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undefined method `[]' for nil:NilClass
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undefined method `[]' for nil:NilClassOn thinpower we got the following error
Error: NoMethodError Message: undefined method `[]' for nil:NilClass Backtrace: /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' /usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:131:in `[]' /var/www/oddb.org/src/plugin/yaml.rb:87:in `block (3 levels) in export_fachinfos' /var/www/oddb.org/src/plugin/yaml.rb:86:in `each' /var/www/oddb.org/src/plugin/yaml.rb:86:in `block (2 levels) in export_fachinfos' /var/www/oddb.org/src/plugin/yaml.rb:85:in `each' /var/www/oddb.org/src/plugin/yaml.rb:85:in `block in export_fachinfos' /var/www/oddb.org/src/plugin/yaml.rb:32:in `call' /var/www/oddb.org/src/plugin/yaml.rb:32:in `check_infos' /var/www/oddb.org/src/plugin/yaml.rb:84:in `export_fachinfos' /var/www/oddb.org/src/util/exporter.rb:307:in `block in export_fachinfo_yaml' /var/www/oddb.org/src/util/exporter.rb:425:in `call' /var/www/oddb.org/src/util/exporter.rb:425:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:306:in `export_fachinfo_yaml' /var/www/oddb.org/jobs/export_fachinfo_yaml:18: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' /var/www/oddb.org/jobs/export_fachinfo_yaml:13:in `<module:Util>' /var/www/oddb.org/jobs/export_fachinfo_yaml:12:in `<module:ODDB>' /var/www/oddb.org/jobs/export_fachinfo_yaml:11:in `<main>'
Fix was easy. Testing it on my vm. Fix did not work, adding debug output and running import again.
Had to call to_yaml with a rescue clause (needed by exactly 2 fachinfos). Also 224 (of 12886) fachinfos do not have a localized_name and stem probably from unsuccessfull import. May be should delete them.
bin/admin reports 6443 as fachinfos.size. (each with :de and :fr). Also fachinfo.to_yaml is very slow! I took 135 minutes to complete.
For Xeljanz (Iksnr 62630) we still have a sequence 00 after the update from Packungen.xls. This must be corrected. Looking for all sequence['00'] via bin/admin.
$suche = []; registrations.each{ |iksnr, reg| $suche << iksnr if reg.sequences['00'] != nil}; $suche.sizeHash
ch.oddb>
->
ch.oddb> $suche = []; registrations.each{ |iksnr, reg| $suche << iksnr if reg.sequences['00'] != nil}; $suche.size
-> 31
ch.oddb> $suche[0..10]
-> ["00828", "10754", "12498", "17644", "29300", "31919", "33709", "42180", "52265", "57487", "57515"]
-> ["58458", "62438", "62470", "62566", "62583", "62612", "62630", "62658", "62711", "62785", "62786"]
ch.oddb> $suche[22..31]
-> ["62920", "62976", "63029", "63030", "63200", "63257", "67769", "69870", "72736"]
Looking at http://ch.oddb.org/de/gcc/show/reg/00828 we find that we have created a sequence '00' even when we see a "Widerruf der Zulassung 24.10.2013". For unknown reasons http://oddb-ci.dyndns.org/de/gcc/show/reg/00828 does not display. "Widerruf der Zulassung 24.10.2013". Therefore I will drop in reimport the actual database from oddb.org. Then I will try to fix this situation via a bin/admin command, to see how many errors will remain afterwards.
$suche = []; registrations.each{ |iksnr, reg| $suche << iksnr if reg.sequences['00'] != nil and reg.inactive?}; $suche.size
ch.oddb> $suche[0..10]
-> ["Zulassungs-Nummer", "17644", "52265", "62470", "29300", "57487", "67769", "00828", "31919", "57515", "62583"]
ch.oddb> $suche[11..21]
-> ["69870", "10754", "33709", "58458", "72736", "12498", "42180", "62438", "62711", "63257", "63200"]
$deleted = []; registrations.each{ |iksnr, reg| if reg.sequences['00'] != nil and reg.inactive? then $deleted <<iksnr; delete reg.sequence('00').pointer; update(reg.pointer, :sequences => {}); end }; $deleted.size
-> 22
ch.oddb> $suche = []; registrations.each{ |iksnr, reg| $suche << iksnr if reg.sequences['00'] != nil }; $suche.size
-> 14
ch.oddb> $suche[0..14]
-> ["62976", "62658", "63030", "62566", "62785", "62786", "62612", "62920", "62630", "63029", "62672", "65040", "62904", "62453"]
Now looking at
On thinpower we got the following error while running sudo -u apache jobs/update_textinfo_swissmedicinfo --no-download --target=both AstraZeneca --reparse.
