---
Got the following error mail
Plugin: ODDB::TextInfoPlugin Error: ArgumentError Message: invalid byte sequence in US-ASCII Backtrace: (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:319:in `match' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:319:in `match' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:319:in `handle_text' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:214:in `handle_element' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:282:in `block in handle_all_children' (druby://localhost:10002) /usr/local/lib/ruby/gems/1.9.1/gems/hpricot-0.8.6/lib/hpricot/traverse.rb:499:in `each' (druby://localhost:10002) /usr/local/lib/ruby/gems/1.9.1/gems/hpricot-0.8.6/lib/hpricot/traverse.rb:499:in `each_child' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:281:in `handle_all_children' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:200:in `handle_element' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:43:in `chapter' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:89:in `block in extract' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:87:in `each' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/textinfo_hpricot.rb:87:in `extract' (druby://localhost:10002) /var/www/oddb.org/ext/fiparse/src/fiparse.rb:201:in `parse_fachinfo_html' (druby://localhost:10002) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' (druby://localhost:10002) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' (druby://localhost:10002) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:10002) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:10002) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/text_info.rb:107:in `parse_fachinfo' /var/www/oddb.org/src/plugin/text_info.rb:1114:in `block in parse_and_update' /var/www/oddb.org/src/plugin/text_info.rb:1078:in `each' /var/www/oddb.org/src/plugin/text_info.rb:1078:in `parse_and_update' /var/www/oddb.org/src/plugin/text_info.rb:1138:in `block (3 levels) in import_info' /var/www/oddb.org/src/plugin/text_info.rb:1137:in `each' /var/www/oddb.org/src/plugin/text_info.rb:1137:in `block (2 levels) in import_info' /var/www/oddb.org/src/plugin/text_info.rb:1136:in `each_pair' /var/www/oddb.org/src/plugin/text_info.rb:1136:in `block in import_info' /var/www/oddb.org/src/plugin/text_info.rb:1133:in `each_pair' /var/www/oddb.org/src/plugin/text_info.rb:1133:in `import_info' /var/www/oddb.org/src/plugin/text_info.rb:1341:in `block in import_swissmedicinfo_by_index' /var/www/oddb.org/src/plugin/text_info.rb:1340:in `each_pair' /var/www/oddb.org/src/plugin/text_info.rb:1340:in `import_swissmedicinfo_by_index' /var/www/oddb.org/src/plugin/text_info.rb:1395:in `import_swissmedicinfo' /var/www/oddb.org/src/util/updater.rb:525:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:501:in `call' /var/www/oddb.org/src/util/updater.rb:501:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:519:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:308:in `update_textinfo_swissmedicinfo' /var/www/oddb.org/src/util/updater.rb:193:in `run' jobs/import_daily:13:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' jobs/import_daily:12:in `<module:Util>' jobs/import_daily:11:in `<module:ODDB>' jobs/import_daily:10:in `<main>'
Trying to get more info by adding some debug output and reproducing the problem on oddb-ci2 with the following steps
Got an error because flockhart plugin accessed a non existing table.aspx. Decided with Zeno to remove the flockhart plugin.
Pushed commits
Pulled them on thinpower.
Thinpower has another error
Plugin: ODDB::XlsExportPlugin Error: NoMethodError Message: undefined method `sequences' for "format_type":String Backtrace: (druby://localhost:10005) /var/www/oddb.org/src/model/sequence.rb:119:in `comparables' (druby://localhost:10005) /var/www/oddb.org/src/model/package.rb:214:in `comparables' (druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/generics_xls.rb:96:in `block in export_generics' (druby://localhost:10005) /var/www/oddb.org/src/model/sequence.rb:175:in `each' (druby://localhost:10005) /var/www/oddb.org/src/model/sequence.rb:175:in `each_package' (druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://localhost:10005) /var/www/oddb.org/src/model/registration.rb:149:in `block in each_package' (druby://localhost:10005) /var/www/oddb.org/src/model/registration.rb:148:in `each_value' (druby://localhost:10005) /var/www/oddb.org/src/model/registration.rb:148:in `each_package' (druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://localhost:10005) /var/www/oddb.org/src/util/oddbapp.rb:664:in `block in each_package' (druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `each_value' (druby://localhost:10005) /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' (druby://localhost:10005) /var/www/oddb.org/src/util/oddbapp.rb:663:in `each_package' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/generics_xls.rb:94:in `export_generics' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:113:in `block in export_generics_xls' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:286:in `call' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:286:in `block in safe_export' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/tempfile.rb:316:in `open' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:285:in `safe_export' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:111:in `export_generics_xls' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' (druby://localhost:10005) /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' /var/www/oddb.org/src/plugin/xls_export.rb:22:in `export_generics' /var/www/oddb.org/src/util/updater.rb:119:in `block in export_generics_xls' /var/www/oddb.org/src/util/updater.rb:501:in `call' /var/www/oddb.org/src/util/updater.rb:501:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:117:in `export_generics_xls' /var/www/oddb.org/src/util/updater.rb:271:in `update_bsv_followers' /var/www/oddb.org/src/util/updater.rb:204:in `run' jobs/import_daily:13:in `block in <module:Util>' /var/www/oddb.org/src/util/job.rb:40:in `call' /var/www/oddb.org/src/util/job.rb:40:in `run' jobs/import_daily:12:in `<module:Util>' jobs/import_daily:11:in `<module:ODDB>' jobs/import_daily:10:in `<main>'
