20110106-setup-oddb_org-windows

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1. Install gd2 on Windows7 suspend
2. Install de.oddb on Windows7 suspend
3. Check difference between rkj-character-encodings (0.4.1) and character-encodings (0.4.1)

Goal

• Setup oddb.org on Windows7 / 70%

Milestones

1. Install gd2

Summary

• http://masay.ch/2011/01/06/setup-oddb_org-windows/

Commits

ToDo Tomorrow

Keep in Mind

1. swissmedic_followers debug
2. On Ice
3. emerge --sync

Install gd2 on Windows7

Reference

• trying to install gd2-1.1.1 (and turing) in windows with rubygems - ruby 1.8.7

Install de.oddb on Windows7

Reference

• Installing de.oddb on Windows via Rubygems

I got the same

C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/util/known_user.rb:19:in `initialize': invalid encoding ("utf8", "la
tin1") (Iconv::InvalidEncoding)
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/util/known_user.rb:19:in `new'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/util/known_user.rb:19
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/util/server.rb:4
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/util.rb:9
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/bin/oddbd:11
        from C:/Ruby186/bin/oddbd:19:in `load'
        from C:/Ruby186/bin/oddbd:19

• Download data from de.oddb server (save it in home dir)
• Import
  1. [Start Menu] -> [PostgreSQL 8.4] -> [pgAdmin III]
  2. Create database: oddb
  3. Create login role: oddb (passwd: oddb)
  4. [Start Menu] -> [PostgreSQL 8.4] -> [SQL Shell (psql)]
  5. \cd [home dir]
  6. \i [oddb sql] (import a sql file)

Run oddbd (de.oddb)

• 'utf8 latin1' error

Set PATH for postgresql commands

• [Computer] (right click) -> [Eigenschaften] -> [Erweiterte Systemeistellung] -> [Umgebungsvariablen]
• Add 'C:\Program Files (x86)\PostgreSQL\8.4\bin;' to PATH

 C:\Ruby186\bin;C:\Program Files (x86)\Vim\vim73\;C:\Program Files (x86)\PostgreSQL\8.4\bin;

Install devkit

Reference

• http://rubyinstaller.org/downloads/
• http://github.com/downloads/oneclick/rubyinstaller/DevKit-tdm-32-4.5.1-20101214-1400-sfx.exe
• https://github.com/oneclick/rubyinstaller/wiki/development-kit

Then

• I can use make, gcc, etc.

I can also create a database by using 'createdb' command

 createdb -U oddb -E utf8 -T template0 oddb

Install libIconv for Windows

• http://gnuwin32.sourceforge.net/packages/libiconv.htm
• http://gnuwin32.sourceforge.net/downlinks/libiconv.php

Set PATH

 C:\Ruby186\bin;C:\Program Files (x86)\Vim\vim73\;C:\Program Files (x86)\PostgreSQL\8.4\bin;C:\mingw\bin;C:\mingw\mingw\bin;C:\Program Files (x86)\GnuWin32\bin;

Iconv test

C:\Users\masa>type test.rb

require 'iconv'

#i = Iconv.new('utf8','latin1')
i = Iconv.new('UTF-8','LATIN1')
p i

Result

C:\Users\masa>ruby test.rb
#<Iconv:0x42868c8>

Note

• It works
• The names of encode depends on a platform (OS)

Experiment

C:\Users\masa>vim C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/util/known_user.rb

  #@@iconv = Iconv.new('utf8', 'latin1')
  @@iconv = Iconv.new('UTF-8', 'LATIN1')

Run oddbd

C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require': no such file to load -- htmlgrid/divtem
plate (LoadError)
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/view/template.rb:4
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/view/drugs/template.rb:4
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/view/drugs/init.rb:4
         ... 13 levels...
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/bin/oddbd:11
        from C:/Ruby186/bin/oddbd:19:in `load'
        from C:/Ruby186/bin/oddbd:19

Note

• The 'utf8 latin' error has gone
• This code can also run on Linux (Gentoo, Funtoo)

Install

• htmlgrid (gem)
• fastercsv (gem)

