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Modifications for ch.oddb.org from Ruby 1.8.6 to Ruby 1.9.3

09-01-2012

Error (mail_patinfo_invoices)

Error: RuntimeError
Message: can't add a new key into hash during iteration
Backtrace:
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/cache_entry.rb:45:in `store'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/cache_entry.rb:45:in `odba_add_reference'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/cache.rb:310:in `fetch_or_do'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/cache.rb:225:in `fetch'

Commit

• Added exclusive control to update @accessed_by Hash variable in CacheEntry class using mutex (odba)

05-01-2012

Error (rpdf2txt, when creating text_parser(pdftext.rb))

/home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:82:in `make_element': cannot make an element from nil (ArgumentError)
        from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `block in make_elements'
        from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `map'
        from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `make_elements'
        from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:361:in `initialize'
        from /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:484:in `new'

Commit

• Fix parser.rb, text_state.rb, and added grammar files for Ruby 1.9.3 (rpdf2txt)

Error (update_narcotics)

Plugin: ODDB::NarcoticPlugin
Error: ArgumentError
Message: invalid byte sequence in UTF-8
Backtrace:
/usr/local/lib/ruby/site_ruby/1.9.1/rpdf2txt/parser.rb:131:in `scan'
/usr/local/lib/ruby/site_ruby/1.9.1/rpdf2txt/parser.rb:131:in `build_object_catalogue'
/usr/local/lib/ruby/site_ruby/1.9.1/rpdf2txt/parser.rb:48:in `object_catalogue'
/usr/local/lib/ruby/site_ruby/1.9.1/rpdf2txt/parser.rb:163:in `page_tree_root'

NoMethodError: undefined method `collect' for "lt":String when updating index 'substance_index_atc' with a ODDB::Substance
["(eval):2:in `block in proc_instance_target'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/index.rb:249:in `call'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/index.rb:249:in `update_origin'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/index.rb:163:in `update'"]
[...]

Plugin: ODDB::NarcoticPlugin
Error: NoMethodError
Message: undefined method `find' for "utf-8":String
Backtrace:
/home/masa/ywesee/oddb.org/src/model/narcotic.rb:31:in `casrn'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/stub.rb:112:in `method_missing'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:704:in `block in narcotic_by_casrn'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:704:in `each'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:704:in `find'

Plugin: ODDB::NarcoticPlugin
Error: NotImplementedError
Message: method `method_missing' called on terminated object (0x00000007b48190 flags=0x0 klass=0x0)
Backtrace:
/home/masa/ywesee/oddb.org/src/model/narcotic.rb:31:in `casrn'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/stub.rb:112:in `method_missing'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:704:in `block in narcotic_by_casrn'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:704:in `each'

Commit

04-01-2012

Error (update_migel_nonpharma)

Plugin: ODDB::MiGeLPlugin
Error: NoMethodError
Message: undefined method `update_values' for []:Array
Backtrace:
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.7/lib/odba/stub.rb:112:in `method_missing'
/var/www/oddb.org/src/util/language.rb:67:in `update_values'
/var/www/oddb.org/src/util/persistence.rb:236:in `issue_update'
/var/www/oddb.org/src/util/oddbapp.rb:123:in `block in update'

Commits

• Skip error migel items during update_migel_nonpharma (oddb.org)

03-01-2012

Commits

• Fix column separator of oddb.csv export (oddb.org)
• Deleted new line in oddb.csv export (oddb.org)
• Fix import_migel_nonpharma error, cannot convert nil into String in File.expand_path (oddb.org)
• Use Syck for YAML.dump as with Ruby 1.8.6 (oddb.org)
• Added a logging statement during update_bsv for debug (oddb.org)
• Fix migel nonpharma importer for Ruby 1.9.3 (oddb.org)
• Fix export_ouwerkerk error, undefined method empty? for nil:NilClass (oddb.org)

29-12-2011

Error (update_interactions)

Plugin: ODDB::Interaction::InteractionPlugin
Error: NoMethodError
Message: undefined method `keys' for nil:NilClass
Backtrace:
/usr/local/lib/ruby/1.9.1/net/http.rb:1019:in `get'
/home/masa/work/oddb.org_3/src/util/http.rb:102:in `get'
/home/masa/work/oddb.org_3/src/util/http.rb:26:in `http_body'

Error (export_ouwerkerk)

Plugin: ODDB::OuwerkerkPlugin
Error: NoMethodError
Message: undefined method `empty?' for nil:NilClass
Backtrace:
/home/masa/work/oddb.org_3/src/plugin/ouwerkerk.rb:75:in `export_registration'
/home/masa/work/oddb.org_3/src/plugin/ouwerkerk.rb:119:in `block in export_registrations'
/home/masa/work/oddb.org_3/src/plugin/ouwerkerk.rb:117:in `each'

Commit

• Fix test_model/substance.rb (oddb.org)
• Deleted update_swissmedicjournal (oddb.org)
• Deleted update_comarketing (oddb.org)
• Deleted comarketing ext server, and replaced pdf with xls file in update_comarketing (oddb.org)

Error (export_competition_xlss)

Plugin: ODDB::XlsExportPlugin
Error: NoMethodError
Message: undefined method `galenic_form' for #<ODDB::Package:0x0000000aec2e58>
Backtrace:
(druby://localhost:10005) /home/masa/work/oddb.org_2/ext/export/src/competition_xls.rb:80:in `block in export_competition'
(druby://localhost:10005) /home/masa/work/oddb.org_2/ext/export/src/competition_xls.rb:59:in `each'
(druby://localhost:10005) /home/masa/work/oddb.org_2/ext/export/src/competition_xls.rb:59:in `each_with_index'

Commit

• Fix export_competition_xlss, error undefined method galenic_form for Package (oddb.org)

28-12-2011

Commit

• Deleted update_vaccines (oddb.org)
• Deleted testcases for update_vaccines (oddb.org)
• Deleted update_medwin_packages and its testcases (oddb.org)
• Deleted reconsider_bsv and its testcases (oddb.org)
• Fix pointer link in mail_swissmedic_notifications report mail (oddb.org)
• Fix test_model/address2.rb (oddb.org)

Error (update_medwin_companies)

