20120229-check-data-float-error-fix-updating-atc_code-email-testenvironment-check-job-mail-oddb_org

<< Masa.20120301-fix-errors-oddb_org | Index | Masa.20120228-check-accessor-Package-Registration-check-parallel-runs-oddb_org >>

1. Fix updating ATC-Code oddb.org
2. Check job script sending email process oddb.org
3. Check error log oddb.org

Commits

• ATC-Code and testenvironment
  1. Fix updating ATC-Code in admin sequence view (oddb.org)
  2. All accessor check processes / update processes should accept nil object and nil data (oddb.org)
  3. Fix ATC-Request email for testenvironment1.rb, and pointer address in the email (oddb.org)
  4. Added testenvironment1.rb and 2 in test dir, and load them in etc/oddb.yaml (oddb.org)
  5. Added testenvironment1 and 2 to src/config.rb (oddb.org)
• Fix errors from log
  1. Fix data corruption error. NoMethodError undefined method values for H* :String at src/model/sequence.rb:257 (oddb.org)
  2. Fix data floating error. NoMethodError undefined method has_ddd? for #<Array:0x0000001a890110> at src/model/package.rb:207' (oddb.org)
  3. Fix NoMethodError undefined method pointer for ODDB::State::Drugs::PriceHistory::PriceChanges at src/view/analysis/limitationtext.rb:35 (oddb.org)
  4. Fix NoMethodError undefined method fr for ODDB::Analysis::Group at src/view/analysis/limitationtext.rb:19 (oddb.org)
  5. Fix NoMethodError undefined method gsub for ODDB::PatinfoDocument2001 at src/view/analysis/limitationtext.rb:20 (oddb.org)
  6. Fix NoMethodError undefined method registration for st_pharmacode:String at src/model/package.rb:38 (oddb.org)
  7. Fix NoMethodError undefined method registration for String at src/model/package.rb:29 (oddb.org)
  8. Fix NoMethodError undefined method dt for name:String at src/view additional_information.rb:101 (oddb.org)
  9. Fix NoMethodError undefined method galenic_group for String at src/model/composition.rb:57 (oddb.org)
  10. Fix NoMethodError undefined method galenic_group for name:String at src/model/galenicform.rb:18 (oddb.org)
  11. Fix NoMethodError undefined method sort for \:String at src/model/composition.rb:100 (oddb.org)
  12. Fix NoMethodError undefined method de for class:String at src/view/admin/registration.rb:55 (oddb.org)
  13. Fix NoMethodError undefined method company for >:String at src/model/sequence.rb:24 (oddb.org)
  14. Fix NoMethodError undefined method limitation for :String at src/model/package.rb:300 (oddb.org)
  15. Fix NoMethodError undefined method de for String at src/util/resultsort.rb:49 (oddb.org)
  16. Fix NoMethodError undefined method interval for ODDB::State::Drugs::Result at src/view/alphaheader.rb:13 (oddb.org)
  17. Fix TypeError can't convert String into Array at src/model/package.rb:131 (oddb.org)
  18. Fix NoMethodError undefined method each_value for H2:String at src/model/sequence.rb:279 (oddb.org)
  19. Fix NoMethodError undefined method generic_type for Array at src/model/registration.rb:163 (oddb.org)
  20. Fix NoMethodError undefined method commercial_form for 50846:String at src/model/package.rb:153 (oddb.org)
  21. Fix NoMethodError undefined method size for ODDB::Registration at src/model/package.rb:328 (oddb.org)
  22. Fix NoMethodError undefined method name_base for ODDB::SearchResult at src/view/drugs/ddd_price.rb:178 (oddb.org)
  23. Fix NoMethodError private method select called for String at src/view/interactions/resultlist.rb:83 (oddb.org)
  24. Fix NoMethodError undefined method active_package_count for %2C:String at src/view/interactions/resultlist.rb:84 (oddb.org)
  25. Fix NoMethodError undefined method object_count for ODDB::State::Interactions::Basket at src/view/interactions/result.rb:54 (oddb.org)
  26. Fix NoMethodError undefined method active? for 1.9:String at src/model/sequence.rb:70 (oddb.org)
  27. Fix NoMethodError undefined method public_package_count for precision:String at src/model/atcclass.rb:59 (oddb.org)
  28. Fix NoMethodError undefined method public? for =\:String at src/model/sequence.rb:253 (oddb.org)
  29. Fix NoMethodError undefined method atc_class for >:String atsrc/model/registration.rb:90 (oddb.org)

