[BioRuby-cvs]
bioruby/lib/bio/io/flatfile bdb.rb, 1.5, 1.6 index.rb,
1.9, 1.10 indexer.rb, 1.17, 1.18
Katayama Toshiaki
k at pub.open-bio.org
Wed Sep 7 21:22:14 EDT 2005
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1.8 dbget.rb, 1.9, 1.10 flatfile.rb, 1.35, 1.36 pubmed.rb,
1.11, 1.12 registry.rb, 1.12, 1.13 sql.rb, 1.2, 1.3
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Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/io/flatfile
Modified Files:
bdb.rb index.rb indexer.rb
Log Message:
* expanded tab at the line head
Index: bdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/bdb.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** bdb.rb 28 Feb 2003 10:29:40 -0000 1.5
--- bdb.rb 8 Sep 2005 01:22:12 -0000 1.6
***************
*** 31,50 ****
module BDBdefault
def permission
! (0666 & (0777 ^ File.umask))
end
module_function :permission
def flag_read
! BDB::RDONLY
end
module_function :flag_read
def flag_write
! (BDB::CREATE | BDB::TRUNCATE)
end
module_function :flag_write
def flag_append
! 'r+'
end
module_function :flag_append
--- 31,50 ----
module BDBdefault
def permission
! (0666 & (0777 ^ File.umask))
end
module_function :permission
def flag_read
! BDB::RDONLY
end
module_function :flag_read
def flag_write
! (BDB::CREATE | BDB::TRUNCATE)
end
module_function :flag_write
def flag_append
! 'r+'
end
module_function :flag_append
***************
*** 53,112 ****
class BDBwrapper
def initialize(name, filename, *arg)
! @dbname = name
! @file = nil
! @filename = filename
! #self.open(*arg)
end
def filename
! File.join(@dbname, @filename)
end
def open(flag = BDBdefault.flag_read,
! permission = BDBdefault.permission)
! unless @file then
! DEBUG.print "BDBwrapper: open #{filename}\n"
! @file = BDB::Btree.open(filename, nil, flag, permission)
! end
! true
end
def close
! if @file
! DEBUG.print "BDBwrapper: close #{filename}\n"
! @file.close
! @file = nil
! end
! nil
end
def [](arg)
! #self.open
! if @file then
! @file[arg]
! else
! nil
! end
end
def []=(key, val)
! #self.open
! @file[key.to_s] = val.to_s
end
def writeback_array(prefix, array, *arg)
! self.close
! self.open(*arg)
! array.each_with_index do |val, key|
! @file["#{prefix}#{key}"] = val.to_s
! end
end
def keys
! if @file then
! @file.keys
! else
! []
! end
end
end #class BDBwrapper
--- 53,112 ----
class BDBwrapper
def initialize(name, filename, *arg)
! @dbname = name
! @file = nil
! @filename = filename
! #self.open(*arg)
end
def filename
! File.join(@dbname, @filename)
end
def open(flag = BDBdefault.flag_read,
! permission = BDBdefault.permission)
! unless @file then
! DEBUG.print "BDBwrapper: open #{filename}\n"
! @file = BDB::Btree.open(filename, nil, flag, permission)
! end
! true
end
def close
! if @file
! DEBUG.print "BDBwrapper: close #{filename}\n"
! @file.close
! @file = nil
! end
! nil
end
def [](arg)
! #self.open
! if @file then
! @file[arg]
! else
! nil
! end
end
def []=(key, val)
! #self.open
! @file[key.to_s] = val.to_s
end
def writeback_array(prefix, array, *arg)
! self.close
! self.open(*arg)
! array.each_with_index do |val, key|
! @file["#{prefix}#{key}"] = val.to_s
! end
end
def keys
! if @file then
! @file.keys
! else
! []
! end
end
end #class BDBwrapper
***************
*** 114,254 ****
module BDB_1
class BDBMappingFile
! def self.open(*arg)
! self.new(*arg)
! end
! def initialize(filename, flag = BDBdefault.flag_read,
! permission = BDBdefault.permission)
! @filename = filename
! @flag = flag
! @permission = permission
! #@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
! end
! attr_reader :filename
! attr_accessor :flag, :permission
! def open
! unless @bdb then
! DEBUG.print "BDBMappingFile: open #{@filename}\n"
! @bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
! true
! else
! nil
! end
! end
! def close
! if @bdb then
! DEBUG.print "BDBMappingFile: close #{@filename}\n"
! @bdb.close
@bdb = nil
! end
! nil
! end
! def records
! @bdb.size
! end
! alias :size :records
! # methods for writing
! def add(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! s << "\t"
! s << val
! val = s
! end
! @bdb[key] = val
! #DEBUG.print "add: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_exclusive(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! raise RuntimeError, "keys must be unique, but key #{key.inspect} already exists"
! end
! @bdb[key] = val
! #DEBUG.print "add_exclusive: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_overwrite(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! DEBUG.print "Warining: overwrote unique id #{key.inspect}\n"
! end
! @bdb[key] = val
! #DEBUG.print "add_overwrite: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_nr(key, val)
! open
! s = @bdb[key]
! if s then
! a = s.split("\t")
! else
! a = []
! end
! a.concat val.to_a
! a.sort!
! a.uniq!
! str = a.join("\t")
! @bdb[key] = str
! #DEBUG.print "add_nr: key=#{key.inspect}, val=#{str.inspect}\n"
! str
! end
!