Plugin: ODDB::MedwinCompanyPlugin
Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
(druby://localhost:10006) /home/masa/ywesee/oddb.org/ext/meddata/src/session.rb:83:in `match'
(druby://localhost:10006) /home/masa/ywesee/oddb.org/ext/meddata/src/session.rb:83:in `handle_resp!'
(druby://localhost:10006) /home/masa/ywesee/oddb.org/ext/meddata/src/session.rb:59:in `initialize'
...
/home/masa/work/oddb.org_3/src/plugin/medwin.rb:62:in `update_company'
/home/masa/work/oddb.org_3/src/plugin/medwin.rb:54:in `block in update'
/home/masa/work/oddb.org_3/src/plugin/medwin.rb:53:in `each_value'

Plugin: ODDB::MedwinCompanyPlugin
Error: Encoding::CompatibilityError
Message: incompatible character encodings: ASCII-8BIT and UTF-8
Backtrace:
(druby://localhost:10006) /home/masa/ywesee/oddb.org/src/util/html_parser.rb:227:in `send_cdata'
(druby://localhost:10006) /home/masa/ywesee/oddb.org/src/util/html_parser.rb:278:in `send_cdata'
(druby://localhost:10006) /home/masa/ywesee/oddb.org/src/util/html_parser.rb:336:in `send_cdata'

Plugin: ODDB::MedwinCompanyPlugin
Error: NoMethodError
Message: undefined method `[]' for nil:NilClass
Backtrace:
(druby://localhost:76542) /home/masa/work/oddb.org_3/src/plugin/medwin.rb:78:in `update_company_data'
(druby://localhost:76542) /home/masa/work/oddb.org_3/src/plugin/medwin.rb:70:in `block in update_company'
(druby://localhost:76542) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1550:in `call'
(druby://localhost:76542) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1550:in `perform_without_block'

Commit

• Fix encoding errors during update_medwin_companies (oddb.org)

Error (update_swissreg_news)

Plugin: ODDB::SwissregPlugin
Error: NoMethodError
Message: undefined method `values' for nil:NilClass
Backtrace:
/home/masa/work/oddb.org_4/src/model/registration.rb:112:in `each_sequence'
/home/masa/work/oddb.org_4/src/plugin/swissreg.rb:60:in `block in update_news'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.6/lib/odba/stub.rb:112:in `each_key'

Plugin: ODDB::SwissregPlugin
Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/session.rb:88:in `match'
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/session.rb:88:in `view_state'
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/session.rb:54:in `get_result_list'

Plugin: ODDB::SwissregPlugin
Error: NoMethodError
Message: undefined method `Hpricot' for #<Net::HTTP www.swissreg.ch:80 open=false>
Backtrace:
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/session.rb:19:in `extract_result_links'
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/session.rb:75:in `get_result_list'
(druby://localhost:10007) /home/masa/ywesee/oddb.org/ext/swissreg/src/swissreg.rb:10:in `search'

Commit

Commit

• Fix pointer link in feedback log (oddb.org)

Problem

• update_bsv does not run

Refer to baseparser.rb.patch sourch.rb.patch

How to patch

~/software/patches $ patch /usr/local/lib64/ruby/1.9.1/rexml/parsers/baseparser.rb baseparser.rb.patch
~/software/patches $ patch /usr/local/lib64/ruby/1.9.1/rexml/source.rb source.rb.patch

Commit

• Replaced pointer link in a swissindex report mail (oddb.org)

Error (export_index_therapeuticus_csv)

Error: NameError
Message: uninitialized constant CSV::Writer
Backtrace:
(druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/csv_exporter.rb:96:in `dump'
(druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:136:in `block (2 levels) in export_idx_th_csv'
(druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:134:in `each'
...
/home/masa/ywesee/oddb.org/src/plugin/csv_export.rb:85:in `export_index_therapeuticus'
/home/masa/ywesee/oddb.org/src/util/exporter.rb:136:in `block in export_index_therapeuticus_csv'

Commit

• Updated CSV library usage in ext/export for Ruby 1.9.3 (oddb.org)

27-12-2011

Problem (updates_swissmedic)

• It runs everyday

Commit

• Updated update_swissmedic to be executed only if the latest file is different from a downloaded file (oddb.org)
• Updated the conditin to run update_swissmedic in the case of no latest xls file (oddb.org)

Error (export_csv, update_swissmedic)

Error: RuntimeError
Message: can't add a new key into hash during iteration
Backtrace:
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.6/lib/odba/cache.rb:325:in `store'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.6/lib/odba/cache.rb:325:in `block (3 levels) in fetch_or_restore'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.6/lib/odba/cache.rb:313:in `call'
...
/home/masa/ywesee/oddb.org/src/model/atcclass.rb:104:in `block in packages'
/home/masa/ywesee/oddb.org/src/model/atcclass.rb:104:in `packages'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:331:in `block in to_csv'

Note

• This error does not always happen (sometimes)

Commit

• Debugged Hash iteration error during cleaning @fetched and @prefetched objects (odba)

Error (export_csv)

Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:207:in `gsub'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:207:in `limitation_text'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:335:in `block (3 levels) in to_csv'
...
/home/masa/ywesee/oddb.org/src/plugin/csv_export.rb:56:in `_export_drugs'
/home/masa/ywesee/oddb.org/src/plugin/csv_export.rb:26:in `export_drugs'
/home/masa/ywesee/oddb.org/src/util/exporter.rb:86:in `block in export_csv'

Error (export_csv, oddb.csv)

Error: NoMethodError
Message: undefined method `de' for #<Array:0x0000000c869168>
Backtrace:
(eval):2:in `send'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:204:in `limitation_text'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:332:in `block (3 levels) in to_csv'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:330:in `collect'
/home/masa/ywesee/oddb.org/src/view/drugs/csv_result.rb:330:in `block (2 levels) in to_csv'

Check

ch.oddb> ODBA.cache.fetch('218870').sl_entry.limitation_text.class
-> Array
ch.oddb> ODBA.cache.fetch('218870').sl_entry.limitation_text.length
-> 189
ch.oddb> ODBA.cache.fetch('218870').sl_entry.limitation_text.first.class
-> ODDB::Feedback

Note

• Package#sl_entry#limitation_text should be an instance of LimitationText class

Commit

• Fix encoding error and undefined de method error during export_csv (oddb.org)
• Skip feedbacks event with pointer link (oddb.org)

23-12-2011

• Skip price_history event with pointer link (oddb.org)
• Fix all the elements of odba_potentials and odba_exclude_vars to be Symbols for Ruby 1.9.3 (odba)
• Skip compare event with pointer link. Also skip invalid byte sequence error. (oddb.org)
• Skip invalid sequence and package numbers in the link without logging the error message. (oddb.org)
• Replaced every TMail with Mail, namely using mail gem (oddb.org)
• Fix ddd_chart event error in the case of no data (oddb.org)
• Fix FachinfoDocument encoding error (htmlgrid)

