIP that keeps the description of an Adapter.
  • Pyblio.Format.S2.Sum
  • Pyblio.Format.S2.Switch
  • Pyblio.Format.S3.Tag
  • Pyblio.Format.S2.Text
  • Pyblio.Schema.TxoItem: Definition of a taxonomy item.
  • __builtin__.type: type(object) -> the object's type type(name, bases, dict) -> a new type
    • protocols.interfaces.AbstractBaseMeta: Metaclass for 'AbstractBase' - a protocol that's also a class
      • protocols.interfaces.InterfaceClass: Metaclass for 'Interface' - a non-instantiable protocol
  • Pyblio.Cite.Style.Base.Unambiguous: Base class to handle caching of generated keys.
    • Pyblio.Cite.Style.Base.Alpha: Base class to add a disambiguation letter after generated keys that clash with already generated ones.
      • Pyblio.Cite.Style.BibTeX.AlphaKey: Generate keys based on authors and year.
    • Pyblio.Cite.Style.Base.Numeric: Return a numeric key for documents, in the order in which they are requested.
  • Pyblio.Store.View: A view of a Result Set represents the Result Set sorted according to a specific criterion.
    • Pyblio.Stores.bsddbstore.View
  • Pyblio.Stores.filestore.Viewable
    • Pyblio.Stores.filestore.ResultSet
    • Pyblio.Stores.filestore.RODict: Read-only dictionnary
  • Pyblio.External.WOK.WOK: I represent a query session on the Web of Knowledge.
  • Pyblio.Parsers.Syntax.BibTeX.Writer
    • Pyblio.Parsers.Semantic.BibTeX.Writer
  • Pyblio.Parsers.Syntax.XMLEndNote.Writer
  • Pyblio.Parsers.Syntax.XMLMARC.Writer
• exceptions.Exception: Common base class for all exceptions.
  • Pyblio.Exceptions.AdaptError: Raised when an external query failed.
  • Pyblio.Cite.WP.CommunicationError: Raised when an error occurs on the link between pyblio and the word processor.
  • Pyblio.Exceptions.ConstraintError
  • Pyblio.Parsers.Syntax.BibTeX.Parser.EndOfFile
  • Pyblio.Exceptions.InvalidQuery: Raised if an ill-typed query is attempted
  • Pyblio.Cite.WP.OperationError: Raised when the requested operation on the IWordProcessor cannot be completed.
  • Pyblio.Exceptions.ParserError
  • Pyblio.Exceptions.QueryError: Raised when an external query failed.
  • Pyblio.Exceptions.SchemaError
  • Pyblio.Schema.SchemaError
  • exceptions.StandardError: Base class for all standard Python exceptions.
    • exceptions.LookupError: Base class for lookup errors.
      • exceptions.KeyError: Mapping key not found.
        • Pyblio.Format.Base.Missing: This error is raised when a specific attribute is missing.
  • Pyblio.Store.StoreError: Generic error occuring while accessing a database storage
  • Pyblio.Callback.WeakError: Invoked when a function call is performed on a destroyed method
• protocols.interfaces.Protocol: Generic protocol w/type-based adapter registry
  • protocols.interfaces.AbstractBaseMeta: Metaclass for 'AbstractBase' - a protocol that's also a class
    • protocols.interfaces.InterfaceClass: Metaclass for 'Interface' - a non-instantiable protocol
• twisted.internet.protocol.Factory: This is a factory which produces protocols.
  • twisted.internet.protocol.ClientFactory: A Protocol factory for clients.
    • twisted.web.client.HTTPClientFactory: Download a given URL.
      • Pyblio.External.HTTP.HTTPRetrieve: Cancellable HTTP client.