! # methods for searching
! def search(key)
! open
! s = @bdb[key]
! if s then
! a = s.split("\t")
! a
! else
! []
! end
! end
end #class BDBMappingFile
class PrimaryNameSpace < Template::NameSpace
! def mapping(filename)
! BDBMappingFile.new(filename)
! end
! def filename
! File.join(dbname, "key_#{name}")
! end
! def search(key)
! r = super(key)
! unless r.empty? then
! [ r ]
! else
! r
! end
! end
end #class PrimaryNameSpace
class SecondaryNameSpace < Template::NameSpace
! def mapping(filename)
! BDBMappingFile.new(filename)
! end
! def filename
! File.join(dbname, "id_#{name}")
! end #class SecondaryNameSpaces
! def search(key)
! r = super(key)
! file.close
! r
! end
end #class SecondaryNameSpace
end #module BDB_1
--- 114,254 ----
module BDB_1
class BDBMappingFile
! def self.open(*arg)
! self.new(*arg)
! end
! def initialize(filename, flag = BDBdefault.flag_read,
! permission = BDBdefault.permission)
! @filename = filename
! @flag = flag
! @permission = permission
! #@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
! end
! attr_reader :filename
! attr_accessor :flag, :permission
! def open
! unless @bdb then
! DEBUG.print "BDBMappingFile: open #{@filename}\n"
! @bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
! true
! else
! nil
! end
! end
! def close
! if @bdb then
! DEBUG.print "BDBMappingFile: close #{@filename}\n"
! @bdb.close
@bdb = nil
! end
! nil
! end
! def records
! @bdb.size
! end
! alias :size :records
! # methods for writing
! def add(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! s << "\t"
! s << val
! val = s
! end
! @bdb[key] = val
! #DEBUG.print "add: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_exclusive(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! raise RuntimeError, "keys must be unique, but key #{key.inspect} already exists"
! end
! @bdb[key] = val
! #DEBUG.print "add_exclusive: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_overwrite(key, val)
! open
! val = val.to_a.join("\t")
! s = @bdb[key]
! if s then
! DEBUG.print "Warining: overwrote unique id #{key.inspect}\n"
! end
! @bdb[key] = val
! #DEBUG.print "add_overwrite: key=#{key.inspect}, val=#{val.inspect}\n"
! val
! end
! def add_nr(key, val)
! open
! s = @bdb[key]
! if s then
! a = s.split("\t")
! else
! a = []
! end
! a.concat val.to_a
! a.sort!
! a.uniq!
! str = a.join("\t")
! @bdb[key] = str
! #DEBUG.print "add_nr: key=#{key.inspect}, val=#{str.inspect}\n"
! str
! end
!
! # methods for searching
! def search(key)
! open
! s = @bdb[key]
! if s then
! a = s.split("\t")
! a
! else
! []
! end
! end
end #class BDBMappingFile
class PrimaryNameSpace < Template::NameSpace
! def mapping(filename)
! BDBMappingFile.new(filename)
! end
! def filename
! File.join(dbname, "key_#{name}")
! end
! def search(key)
! r = super(key)
! unless r.empty? then
! [ r ]
! else
! r
! end
! end
end #class PrimaryNameSpace
class SecondaryNameSpace < Template::NameSpace
! def mapping(filename)
! BDBMappingFile.new(filename)
! end
! def filename
! File.join(dbname, "id_#{name}")
! end #class SecondaryNameSpaces
! def search(key)
! r = super(key)
! file.close
! r
! end
end #class SecondaryNameSpace
end #module BDB_1
Index: index.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/index.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** index.rb 27 Aug 2003 17:25:21 -0000 1.9
--- index.rb 8 Sep 2005 01:22:12 -0000 1.10
***************
*** 50,56 ****
def closed?
if @db then
! false
else
! true
end
end
--- 50,56 ----
def closed?
if @db then
[...1963 lines suppressed...]
! else
! n2 = names
! p = nil
! end
! s = secondary.search_names(key, *n2)
! s.push p if p
! s.sort!
! s.uniq!
! s
end
def search_namespaces(key, *names)
! s = search_namespaces_get_unique_id(key, *names)
! search_primary(*s)
end
def check_consistency
! fileids.check_all
end
end #class DataBank
Index: indexer.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/indexer.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** indexer.rb 27 Aug 2003 17:25:21 -0000 1.17
--- indexer.rb 8 Sep 2005 01:22:12 -0000 1.18
***************
*** 27,702 ****
class NameSpace
! def initialize(name, method)
! @name = name
! @proc = method
! end
! attr_reader :name, :proc
end #class NameSpace
class NameSpaces < Hash
[...1427 lines suppressed...]
! Indexer::makeindexFlat(dbname, parser, options, *files)
end
end #def makeindex
***************
*** 752,758 ****
def self.update_index(dbname, format, options, *files)
if format then
! parser = Indexer::Parser.new(dbclass)
else
! parser = nil
end
Indexer::update_index(dbname, parser, options, *files)
--- 752,758 ----
def self.update_index(dbname, format, options, *files)
if format then
! parser = Indexer::Parser.new(dbclass)
else
! parser = nil
end
Indexer::update_index(dbname, parser, options, *files)
- Previous message: [BioRuby-cvs] bioruby/lib/bio/io brdb.rb, 1.2, 1.3 das.rb, 1.7,
1.8 dbget.rb, 1.9, 1.10 flatfile.rb, 1.35, 1.36 pubmed.rb,
1.11, 1.12 registry.rb, 1.12, 1.13 sql.rb, 1.2, 1.3
- Next message: [BioRuby-cvs] bioruby/lib/bio/util sirna.rb,1.3,1.4
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