22-12-2011

Error (Update sequence data)

instance of Date needs to have method `marshal_load'
(druby://localhost:37039) /usr/lib64/ruby/1.8/drb/drb.rb:585:in `load'
(druby://localhost:37039) /usr/lib64/ruby/1.8/drb/drb.rb:585:in `load'
(druby://localhost:37039) /usr/lib64/ruby/1.8/drb/drb.rb:581:in `exclusive'
(druby://localhost:37039) /usr/lib64/ruby/1.8/drb/drb.rb:581:in `load'
(druby://localhost:37039) /usr/lib64/ruby/1.8/drb/drb.rb:633:in `recv_reply'

Commit

• Fix Date object loading error (sbsm)

21-12-2011

• http://dev.ywesee.com/wiki.php/Choddb/Ruby193p0todo

Rescue pointer link acccess

• Rescued print event with pointer link (oddb.org)

Delete notify event

• Deleted notfiy event (oddb.org)

Fix pointer link address suggestion

• Fix pointer link to a doctor view in suggest address view (oddb.org)
• Fix pointer link of Zurück zur Detailansicht in suggeset address confirm view (oddb.org)
• Fix pointer link to create a new doctor address (oddb.org)
• Fix address index when creating a new address (oddb.org)
• Fix doctor#addresses update without updating email address (oddb.org)

20-12-2011 Debug App#update

Error (doctors)

ch.oddb> doctors.length
-> dump format error for symbol(0xaf)

failsafe rescued ArgumentError < StandardError
dump format error for symbol(0xaf)
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1472:in `instance_eval'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.4/lib/odba/marshal.rb:15:in `load'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.4/lib/odba/cache.rb:628:in `restore'
...
(eval):1:in `block (2 levels) in _admin'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1472:in `instance_eval'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1472:in `block (2 levels) in _admin'
/home/masa/ywesee/oddb.org/src/util/failsafe.rb:10:in `call'
/home/masa/ywesee/oddb.org/src/util/failsafe.rb:10:in `failsafe'
/home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1471:in `block in _admin'

Problem

• It looks like that App#update does not work for Non-Persistable object

Commit

• Modified doctor address suggestion for Ruby 1.9.3 (oddb.org)
• Added attr_accessor :odba_persistent (odba)

19-12-2011 Fix online

Error (suggest_address.rb)

/usr/local/lib/ruby/gems/1.9.1/gems/tmail-1.2.0/lib/tmail/scanner_r.rb:108: warning: variable $KCODE is no longer effective
error in SBSM::Session#process: /de/gcc
NoMethodError
undefined method `match' for nil:NilClass
/usr/local/lib/ruby/gems/1.9.1/gems/tmail-1.2.0/lib/tmail/scanner_r.rb:234:in `readstr'
/usr/local/lib/ruby/gems/1.9.1/gems/tmail-1.2.0/lib/tmail/scanner_r.rb:146:in `scan_main'
/usr/local/lib/ruby/gems/1.9.1/gems/tmail-1.2.0/lib/tmail/scanner_r.rb:125:in `scan'
parser.y:375:in `parse_in'
racc/parser.rb:152:in `_racc_yyparse_c'

Commit

• Skip GLOBAL_MAP events with pointer link (oddb.org)
• Fix navigator link in galenic form view (oddb.org)
• Fix pageing with big search results and many ATC-Codes, i.e. Novartis (oddb.org)
• Don't force_encoding nil data (oddb.org)
• Replaced TMail with Mail. Updated grammar for content_type (oddb.org)

16-12-2011 Fix online

Remove feedback pager

Commit

• Removed feedbacks pager (oddb.org)

update_company_textinfo

Error (Updater.new(self).update_company_textinfos 'Teva')

Plugin: ODDB::TextInfoPlugin
Error: NoMethodError
Message: undefined method `u' for :ODDB::Text::Paragraph
Backtrace:
(druby://localhost:10002) /home/masa/work/commit/oddb.org/src/model/text.rb:115:in `set_format'
(druby://localhost:10002) /home/masa/work/commit/oddb.org/src/model/text.rb:76:in `clear!'
(druby://localhost:10002) /home/masa/work/commit/oddb.org/src/model/text.rb:62:in `initialize'
(druby://localhost:10002) /usr/local/lib/ruby/gems/1.9.1/gems/hpricot-0.8.4/lib/hpricot/traverse.rb:499:in `each'
(druby://localhost:10002) /usr/local/lib/ruby/gems/1.9.1/gems/hpricot-0.8.4/lib/hpricot/traverse.rb:499:in `each_child'
/home/masa/work/oddb.org/src/plugin/text_info.rb:198:in `parse_fachinfo'
/home/masa/work/oddb.org/src/plugin/text_info.rb:328:in `block in update_product'
/home/masa/work/oddb.org/src/plugin/text_info.rb:327:in `each'

Commit

• Fix update_company_textinfo for Ruby 1.9.3 (oddb.org)

mod_ruby compiled on Ruby 1.9.3

Error

/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/local/lib/libruby-static.a(array.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libruby-static.a: could not read symbols: Bad value
collect2: ld gab 1 als Ende-Status zurück
make: *** [mod_ruby.so] Fehler 1

Commits

• Replaced notify link with mailto (oddb.org)
• Fix mailto link event from drug to show (oddb.org)
• Added notify link for migel (oddb.org)
• Changed Ruby interpreter path for jobs/* (oddb.org)

Replace feedbacks captcha

Error (when feedback save button is clicked)

invalid byte sequence in UTF-8
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/component.rb:230:in `gsub'
/usr/local/lib/ruby/1.9.1/cgi/html.rb:433:in `block in html'
/home/masa/work/oddb.org/src/view/rss/feedback.rb:73:in `block (2 levels) in to_html'
/home/masa/work/oddb.org/src/view/rss/feedback.rb:53:in `each'
/home/masa/work/oddb.org/src/view/rss/feedback.rb:53:in `block in to_html'
/usr/local/lib/ruby/1.9.1/rss/maker/base.rb:439:in `make'
/usr/local/lib/ruby/1.9.1/rss/maker/base.rb:403:in `make'
/usr/local/lib/ruby/1.9.1/rss/maker.rb:10:in `make'
/home/masa/work/oddb.org/src/view/rss/feedback.rb:44:in `to_html'
/home/masa/work/oddb.org/src/util/oddbapp.rb:1555:in `block (2 levels) in update_feedback_rss_feed'
/home/masa/work/oddb.org/src/util/oddbapp.rb:1552:in `block in update_feedback_rss_feed'

