20110114-setup-de_oddb_org-on-ubuntu

<< | 2011 | >>

1. warning when emerge --sync
2. Debug import_gkv

Goal

• Set up de.oddb.org on Windows7 / 80%

Milestones

1. Debug import_gkv
2. Virtual Host setting on Win
3. Set up de.oddb.org on Win through gem
4. Confirm de.oddb.org running on Win

Summary

Commits

ToDo Tomorrow

Keep in Mind

1. emerge portage warning
2. On Ice
3. emerge --sync

warning when emerge --sync

When I run 'emerge --sync' the following warning comes

Performing Global Updates: /usr/portage/profiles/updates/1Q-2011
(Could take a couple of minutes if you have a lot of binary packages.)
  .='update pass'  *='binary update'  #='/var/db update'  @='/var/db move'
  s='/var/db SLOT move'  %='binary move'  S='binary SLOT move'
  p='update /etc/portage/package.*'
....



 * An update to portage is available. It is _highly_ recommended
 * that you update portage now, before any other packages are updated.

 * To update portage, run 'emerge portage' now.

masa@masa ~ $ sudo emerge portage
Passwort: 
Calculating dependencies... done!

>>> Verifying ebuild manifests

!!! A file listed in the Manifest could not be found: /usr/portage/sys-apps/portage/portage-9999.ebuild

Note

• An error comes when 'emerge portage'

Debug import_gkv

• Email Fri Jan 14 02:06:34 2011: de.oddb.org Zubef (PDF)

Fri Jan 14 02:00:06 2011: de.oddb.org ODDB::Import::Gkv#import
NoMethodError
private method `gsub' called for nil:NilClass
/var/www/de.oddb.org/lib/oddb/util/multilingual.rb:60:in `all'
/var/www/de.oddb.org/lib/oddb/util/multilingual.rb:60:in `collect'
/var/www/de.oddb.org/lib/oddb/util/multilingual.rb:60:in `all'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:175:in `import_active_agent'
/var/www/de.oddb.org/lib/oddb/util/multilingual.rb:60:in `find'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:174:in `each'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:174:in `find'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:174:in `import_active_agent'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:160:in `import_row'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:458:in `process_page'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:457:in `each'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:457:in `process_page'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:40:in `call'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:40:in `send_page'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:42:in `extract_text'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/object.rb:479:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/object.rb:442:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/object.rb:479:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/object.rb:478:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/object.rb:463:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:40:in `extract_text'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:100:in `import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:106:in `reported_import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:113:in `call'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:113:in `_reported_import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:106:in `reported_import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:58:in `import_gkv'
/usr/lib64/ruby/1.8/open-uri.rb:32:in `open_uri_original_open'
/usr/lib64/ruby/1.8/open-uri.rb:32:in `open'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:77:in `download_latest'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:57:in `import_gkv'
/var/www/de.oddb.org/jobs/import_gkv:16
/var/www/de.oddb.org/lib/oddb/util/job.rb:16:in `call'
/var/www/de.oddb.org/lib/oddb/util/job.rb:16:in `run'
/var/www/de.oddb.org/jobs/import_gkv:15
Imported   191 Zubef-Entries on 14.01.2011:
Visited    191 existing Zubef-Entries
Visited     13 existing Companies
Visited      8 existing Substances
Created      0 new Zubef-Entries
Created      0 new Products
Created      0 new Sequences
Created    178 new Companies
Created    179 new Substances
Assigned     0 Chemical Equivalences
Assigned     0 Companies
Created      0 Incomplete Packages:
Created      0 Product(s) without a name (missing product name):