Fix updating ATC-Code oddb.org

Problem

• ATC-Code is not updated from admin sequence view
• z.B search by 'atcless' -> http://oddb.masa.org/de/gcc/drug/reg/62084/seq/01 (ATC-Code should be L02BX03)
• 'Speichern' button does not work

Commit

• Fix updating ATC-Code in admin sequence view (oddb.org)
• All accessor check processes / update processes should accept nil object and nil data (oddb.org)
• Fix ATC-Request email for testenvironment1.rb, and pointer address in the email (oddb.org)
• Added testenvironment1.rb and 2 in test dir, and load them in etc/oddb.yaml (oddb.org)
• Added testenvironment1 and 2 to src/config.rb (oddb.org)

Check job script sending email process oddb.org

Note

• Job script should run and send an email even if the main application is not running
• But after the sending an email, the following error will come

/usr/local/lib/ruby/1.9.1/drb/drb.rb:736:in `rescue in block in open': druby://localhost:10000 - #<Errno::ECONNREFUSED: Connection refused - connect(2)> (DRb::DRbConnError)
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:730:in `block in open'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:729:in `each'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:729:in `open'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1192:in `initialize'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1172:in `new'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1172:in `open'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1088:in `block in method_missing'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1106:in `with_friend'
        from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1087:in `method_missing'
        from /home/masa/ywesee/oddb.org/src/util/job.rb:20:in `run'
        from jobs/import_bsv:12:in `<module:Util>'
        from jobs/import_bsv:11:in `<module:ODDB>'
        from jobs/import_bsv:10:in `<main>'

• This connection error happens because the job process tries to kill the link to cache of the main application
• But no problem for the data updating

Check error log oddb.org

Refer to Attach:error_log1.20120229.txt

Error

error in SBSM::Session#http_headers: /de/gcc/search/search_type/st_oddb/zone/drugs/search_query/Carmol+Hustentee/currency/USD
NoMethodError
undefined method `values' for "H*":String
/var/www/oddb.org/src/model/sequence.rb:257:in `public_packages'
usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.8/lib/odba/stub.rb:112:in `method_missing'

• Attach:all_err_message.20120229.txt
• bin/admin (online)

ch.oddb> atc_classes.values.map{|atc| atc.sequences.map{|seq| seq.packages.to_s if seq.packages.is_a?(String)} if atc.sequences}.flatten.uniq
-> [nil, "H2", "H*"]
ch.oddb> atc_classes.values.map{|atc| atc.sequences.map{|seq| seq.iksnr.to_s + seq.seqnr.to_s if seq.packages.is_a?(String)} if atc.sequences}.flatten.uniq
-> [nil, "4388901", "6120701", "5949701"]
ch.oddb> atc_classes.values.map{|atc| atc.sequences.map{|seq| seq.odba_id if seq.packages.is_a?(String)} if atc.sequences}.flatten.uniq
-> [nil, 77089, 25647736, 11780537]
ch.oddb> registration('43889').sequence('01').packages.class
-> Hash
ch.oddb> registration('43889').sequence('01').packages.is_a?(String)
-> false
ch.oddb> ODBA.cache.fetch('25647736').packages.class
-> Hash

Note

• This is strange.
• If I search the invalid sequence object via 'registration' object or ODBA.cache.fetch, the packages is a Hash
• but the packages is a String if I search it via 'atc_class' object

ch.oddb> atc_classes.values.map{|atc| atc.sequences.map{|seq| atc.code if seq.packages.is_a?(String)} if atc.sequences}.flatten.uniq
-> [nil, "A16AZ", "N05CZ", "R05CA10"]
ch.oddb> atc_class('A16AZ').sequences.map{|seq| seq.packages.to_s if seq.packages.is_a?(String)}.uniq
-> [nil, "H2"]
ch.oddb> atc_class('A16AZ').sequences[29].packages.class
-> String
ch.oddb> atc_class('A16AZ').sequences[29].packages
-> H2

• Access: http://ch.oddb.org/de/gcc/search/search_query/A16AZ => 'working!!'
• But still the String is includes in the atc_class

ch.oddb> atc_class('A16AZ').sequences.map{|seq| seq.packages.to_s if seq.packages.is_a?(String)}.uniq
-> [nil, "H2"]