Note

• feedback data is saved but the rss failed

Commit

• Updated captcha for Feedback (oddb.org)
• Fix dictionaries for feedback (oddb.org)

15-12-2011 Debug online

Error (Feedbacks, Turing, call method, http://oddb.masa.org/de/gcc/feedbacks/reg/31862/seq/02/pack/078)

error in SBSM::Session#to_html: /de/gcc/feedbacks/reg/31862/seq/02/pack/078
RuntimeError
Failed to generate: undefined method `call' for 140136148846688:Fixnum
/usr/local/lib/ruby/gems/1.9.1/gems/turing-0.0.11/lib/turing/challenge.rb:114:in `generate_challenge'
/home/masa/work/oddb.org/src/view/captcha.rb:6:in `challenge'
/home/masa/work/oddb.org/src/view/captcha.rb:9:in `captcha'
/home/masa/work/oddb.org/src/view/feedbacks.rb:43:in `init'

Error (Feedbacks, Turing, generate method, http://oddb.masa.org/de/gcc/feedbacks/reg/31862/seq/02/pack/078)

error in SBSM::Session#to_html: /de/gcc/feedbacks/reg/31862/seq/02/pack/078
RuntimeError
Failed to generate: plugin Turing::Image::WhiteSquaring doesn't have generate method
/usr/local/lib/ruby/gems/1.9.1/gems/turing-0.0.11/lib/turing/challenge.rb:114:in `generate_challenge'
/home/masa/work/oddb.org/src/custom/lookandfeelbase.rb:4210:in `generate_challenge'
/home/masa/work/oddb.org/src/view/captcha.rb:6:in `challenge'
/home/masa/work/oddb.org/src/view/captcha.rb:9:in `captcha'

Note Important

• Class#instance_methods becomes an Array of Sympols (method name) in Ruby 1.9.3
• It is an Array of String (method name) in Ruby 1.8

Error (New indication button, http://oddb.masa.org/de/gcc/indications/)

error in SBSM::Session#to_html: /de/gcc
NoMethodError
undefined method `join' for nil:NilClass
/home/masa/work/oddb.org/src/view/admin/indication.rb:18:in `synonym_list'
/home/masa/work/oddb.org/src/view/descriptionform.rb:29:in `init'
/home/masa/work/oddb.org/src/view/publictemplate.rb:54:in `new'
/home/masa/work/oddb.org/src/view/publictemplate.rb:54:in `content'
/home/masa/work/oddb.org/src/view/publictemplate.rb:51:in `init'
/home/masa/work/oddb.org/src/view/privatetemplate.rb:17:in `init'

Commit

• Fix new indication button (oddb.org)

Error (tmail)

Oddb (OddbApp): symbol lookup error:
/usr/local/lib/ruby/gems/1.9.1/gems/tmail-1.2.7.1/ext/tmailscanner/tmail/tmailscanner.so: undefined symbol: rb_get_kcode

 tmail-1.2.0 should work. The other version is not compatible with with MRI 1.9.2
 We should use "Mail" instead.

Error (http://ch.oddb.org/de/gcc/effective_substances/)

error in SBSM::Session#process: /de/gcc/effective_substances/
Encoding::CompatibilityError
incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
/home/masa/work/oddb.org/src/util/interval.rb:46:in `match'
...
NoMethodError
undefined method `interval' for #<ODDB::State::Migel::Product:0x00000004385050>
/home/masa/work/oddb.org/src/view/alphaheader.rb:12:in `compose_header'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/list.rb:49:in `compose'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:55:in `init'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/list.rb:129:in `init'

Commit

• Fix effective_substances error for Ruby 1.9.3 (oddb.org)

Error (http://oddb.masa.org/de/gcc/indications/)

error in SBSM::Session#to_html: /de/gcc/indications/
Encoding::CompatibilityError
incompatible character encodings: UTF-8 and ASCII-8BIT
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:268:in `to_html'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:268:in `to_html'
...

Check

 ch.oddb> indications.values.select{|ind| ind.description.encoding.to_s != "UTF-8"}.length
 -> 249

Commit

• Fix incompatible encoding regexp match error accessing to /de/gcc/indications/ (oddb.org)

Error (when segmentation fault)

error in SBSM::Session#to_html: /
NoMethodError
undefined method `iksnr' for "#":String
/var/www/oddb.org/src/model/package.rb:37:in `block (2 levels) in sequence_data'
/var/www/oddb.org/src/view/drugs/centeredsearchform.rb:199:in `heading'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/composite.rb:141:in `create'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/divcomposite.rb:33:in `block in compose'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/divcomposite.rb:13:in `each'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/divcomposite.rb:13:in `compose'

error in SBSM::Session#http_headers: /
NoMethodError
undefined method `iksnr' for "#":String
/var/www/oddb.org/src/model/package.rb:37:in `block (2 levels) in sequence_data'
/var/www/oddb.org/src/view/drugs/centeredsearchform.rb:199:in `heading'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/composite.rb:141:in `create'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/divcomposite.rb:33:in `block in compose'
/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.1/lib/htmlgrid/divcomposite.rb:13:in `each'

14-12-2011 setup oddb.org online

Error (ch.oddb-fiparse)

/var/www/oddb.org/ext/fiparse $ ruby193 bin/fiparsed 
/usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead.
/usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': cannot load such file -- rwv2 (LoadError)
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require'
        from /usr/local/lib/ruby/gems/1.9.1/gems/rwv2-0.6.0/lib/rwv2/rwv2.rb:25:in `<top (required)>'
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:59:in `require'
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:59:in `rescue in require'

• Copy the rwv2.so to lib director for Ruby 1.9.3

 cp /usr/lib64/ruby/site_ruby/1.8/x86_64-linux/rwv2.so /usr/local/lib64/ruby/site_ruby/1.9.1/x86_64-linux

Error (ch.oddb-fiparse)

/var/www/oddb.org/ext/fiparse $ ruby193 bin/fiparsed 
/usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead.
/usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': /var/www/oddb.org/ext/fiparse/src/fachinfo_pdf.rb:141: invalid multibyte char (US-ASCII) (SyntaxError)
/var/www/oddb.org/ext/fiparse/src/fachinfo_pdf.rb:141: invalid multibyte char (US-ASCII)
/var/www/oddb.org/ext/fiparse/src/fachinfo_pdf.rb:141: syntax error, unexpected $end, expecting ')'
                                self.out << data.gsub(/&#9632;/u, '')
                                                         ^
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require'
        from /var/www/oddb.org/ext/fiparse/src/fiparse.rb:10:in `<top (required)>'
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require'
        from /usr/local/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require'
        from bin/fiparsed:9:in `<main>'