seen in log/oddb/debug/2014/07.log
2014-07-01 12:51:32 CEST Util.log_and_deliver_mail to=["Tim.Suter@just-medical.com", "matthijs.ouwerkerk@just-medical.com", "ngiger@ywesee.com", "ouwerkerk@bluewin.ch", "zdavatz@ywesee.com"] subject ch.ODDB.org Report - Med-Drugs - Swissmedic 05/2014 - SL 07/2014 size swissdrug update Swissmedic 05/2014 - SL 07/2014 Error registrations (Swissmedic Number): 17233 2014-07-01 12:51:36 CESTlog notify Med-Drugs: sent mail
I get the same error NoMethodError undefined method `description' for "format_type":String when trying to display the drug with iksnr 17233 via the web interface. bin/oddbd displays even more info
NoMethodError undefined method `description' for "format_type":String /var/www/oddb.org/src/view/additional_information.rb:81:in `atc_description' /var/www/oddb.org/src/view/drugs/package.rb:175:in `atc_class' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:68:in `create' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:286:in `compose_component' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:211:in `block in compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:57:in `init' /var/www/oddb.org/src/view/drugs/package.rb:170:in `init' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/component.rb:139:in `initialize' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:61:in `new' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:61:in `create' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:286:in `compose_component' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:211:in `block in compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:57:in `init' /var/www/oddb.org/src/view/drugs/package.rb:301:in `init' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/component.rb:139:in `initialize' /var/www/oddb.org/src/view/publictemplate.rb:63:in `new' /var/www/oddb.org/src/view/publictemplate.rb:63:in `content' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:68:in `create' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:286:in `compose_component' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:211:in `block in compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:205:in `compose' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:57:in `init' /var/www/oddb.org/src/view/publictemplate.rb:60:in `init' /var/www/oddb.org/src/view/privatetemplate.rb:17:in `init' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/component.rb:139:in `initialize' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/state.rb:245:in `new' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/state.rb:245:in `view' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/state.rb:181:in `to_html' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/session.rb:447:in `to_html' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/session.rb:173:in `block in drb_process' <internal:prelude>:10:in `synchronize' /usr/local/lib/ruby/gems/1.9.1/gems/sbsm-1.2.3/lib/sbsm/session.rb:171:in `drb_process' /usr/local/lib/ruby/1.9.1/drb/drb.rb:1548:in `perform_without_block' /usr/local/lib/ruby/1.9.1/drb/drb.rb:1508:in `perform' /usr/local/lib/ruby/1.9.1/drb/drb.rb:1586:in `block (2 levels) in main_loop' /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `loop' /usr/local/lib/ruby/1.9.1/drb/drb.rb:1582:in `block in main_loop' ODDB::View::Drugs::PackageInnerComposite::COMPONENTS[[0, 3, 0]] in create(atc_class) ODDB::View::Drugs::PackageComposite::COMPONENTS[[0, 1]] in create(ODDB::View::Drugs::PackageInnerComposite) ODDB::View::Drugs::Package::COMPONENTS[[0, 3]] in create(content) error in SBSM::Session#http_headers: /de/gcc NoMethodError undefined method `description' for "format_type":String /var/www/oddb.org/src/view/additional_information.rb:81:in `atc_description' /var/www/oddb.org/src/view/drugs/package.rb:175:in `atc_class' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:68:in `create' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:286:in `compose_component' /usr/local/lib/ruby/gems/1.9.1/gems/htmlgrid-1.0.6/lib/htmlgrid/composite.rb:211:in `block in compose'
Using bin/admin shows a very curious result
ch.oddb> registration('17233').sequence('02').package('001').atc_class
-> format_type
Found it as a change /var/www/oddb.org/data/xls/Präparateliste-latest.xlsx with the following details "17233"=>[:name_base, :index_therapeuticus, :production_science, :registration_date, :expiry_date, :ikscd, :size, :unit, :ikscat, :substances, :composition, :indication_registration]. It looks that our handling for this kind of change is wrong! Reparsing FI/PI for 17233. Did not help.
Using bin/admin found that we have exactly two packages (both belonging to IKSNR 17233) where the atc_class is a String.
$all = []; packages.collect {|x| $all << x if x.atc_class.is_a?(String)}; $all.size
-> 2
ch.oddb> $all.first
-> #<ODDB::Package:0x0000000a3b1140>
ch.oddb> $all.first.iksnr
-> 17233
ch.oddb> $all.first.ikscd
-> 068
ch.oddb> $all.last.iksnr
-> 17233
ch.oddb> $all.last.ikscd
-> 001
ch.oddb> $all = []; packages.collect {|x| $all << x unless x.atc_class.is_a?(ODDB::AtcClass)}; $all.size
-> 43
ch.oddb> $classes = $all.collect{ |x| x.atc_class.class.to_s }.sort.uniq
-> ["NilClass", "String"]
And we have 41 where the atc_class is nil.
Discovered that when calling jobs/update_textinfo_swissmedicinfo with an IKSNR which does not yet have a registration, that it will fail, because of a missing app.registrations.odba_store. But somehow, also the package name does not get updated correctly, probably because name_base is nil. Why?
The patinfo works and is shown under http://oddb-ci2.dyndns.org/de/gcc/patinfo/reg/17233/seq/00. Importing the fachinfo still fails.