Run oddbd

C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require': C:/Ruby186/lib/ruby/gems/1.8/gems/de.od
db-2.0.0/lib/oddb/import/pharmnet.rb:556: undefined (?...) sequence: /(?<!nicht )akzeptieren/ (SyntaxError)
C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/import/pharmnet.rb:788: undefined (?...) sequence: /^(?<name>.*?)\s*-\s*O
P((?<size>\d+)|\((?<multi>\d+)x(?<size>\d+)\))(\((?<unit>[^)]+)\))?$/
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/state/drugs/admin/package.rb:6
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/state/viral/admin.rb:4
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/state/login.rb:4
         ... 16 levels...
        from C:/Ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
        from C:/Ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/bin/oddbd:11
        from C:/Ruby186/bin/oddbd:19:in `load'
        from C:/Ruby186/bin/oddbd:19

Note

• This is the oniguruma problem

Check Ruby version

C:\Users\masa>ruby -v
ruby 1.8.6 (2010-02-04 patchlevel 398) [i386-mingw32]

Install win-bash

• http://win-bash.sourceforge.net/
• http://sourceforge.net/projects/win-bash/files/win-bash/0.6/win-bash.exe/download

Put win-bash.exe in the directory of PATH (anywere)

• Then we can use bash commands from dos prompt

Install patch for windows

• http://gnuwin32.sourceforge.net/packages/patch.htm
• http://gnuwin32.sourceforge.net/downlinks/patch.php

Install tar for windows

• http://gnuwin32.sourceforge.net/packages/gtar.htm
• http://gnuwin32.sourceforge.net/downlinks/tar-bin.php

Install gzip for windows

• http://gnuwin32.sourceforge.net/packages/gzip.htm
• http://gnuwin32.sourceforge.net/downlinks/gzip.php

Install Ruby 1.8.6 with oniguruma patch

• Ruby source code: ftp://ftp.fu-berlin.de/unix/languages/ruby/1.8/ruby-1.8.6-p369.tar.gz
• Oniguruma patch: http://dev.ywesee.com/uploads/$PageName//oniguruma_patch_for_ruby-1.8.6_p369.20100615_from_Hannes-san.tar.gz

Reference

• http://dev.ywesee.com/wiki.php/Masa/20100907-install-ruby

Result

• make error

ruby.c: In function 'ruby_init_loadpath':
ruby.c:318:42: warning: universal character names are only valid in C++ and C99
ruby.c:318:42: error: incomplete universal character name \U
ruby.c:318:42: warning: unknown escape sequence: '\m'
ruby.c:318:42: warning: unknown escape sequence: '\w'
ruby.c:322:45: warning: universal character names are only valid in C++ and C99
ruby.c:322:45: error: incomplete universal character name \U
ruby.c:322:45: warning: unknown escape sequence: '\m'
ruby.c:322:45: warning: unknown escape sequence: '\w'
ruby.c:323:41: warning: universal character names are only valid in C++ and C99
ruby.c:323:41: error: incomplete universal character name \U
ruby.c:323:41: warning: unknown escape sequence: '\m'
ruby.c:323:41: warning: unknown escape sequence: '\w'
make: *** [ruby.o] Error 1

Install Ruby 1.8.6 with oniguruma patch on Cygwin

• Success

Install de.oddb through gem

1. de.oddb
2. rclconf
3. facets (-v=1.8.54)
4. odba
5. pg (-v=0.9.0)
6. dbd-pg
   • dbi
   • deprecated
7. sbsm
8. mod: /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/util/known_user.rb

 #@@iconv = Iconv.new('utf8', 'latin1')
 @@iconv = Iconv.new('UTF-8', 'LATIN1')

1. htmlgrid
2. fastercsv
3. htmlentities
4. mechanize
   • nokogiri

• Error when mechanize is installed

$ ./gem install mechanize
Fetching: nokogiri-1.4.4.gem (100%)
Building native extensions.  This could take a while...
ERROR:  Error installing mechanize:
        ERROR: Failed to build gem native extension.