• Put magic comment '# encoding: utf-8' to the error files
• Install rwv2

 # /usr/local/bin/gem193 install rwv2

Error (ch.oddb-readonly)

@400000004ee8c16e17a9da8c /usr/local/lib/ruby/1.9.1/drb/drb.rb:861:in `initialize': Address already in use - bind(2) (Errno::EADDRINUSE)
@400000004ee8c16e17a9e644       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:861:in `open'
@400000004ee8c16e17a9e644       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:861:in `open_server'
@400000004ee8c16e17a9ea2c       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:759:in `block in open_server'
@400000004ee8c16e17a9ea2c       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:757:in `each'
@400000004ee8c16e17a9ea2c       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:757:in `open_server'
@400000004ee8c16e17aaefe4       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1342:in `initialize'
@400000004ee8c16e17aaf3cc       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1624:in `new'
@400000004ee8c16e17aaf3cc       from /usr/local/lib/ruby/1.9.1/drb/drb.rb:1624:in `start_service'
@400000004ee8c16e17aaf3cc       from /var/www/oddb.org/ext/readonly/bin/readonlyd:15:in `<main>'

• Kill the old readonly process

Warning (ch.oddb-readonly, gd2.rb)

@400000004ee8beb70a1fca0c /usr/local/lib/ruby/gems/1.9.1/gems/gd2-1.1.1/lib/gd2.rb:30: Use RbConfig instead of obsolete and deprecated Config.

• Replace Config to RbConfig

12-12-2012 ydim injection from oddb.org client (Ruby 1.9.3) to ydim server (Ruby 1.8.6)

Commit

• Debugged Date incompatibility between Ruby 1.8 and 1.9 in invoice.rb (ydim)

rpdf2txt

Most of testcase error is related to rockit

  1) Error:
test_tree_node1(Rpdf2txt::TestPdfObject):
ArgumentError: cannot make an element from nil
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:82:in `make_element'
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `block in make_elements'
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `map'
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:92:in `make_elements'
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:361:in `initialize'
    /home/masa/work/rpdf2txt/lib/rpdf2txt-rockit/grammar.rb:484:in `new'
...

Testcases on Ruby 1.9.3

 135 tests, 19 assertions, 15 failures, 118 errors, 0 skips

09-12-2011 compatible updates of ywesee libraries to work on both Ruby 1.8.6 and 1.9.3

1. htmlgrid
2. odba
3. sbsm
4. ydim
5. rpdf2txt

1. htmlgrid

Memo

• The install place is different in the cases through 1. gem 2. setup.rb

Commit

• Fixed require grid.o for gem install case (htmlgrid)
• Updated component.rb to be compatible for both Ruby 1.8 and 1.9 (htmlgrid)

2. odba

Commit

• Updated cache.rb persitatble.rb 18_19_loading_compatibility.rb to be compatible for both Ruby 1.8 and 1.9 (odba)

3. sbsm

Commit

• Updated session.rb to be compatible for both Ruby 1.8 and 1.9 (sbsm)

4. ydim

Error (mail_patinfo_invoices)

• Email ch.ODDB.org Report - Error Invoice: - 09/12/2011

Invoicer#send_invoice(2011-12-08, mhatakeyama@ywesee.com, 39828 02, 2011-12-08)
Error: NoMethodError
Message: undefined method `dbi_args' for #<DBI::DatabaseHandle:0x7f60dd1063d8>
Backtrace:
(druby://localhost:12375) /usr/lib64/ruby/site_ruby/1.8/odba/cache.rb:401:in `next_id'
(druby://localhost:12375) /usr/lib64/ruby/site_ruby/1.8/odba/persistable.rb:261:in `odba_id'

Note

• ODBA.storage.dbi is not always an instance of ODBA::ConnectionPool (oddb.org uses ODBA::ConnectionPool instance)
  • see ODBA::Storage#dbi method
• ODBA.storage.instance_variable_get('@dbi') is always of ODBA::ConnectionPool

Commit

• Debugged ODBA::Cache#next_id (odba)
• Added require odba/18_19_loading_compatibility for the compatibility between Ruby 1.8 and 1.9 (ydim)

Note

• But it fails in injecting invoices from Ruby 1.9 (oddb.org) to 1.8 (ydim server)

02-12-2011 mail_invoices

Error (mail_fachinfo_log)

• Eamil ch.ODDB.org Report - Error Export: Mail Fachinfo-Invoices - 02/12/2011

Error: NameError
Message: undefined local variable or method `subject' for #<ODDB::FachinfoInvoicer:0x00000007a40d38>
Backtrace:
/home/masa/work/oddb.org_1/src/plugin/invoicer.rb:61:in `rescue in send_invoice'
/home/masa/work/oddb.org_1/src/plugin/invoicer.rb:47:in `send_invoice'
/home/masa/work/oddb.org_1/src/plugin/info_invoicer.rb:323:in `block in send_daily_invoices'
/home/masa/work/oddb.org_1/src/plugin/info_invoicer.rb:311:in `each'
/home/masa/work/oddb.org_1/src/plugin/info_invoicer.rb:311:in `send_daily_invoices'
/home/masa/work/oddb.org_1/src/plugin/info_invoicer.rb:13:in `run'

Refer to invoicer.rb.patch

Error (mail_fachinfo_log)

• Email ch.ODDB.org Report - Error Export: Mail Fachinfo-Invoices - 02/12/2011

Error: TypeError
Message: can't iterate from Time
Backtrace:
/home/masa/work/oddb.org_1/src/plugin/fachinfo_invoicer.rb:35:in `each'
/home/masa/work/oddb.org_1/src/plugin/fachinfo_invoicer.rb:35:in `include?'
/home/masa/work/oddb.org_1/src/plugin/fachinfo_invoicer.rb:35:in `include?'
/home/masa/work/oddb.org_1/src/plugin/fachinfo_invoicer.rb:35:in `block (2 levels) in report_edited_fachinfos'

Refer to fachinfo_invoicer.rb.patch

01-12-2011 mail_invoices, export_oddbdat

Error (mail_patinfo_invoices)

