20101122-debug-import_gkv

1. Confirm the error

Goal

• Debug import_gkv / 100%

Milestones

1. Confirm the error
   • Traceback the error message

Summary

• http://masay.ch/2010/11/22/debug-import_gkv-2/

Commits

ToDo Tomorrow

Keep in Mind

1. A bug import_gkv Tue Nov 16 02:00:10 2010: de.oddb.org Zubef (PDF)
2. Compression (refer to lib/oddb/export/server.rb), Test cases (grant_download, Logging, Reporting)
3. Log Error: on production server, de.oddb.org/log/import_dimdi, import_pharmnet
4. On Ice
5. emerge --sync

Confirm the error

Tue Nov 16 14:40:39 2010: de.oddb.org Zubef (PDF)

Tue Nov 16 14:40:35 2010: de.oddb.org ODDB::Import::Gkv#import
NoMethodError
undefined method `[]' for nil:NilClass
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:146:in `scan_object_stream'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:137:in `build_object_catalogue'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:134:in `each'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:134:in `build_object_catalogue'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:47:in `object_catalogue'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:160:in `page_tree_root'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:142:in `build_page_tree'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:50:in `page_tree'
/usr/lib64/ruby/site_ruby/1.8/rpdf2txt/parser.rb:40:in `extract_text'
/var/www/de.oddb.org/lib/oddb/import/gkv.rb:96:in `import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:110:in `reported_import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:117:in `call'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:117:in `_reported_import'
/var/www/de.oddb.org/lib/oddb/util/updater.rb:110: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'
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'
jobs/import_gkv:15
Imported     0 Zubef-Entries on 16.11.2010:
Visited      0 existing Zubef-Entries
Visited      0 existing Companies
Visited      0 existing Substances
Created      0 new Zubef-Entries
Created      0 new Products
Created      0 new Sequences
Created      0 new Companies
Created      0 new Substances
Assigned     0 Chemical Equivalences
Assigned     0 Companies
Created      0 Incomplete Packages:
Created      0 Product(s) without a name (missing product name):

Confirm the same error locally

Run de.oddb.org/bin/oddbd

Run jobs/import_gkv

Result