/cygdrive/c/Users/masa/ruby186/bin/ruby.exe extconf.rb
checking for #include <libxml/parser.h>
... no
-----
libxml2 is missing.  please visit http://nokogiri.org/tutorials/installing_nokogiri.html for help with installing dependencies.
-----

Install libxml2, libxml2-devel and libxsl, libxsl-devel through cygwin setup.exe

Install openssl, openssl-devel through cygwin

Error

/cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `gem_original_require': no such file to load --
openssl (LoadError)
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/1.8/net/https.rb:102
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `gem_original_require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/gems/1.8/gems/mechanize-1.0.0/lib/mechanize.rb:2
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:34:in `gem_original_require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:34:in `require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/import/pharmnet.rb:6
         ... 25 levels...
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/bin/oddbd:11
        from /usr/bin/oddbd:19:in `load'
        from /usr/bin/oddbd:19

Note

• 'openssl' is a standard library for Ruby 1.8.6
• I guess openssl and openssl-devel libraries should be installed before compiling Ruby

Re-conpile Ruby

• Then the openssl error has gone

Error

/cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `gem_original_require': no such file to load -
- encoding/character/utf-8 (LoadError)
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/import/importer.rb:1
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `gem_original_require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/import/pharmnet.rb:7
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `gem_original_require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/lib/oddb/html/state/drugs/admin/package.rb:6
         ... 22 levels...
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:29:in `require'
        from /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/de.oddb-2.0.0/bin/oddbd:11
        from /usr/bin/oddbd:19:in `load'
        from /usr/bin/oddbd:19

Install character-encodings

make
gcc -I. -I/cygdrive/c/Users/masa/ruby186_2/lib/ruby/1.8/i386-cygwin -I/cygdrive/c/Users/masa/ruby186_2/lib/ruby/1.8/i386-cygwin -I. -DH
AVE_ASSERT_H -DHAVE_LIMITS_H -DHAVE_LOCALE_H -DHAVE_STDBOOL_H -DHAVE_STDDEF_H -DHAVE_STDINT_H -DHAVE_STDIO_H -DHAVE_STDLIB_H -DHAVE_STR
ING_H -DHAVE_SYS_TYPES_H -DHAVE_WCHAR_H   -g -O2  -std=c99 -finline-functions -Wall -Wextra -Wwrite-strings -Waggregate-return -Wmissin
g-prototypes -Wmissing-declarations -Wnested-externs -Wundef -Wpointer-arith -Wcast-align -Werror -Winline  -c break.c
gcc -I. -I/cygdrive/c/Users/masa/ruby186_2/lib/ruby/1.8/i386-cygwin -I/cygdrive/c/Users/masa/ruby186_2/lib/ruby/1.8/i386-cygwin -I. -DH
AVE_ASSERT_H -DHAVE_LIMITS_H -DHAVE_LOCALE_H -DHAVE_STDBOOL_H -DHAVE_STDDEF_H -DHAVE_STDINT_H -DHAVE_STDIO_H -DHAVE_STDLIB_H -DHAVE_STR
ING_H -DHAVE_SYS_TYPES_H -DHAVE_WCHAR_H   -g -O2  -std=c99 -finline-functions -Wall -Wextra -Wwrite-strings -Waggregate-return -Wmissin
g-prototypes -Wmissing-declarations -Wnested-externs -Wundef -Wpointer-arith -Wcast-align -Werror -Winline  -c decompose.c
decompose.c: In function `_utf_normalize_wc':
decompose.c:410: Warnung: Sichtbarkeitsattribute werden in dieser Konfiguration nicht unterst"utzt; ignoriert
make: *** [decompose.o] Fehler 1


Gem files will remain installed in /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/character-encodings-0.4.1 for inspection.
Results logged to /cygdrive/c/Users/masa/ruby186_2/lib/ruby/gems/1.8/gems/character-encodings-0.4.1/ext/encoding/character/utf-8/gem_ma
ke.out

Note

• This is what we got before

suspend

Check difference between rkj-character-encodings (0.4.1) and character-encodings (0.4.1)

Install character-encodings and rkj-character-encodings

masa@masa ~/work $ gem search character-encoding 

*** LOCAL GEMS ***

character-encodings (0.4.1)
rkj-character-encodings (0.4.1)

sample

require 'encoding/character/utf-8'
str = u"hëllö"
p str.length
  #=> 5
p str.reverse.length
  #=> 5
p str[/ël/]
  #=> "ël"

Reference

• http://stackoverflow.com/questions/3818518/encoding-in-ruby-1-8-7-or-1-9-2