• Email ch.ODDB.org Report - Error Invoice: - 01/12/2011

Invoicer#send_invoice(2011-11-30, mhatakeyama@ywesee.com, 47721 01, 2011-11-30)
Error: TypeError
Message: instance of Date needs to have method `marshal_load'
Backtrace:
(druby://localhost:12375) /usr/lib64/ruby/1.8/drb/drb.rb:585:in `load'
(druby://localhost:12375) /usr/lib64/ruby/1.8/drb/drb.rb:585:in `load'
(druby://localhost:12375) /usr/lib64/ruby/1.8/drb/drb.rb:581:in `exclusive'
(druby://localhost:12375) bin/ydimd:46
/home/masa/work/oddb.org_2/src/plugin/ydim.rb:122:in `block in inject_from_items'
/home/masa/work/oddb.org_2/src/plugin/ydim.rb:252:in `call'
/home/masa/work/oddb.org_2/src/plugin/ydim.rb:252:in `ydim_connect'
/home/masa/work/oddb.org_2/src/plugin/ydim.rb:119:in `inject_from_items'

Error (export_oddbdat)

• Email ch.ODDB.org Report - Error Export: oddbdat - 30/11/2011

Error: NoMethodError
Message: undefined method `[]' for nil:NilClass
Backtrace:
(druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/stub.rb:112:in `method_missing'
(druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/stub.rb:131:in `[]'
/home/masa/work/oddb.org_2/src/plugin/oddbdat_export.rb:68:in `export'
/home/masa/work/oddb.org_2/src/util/exporter.rb:160:in `block in export_oddbdat'

Solution

• skip the error data (ODDB::Substance instance)

Refer to substance.rb.patch

30-11-2011 update_price_feeds, exporters

Error (mail_patinfo_invoices)

• Email ch.ODDB.org Report - Error Export: Mail Patinfo-Invoices - 30/11/2011

Error: TypeError
Message: can't iterate from Time
Backtrace:
/home/masa/work/oddb.org_2/src/plugin/info_invoicer.rb:209:in `each'
/home/masa/work/oddb.org_2/src/plugin/info_invoicer.rb:209:in `include?'
/home/masa/work/oddb.org_2/src/plugin/info_invoicer.rb:209:in `include?'

Refer to info_invoicer.rb.patch

Error

• Email ch.ODDB.org Report - Error Export: Mail Patinfo-Invoices - 30/11/2011

Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
/home/masa/work/oddb.org_2/src/plugin/patinfo_invoicer.rb:69:in `match'
/home/masa/work/oddb.org_2/src/plugin/patinfo_invoicer.rb:69:in `unique_name'
/home/masa/work/oddb.org_2/src/plugin/info_invoicer.rb:124:in `block (2 levels) in filter_paid'

Refer to patinfo_invoicer.rb.patch

Error (export_index_therapeuticus_csv)

• Email ch.ODDB.org Report - Error Export: index_therapeuticus - 30/11/2011

Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
(druby://localhost:10005) /home/masa/work/oddb.org/ext/export/src/csv_exporter.rb:87:in `gsub'
(druby://localhost:10005) /home/masa/work/oddb.org/ext/export/src/csv_exporter.rb:87:in `block in collect_languages'
/home/masa/work/oddb.org/src/plugin/csv_export.rb:85:in `export_index_therapeuticus'
/home/masa/work/oddb.org/src/util/exporter.rb:137:in `block in export_index_therapeuticus_csv'
/home/masa/work/oddb.org/src/util/exporter.rb:317:in `call'
/home/masa/work/oddb.org/src/util/exporter.rb:317:in `safe_export'

Error (export_doc_csv, export_index_therapeuticus_csv, export_price_history_csv)

• Email ch.ODDB.org Report - Error Export: doctors.csv - 30/11/2011

Error: NameError
Message: uninitialized constant CSV::Writer
Backtrace:
(druby://localhost:10005) /home/masa/work/oddb.org/ext/export/src/csv_exporter.rb:97:in `dump'
(druby://localhost:10005) /home/masa/work/oddb.org/ext/export/src/odba_exporter.rb:92:in `block (2 levels) in export_doc_csv'
/home/masa/work/oddb.org_3/src/plugin/csv_export.rb:21:in `export_doctors'
/home/masa/work/oddb.org_3/src/util/exporter.rb:102:in `block in export_doc_csv'
/home/masa/work/oddb.org_3/src/util/exporter.rb:315:in `call'

Note

• CSV::Reader, CSV::Writer class are gone from Ruby 1.9

Refer to csv_exporter.rb.patch odba_exporter.rb.patch

Error (export_oddbdat)

• Email ch.ODDB.org Report - Error Export: oddbdat - 30/11/2011

Error: DRb::DRbConnError
Message: connection closed
Backtrace:
/usr/local/lib/ruby/1.9.1/drb/drb.rb:570:in `load'
/usr/local/lib/ruby/1.9.1/drb/drb.rb:632:in `recv_reply'
/usr/local/lib/ruby/1.9.1/drb/drb.rb:918:in `recv_reply'
/home/masa/work/oddb.org/src/plugin/oddbdat_export.rb:59:in `export'
/home/masa/work/oddb.org/src/util/exporter.rb:160:in `block in export_oddbdat'

Note

• Do not run 2 exporters at the same time
• After one exporter method is done, the exported is killed and it starts again after 30 seconds

Error (update_price_feeds)

/home/masa/work/oddb.org/src/plugin/plugin.rb:84:in `block in update_rss_feeds': undefined method `mv' for File:Class (NoMethodError)
        from /home/masa/work/oddb.org/src/plugin/plugin.rb:48:in `call'
        from /home/masa/work/oddb.org/src/plugin/plugin.rb:48:in `block in l10n_sessions'
        from /home/masa/work/oddb.org/src/plugin/plugin.rb:45:in `each_key'

Refer to plugin.rb.patch

29.11.2011 update_bsv, update_swissmedic and followers

Error (update_swissmedic)

NoMethodError: undefined method `values' for nil:NilClass when updating index 'sequence_vaccine' with a ODDB::Registration
["(eval):2:in `block in proc_instance_target'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:265:in `call'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:265:in `update_origin'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:170:in `update'"]
[...]