• Question: Is it possible to be a different object even if the odba_id is same

ch.oddb> atc_class('A16AZ').sequences[29].odba_id
-> 77089
ch.oddb> registration('43889').sequence('01').odba_id
-> 77089
ch.oddb> atc_class('A16AZ').sequences[29].packages.class
-> String
ch.oddb> atc_class('A16AZ').sequences[29].packages
-> H2
ch.oddb> registration('43889').sequence('01').packages.class
-> Hash
ch.oddb> registration('43889').sequence('01').packages
-> {"028"=>#<ODBA::Stub:85543860#239815 @odba_class=ODDB::Package @odba_container=98246420#105071>}

Note

• These are gone after reboot, so it is caused by probably the cache data floating
• Temporary solution
  • we should skip the invalid data in the view process, and wait the cache data is corrected after some time or rebooting
  • fix the data floating error one by one

Commit

• Fix data corruption error. NoMethodError undefined method values for H* :String at src/model/sequence.rb:257 (oddb.org)
• Fix data floating error. NoMethodError undefined method has_ddd? for #<Array:0x0000001a890110> at src/model/package.rb:207' (oddb.org)

Refer to Attach:error_log2.20120229.txt

Commit

• Fix NoMethodError undefined method pointer for ODDB::State::Drugs::PriceHistory::PriceChanges at src/view/analysis/limitationtext.rb:35 (oddb.org)
• Fix NoMethodError undefined method fr for ODDB::Analysis::Group at src/view/analysis/limitationtext.rb:19 (oddb.org)
• Fix NoMethodError undefined method gsub for ODDB::PatinfoDocument2001 at src/view/analysis/limitationtext.rb:20 (oddb.org)
• Fix NoMethodError undefined method registration for st_pharmacode:String at src/model/package.rb:38 (oddb.org)
• Fix NoMethodError undefined method registration for String at src/model/package.rb:29 (oddb.org)
• Fix NoMethodError undefined method dt for name:String at src/view additional_information.rb:101 (oddb.org)

Refer to Attach:error_log3.20120229.txt

Commit

• Fix NoMethodError undefined method galenic_group for String at src/model/composition.rb:57 (oddb.org)
• Fix NoMethodError undefined method galenic_group for name:String at src/model/galenicform.rb:18 (oddb.org)

Refer to Attach:error_log4.20120229.txt

Commit

• Fix NoMethodError undefined method sort for \:String at src/model/composition.rb:100 (oddb.org)
• Fix NoMethodError undefined method de for class:String at src/view/admin/registration.rb:55 (oddb.org)
• Fix NoMethodError undefined method company for >:String at src/model/sequence.rb:24 (oddb.org)
• Fix NoMethodError undefined method limitation for :String at src/model/package.rb:300 (oddb.org)
• Fix NoMethodError undefined method de for String at src/util/resultsort.rb:49 (oddb.org)

Refer to Attach:error_log5.20120229.txt

Commit

• Fix NoMethodError undefined method interval for ODDB::State::Drugs::Result at src/view/alphaheader.rb:13 (oddb.org)
• Fix TypeError can't convert String into Array at src/model/package.rb:131 (oddb.org)
• Fix NoMethodError undefined method each_value for H2:String at src/model/sequence.rb:279 (oddb.org)

Refer to Attach:error_log6.20120229.txt

Commit

• Fix NoMethodError undefined method generic_type for Array at src/model/registration.rb:163 (oddb.org)
• Fix NoMethodError undefined method commercial_form for 50846:String at src/model/package.rb:153 (oddb.org)
• Fix NoMethodError undefined method size for ODDB::Registration at src/model/package.rb:328 (oddb.org)
• Fix NoMethodError undefined method name_base for ODDB::SearchResult at src/view/drugs/ddd_price.rb:178 (oddb.org)

Refer to Attach:error_log7.20120229.txt

Commit

• Fix NoMethodError private method select called for String at src/view/interactions/resultlist.rb:83 (oddb.org)
• Fix NoMethodError undefined method active_package_count for %2C:String at src/view/interactions/resultlist.rb:84 (oddb.org)

Refer to Attach:error_log8.20120229.txt

Commit

• Fix NoMethodError undefined method object_count for ODDB::State::Interactions::Basket at src/view/interactions/result.rb:54 (oddb.org)

Refer to Attach:error_log9.20120229.txt

Commit

• Fix NoMethodError undefined method active? for 1.9:String at src/model/sequence.rb:70 (oddb.org)
• Fix NoMethodError undefined method public_package_count for precision:String at src/model/atcclass.rb:59 (oddb.org)
• Fix NoMethodError undefined method public? for =\:String at src/model/sequence.rb:253 (oddb.org)
• Fix NoMethodError undefined method atc_class for >:String atsrc/model/registration.rb:90 (oddb.org)