Error (update_price_feeds)

/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html': incompatible character encodings: ASCII-8BIT and UTF-8 (Encoding::CompatibilityError)
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/template.rb:123:in `block in to_html'

Refer to component.rb.patch

Error (export_oddb_csv)

• Email ch.ODDB.org Report - Error: oddb.csv - 29/11/2011

Plugin: ODDB::CsvExportPlugin
Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
/home/masa/work/oddb.org_3/src/model/dose.rb:32:in `match'
/home/masa/work/oddb.org_3/src/model/dose.rb:32:in `initialize'
/home/masa/work/oddb.org_3/src/model/dose.rb:16:in `new'
/home/masa/work/oddb.org_3/src/model/dose.rb:16:in `from_quanty'

Refer to dose.rb.patch

Error

• Email ch.ODDB.org Report - Error: oddb.csv - 29/11/2011

Plugin: ODDB::CsvExportPlugin
Error: TypeError
Message: can't convert String into Hash
Backtrace:
(eval):3:in `merge'
(eval):3:in `merge'
/usr/local/lib/ruby/1.9.1/csv.rb:1274:in `generate_line'
/home/masa/work/oddb.org_3/src/view/drugs/csv_result.rb:343:in `block in to_csv'
/home/masa/work/oddb.org_3/src/view/drugs/csv_result.rb:342:in `collect'
/home/masa/work/oddb.org_3/src/view/drugs/csv_result.rb:342:in `to_csv'

Note

• CSV class has changed drastically from Ruby 1.8 to 1.9

Warning

 /usr/local/lib/ruby/1.9.1/net/protocol.rb:313: warning: regexp match /.../n against to ISO-8859-1 string

Refer to csv_result.rb.patch

Error (update_bsv)

• Email ch.ODDB.org Report - Error: SL-Update (XML) - 28/11/2011

Plugin: ODDB::BsvXmlPlugin
Error: NoMethodError
Message: undefined method `[]=' for nil:NilClass
Backtrace:
/home/masa/work/oddb.org/src/util/log.rb:68:in `block in notify'
/home/masa/work/oddb.org/src/util/log.rb:67:in `each'
/home/masa/work/oddb.org/src/util/log.rb:67:in `notify'
/home/masa/work/oddb.org/src/util/updater.rb:456:in `log_notify_bsv'
/home/masa/work/oddb.org/src/util/updater.rb:257:in `block in update_bsv'

Refer to log.rb.patch

Warning

 /usr/local/lib/ruby/1.9.1/net/protocol.rb:313: warning: regexp match /.../n against to UTF-8 string

28.11.2011 update_bsv and update_bsv_followers

Error (update_price_feeds)

/home/masa/work/oddb.org_2/src/plugin/rss.rb:23:in `each': can't iterate from Time (TypeError)
        from /home/masa/work/oddb.org_2/src/plugin/rss.rb:23:in `include?'
        from /home/masa/work/oddb.org_2/src/plugin/rss.rb:23:in `include?'
        from /home/masa/work/oddb.org_2/src/plugin/rss.rb:23:in `block in update_price_feeds'
        from /home/masa/work/oddb.org_2/src/model/sequence.rb:140:in `each'
        from /home/masa/work/oddb.org_2/src/model/sequence.rb:140:in `each_package'

Refer to rss.rb.patch

/usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html': incompatible character encodings: ASCII-8BIT and UTF-8 (Encoding::CompatibilityError)
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/composite.rb:263:in `to_html'
        from /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.0/lib/htmlgrid/template.rb:123:in `block in to_html'

Refer to composite.rb.patch

Error (update_lppv)

• Email ch.ODDB.org Report - Error: Lppv prices - 28/11/2011

Plugin: ODDB::LppvPlugin
Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
/home/masa/work/oddb.org_2/src/util/html_parser.rb:153:in `gsub'
/home/masa/work/oddb.org_2/src/util/html_parser.rb:153:in `feed'
/home/masa/work/oddb.org_2/src/plugin/lppv.rb:103:in `get_prices'
/home/masa/work/oddb.org_2/src/plugin/lppv.rb:92:in `block (2 levels) in update'
/home/masa/work/oddb.org_2/src/plugin/lppv.rb:91:in `upto'

Refer to html_parser.rb.patch

Error

• Email ch.ODDB.org Report - Error: SL-Update (XML) - 25/11/2011

Plugin: ODDB::BsvXmlPlugin
Error: NoMethodError
Message: undefined method `diff' for #<RuntimeError: can't add a new key into hash during iteration>
@report: {:name_base=>"Allergovit Mix Gramin/Artemi/Secale", :name_descr=>"Inj Susp Stärke B", :swissmedic_no5_bag=>"60621", :deductible=>:deductible_g, :generic_type=>:unknown, :atc_class=>"V01AA20", :pharmacode_bag=>"4880127", :swissmedic_no5_oddb=>"60621", :swissmedic_no8_bag=>"60621002", :pharmacode_oddb=>"4880127"}
Backtrace:
/home/masa/work/oddb.org/src/util/persistence.rb:234:in `issue_update'
/home/masa/work/oddb.org/src/util/oddbapp.rb:122:in `block in update'
/home/masa/work/oddb.org/src/util/failsafe.rb:10:in `call'
/home/masa/work/oddb.org/src/util/failsafe.rb:10:in `failsafe'
/home/masa/work/oddb.org/src/util/oddbapp.rb:121:in `update'

Console Log

failsafe rescued RuntimeError < StandardError
can't add a new key into hash during iteration
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/cache.rb:488:in `store'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/cache.rb:488:in `block in store_cache_entry'
<internal:prelude>:10:in `synchronize'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/cache.rb:482:in `store_cache_entry'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/cache.rb:474:in `store'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/persistable.rb:267:in `odba_isolated_store'
/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/persistable.rb:385:in `block in odba_store_unsaved'

Refer to cache.rb.patch

Note

• This Hash iteration error also can be caused by a Hash iteration in the different thread from the one where a new key is added into the Hash
• Do not forget exclusive access control (ex. using Mutex) in such a Hash interation process shared with another thread

Sample1 (This causes the error)

hash = {1=>2, 3=>4}
p hash

cleaner = Thread.new {
  hash.each do |k,v|
    sleep(10)
  end
}

sleep(1)
hash.store(2,3)
p hash

Sample2 (This is safe)

hash = {1=>2, 3=>4}
p hash

mutex = Mutex.new
cleaner = Thread.new do
  mutex.synchronize do
    hash.each do |k,v|
      sleep(10)
    end
  end
end

sleep(1)
mutex.synchronize do
  hash.store(2,3)
end
p hash

24.11.2011 Setup script

Apache error log

• /var/log/apache2/error_log

[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: Wed Nov 23 11:00:35 +0100 2011 - 70317589258020 - TypeError - can't iterate from Time
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:29:in `each'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:29:in `include?'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:29:in `include?'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:29:in `block in init'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:24:in `select'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /home/masa/work/oddb.org/src/state/drugs/init.rb:24:in `init'
[Wed Nov 23 11:00:35 2011] [error] access to / failed for (null), reason: (druby://localhost:10000) /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.0.0/lib/sbsm/session.rb:287:in `logout'
...

Update

• src/state/drugs/init.rb

      @model.fachinfo_news = fachinfos.select { |fi|
        #range.include? fi.revision
        range.cover? fi.revision
      }

Reference

• Range.cover? http://redmine.ruby-lang.org/issues/3623

update_swissmedic

Error

TypeError: can't convert String into Integer when updating index 'sequence_generic_type_index' with a ODDB::Sequence
["/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:301:in `[]'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:301:in `block in current_ids'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:299:in `collect'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.0.0/lib/odba/index.rb:299:in `current_ids'"]
[...]

Refer to

• statement.rb.patch
• row.rb.patch

update_bsv

Errors

• Email ch.ODDB.org Report - Error: SL-Update (XML) - 24/11/2011

Plugin: ODDB::BsvXmlPlugin
Error: Encoding::CompatibilityError
Message: incompatible encoding regexp match (UTF-8 regexp with ASCII-8BIT string)
Backtrace:
/usr/local/lib/ruby/1.9.1/rexml/source.rb:210:in `match'
/usr/local/lib/ruby/1.9.1/rexml/source.rb:210:in `match'
/usr/local/lib/ruby/1.9.1/rexml/parsers/baseparser.rb:440:in `pull'
/usr/local/lib/ruby/1.9.1/rexml/parsers/streamparser.rb:17:in `parse'
/usr/local/lib/ruby/1.9.1/rexml/document.rb:205:in `parse_stream'

Refer to baseparser.rb.patch sourch.rb.patch

• Email ch.ODDB.org Report - Error: SL-Update (XML) - 24/11/2011

Plugin: ODDB::BsvXmlPlugin
Error: NoMethodError
Message: undefined method `each' for "Gesamthaft zugelassen 120 Punkte. Iniectabilia sine limitatione":String
Backtrace:
/home/masa/work/oddb.org/src/plugin/bsv_xml.rb:59:in `update_chapter'
/home/masa/work/oddb.org/src/plugin/bsv_xml.rb:123:in `block in tag_end'
/home/masa/work/oddb.org/src/plugin/bsv_xml.rb:120:in `each_key'
/home/masa/work/oddb.org/src/plugin/bsv_xml.rb:120:in `tag_end'

Refer to bsv_xml.rb.patch

DBI patches

• Attach:statement.rb.patch.20111125.txt (Debugged DBI library)
• Attach:row.rb.patch.20111125.txt (Debugged DBI library)
• Attach:columninfo.rb.patch.20111123.txt

CSV.rb patch

• Attach:csv.rb.patch.20111123.txt

Patches

• Attach:object.rb.patch.20111123.txt
• Attach:chapter.rb.patch.20111123.txt
• Attach:who.rb.patch.20111123.txt
• Attach:assign_patinfo.rb.patch.20111123.txt
• Attach:notification.rb.patch.20111123.txt
• Attach:statement.rb.patch.20111123.txt
• Attach:18_19_loading_compatibility.rb.patch.20111207.txt
• Attach:init.rb.patch.20111123.txt
• Attach:interval.rb.patch.20111202.txt
• Attach:session.rb.patch.20111123.txt
• Attach:additional_information.rb.patch.20111123.txt
• Attach:log.rb.patch.20111129.txt
• Attach:activeagent.rb.patch.20111123.txt
• Attach:searchterms.rb.patch.20111123.txt
• Attach:composition.rb.patch.20111123.txt
• Attach:doctor.rb.patch.20111123.txt
• Attach:galenicform.rb.patch.20111123.txt
• Attach:product.rb.patch.20111123.txt
• Attach:package.rb.patch.20111123.txt
• Attach:part.rb.patch.20111123.txt
• Attach:registration.rb.patch.20111123.txt
• Attach:sequence.rb.patch.20111123.txt
• Attach:slentry.rb.patch.20111123.txt
• Attach:substance.rb.patch.20111123.txt
• Attach:address.rb.patch.20111123.txt
• Attach:source.rb.patch.20111124.txt
• Attach:baseparser.rb.patch.20111124.txt
• Attach:persistable.rb.patch.20111124.txt
• Attach:bsv_xml.rb.patch.20111124.txt
• Attach:persistence.rb.patch.20111125.txt
• Attach:cache.rb.patch.20111128.txt (Debugged Hash iteration error (ODBA bug on Ruby 1.9.3))
• Attach:html_parser.rb.patch.20111128.txt (Debugged update_lppv)
• Attach:rss.rb.patch.20111128.txt (Debugged update_price_feeds)
• Attach:dose.rb.patch.20111129.txt (Debugged export_oddb_csv)
• Attach:csv_result.rb.patch.20111129.txt (Debugged export_oddb_csv)
• Attach:plugin.rb.patch.20111130.txt (Debugged update_price_feeds)
• Attach:oddbdat.rb.patch.20111130.txt (to run exportd)
• Attach:component.rb.patch.20111130.txt (Debugged update_price_feeds)
• Attach:csv_exporter.rb.patch.20111130.txt (Debugged export_doc_csv)
• Attach:odba_exporter.rb.patch.20111130.txt (Debugged export_doc_csv)
• Attach:info_invoicer.rb.patch.20111130.txt (Debugged mail_patinfo_invoices)
• Attach:patinfo_invoicer.rb.patch.20111130.txt (Debugged mail_patinfo_invoices)
• Attach:substance.rb.patch.20111201.txt (Deubugged export_oddbdat)
• Attach:server.rb.patch.20111201.txt (Debugged mail_patinfo_invoices)
• Attach:fachinfo_invoicer.rb.patch.20111202.txt (Debugged mail_fachinfo_log)
• Attach:invoicer.rb.patch.20111202.txt (Debugged mail_fachinfo_log)
• Attach:iso-latin1.rb.patch.20111202.txt (Debugged migel)

Scripts

• Attach:install_ruby193.20111123.txt
• Attach:install_git.sh.20111208.txt.txt
• Attach:install_gem.sh.20111201.txt
• Attach:oddb_patches.sh.20111208.txt
• Attach:gem_patches.sh.20111209.txt
• Attach:add_magic_comment.rb.20111123.txt