Plugin: ODDB::TextInfoPlugin Error: NoMethodError Message: undefined method `create_package' for nil:NilClass Backtrace: /var/www/oddb.org/src/plugin/text_info.rb:582:in `create_dummy_package_if_necessary' /var/www/oddb.org/src/plugin/text_info.rb:1365:in `block in import_swissmedicinfo_by_iksnrs' /var/www/oddb.org/src/plugin/text_info.rb:1362:in `each' /var/www/oddb.org/src/plugin/text_info.rb:1362:in `import_swissmedicinfo_by_iksnrs' /var/www/oddb.org/src/plugin/text_info.rb:1383:in `import_swissmedicinfo_by_companies' /var/www/oddb.org/src/plugin/text_info.rb:1397:in `import_swissmedicinfo' /var/www/oddb.org/src/util/updater.rb:512:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:303:in `update_textinfo_swissmedicinfo' jobs/update_textinfo_swissmedicinfo:39: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/update_textinfo_swissmedicinfo:12:in `<module:Util>' jobs/update_textinfo_swissmedicinfo:11:in `<module:ODDB>' jobs/update_textinfo_swissmedicinfo:10:in `<main>'
Trying to reproduce the problem here on my VM. Could reproduce the problem here. Situation for IKSNR 52110 'Beloc Zok' is that there exist 4 sequences but no package at all. Adapted handling the code to handle this situation and rerunning the import.
I pose myself the question, how we got into this situation and why parsing the Packungen.xls this situation was not fixed. Running registrations.each{ |iksnr, reg| $stdout.puts "iksrn #{iksnr} reg #{reg.inspect}" if reg.packages.size == 0 and not reg.expired?} in bin/admin returns quite a few packages, eg. 00709 which is not found in Packungen.xls
Found 388 registrations where noc packages are defined. Used bin/admin
ch.oddb> $suche = []; registrations.each{ |iksnr, reg| $suche << iksnr if reg.packages.size == 0 and reg.active?}; $suche.size
-> 388
Solution is: create_dummy_package_if_necessary must exclude the following registrations
Rename the method to create_sequence_and_package_if_necessary to better reflect the actual work done. Now the import worked correctly. Pushed commit Fix importing expired registrations
Plugin: ODDB::SwissindexPharmaPlugin Error: ArgumentError Message: invalid value for Integer(): "7680274.00017" Backtrace: /var/www/oddb.org/src/plugin/swissindex.rb:234:in `sprintf' /var/www/oddb.org/src/plugin/swissindex.rb:234:in `block in report' /var/www/oddb.org/src/plugin/swissindex.rb:233:in `each' /var/www/oddb.org/src/plugin/swissindex.rb:233:in `report' /var/www/oddb.org/src/plugin/plugin.rb:54:in `block in log_info' /var/www/oddb.org/src/plugin/plugin.rb:53:in `each' /var/www/oddb.org/src/plugin/plugin.rb:53:in `inject' /var/www/oddb.org/src/plugin/plugin.rb:53:in `log_info' /var/www/oddb.org/src/util/updater.rb:144:in `log_info' /var/www/oddb.org/src/util/updater.rb:514:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:423:in `update_package_trade_status_by_swissindex' jobs/update_swissindex_pharma:16: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/update_swissindex_pharma:13:in `<module:Util>' jobs/update_swissindex_pharma:11:in `<module:ODDB>' jobs/update_swissindex_pharma:10:in `<main>'
Adding a debug printf to see which reg is updated.
Question is, wherefrom does the pack.barcode get the value "7680274.00017"? Adding also a printf when the @out_of_trade_true_list is set.
Tried to run the import, but got an Message: druby://oddb-ci.dyndns.org:45291 - #<Errno::ETIMEDOUT: Connection timed out - connect(2)> error.
Runing oddbd in a separate screen and rerunning the import. This time I got druby://oddb-ci.dyndns.org:48310 - #<Errno::ETIMEDOUT: Connection timed out - connect(2)>. Running jobs /var/www/oddb.org/ext/swissindex/bin/swissindex_nonpharmad and /var/www/oddb.org/ext/swissindex/bin/swissindex_pharmad in separate screens.
I thinks I have a problem with my network configuration. Unfortunately http://www.funtoo.org/ answers with nginx: 502 Bad Gateway. Attacking therefore another problem.
Once each week we get the following error:
Plugin: ODDB::SwissindexPharmaPlugin Error: ArgumentError Message: wrong number of arguments (2 for 1) Backtrace: /var/www/oddb.org/src/plugin/plugin.rb:40:in `initialize' /var/www/oddb.org/src/util/updater.rb:508:in `new' /var/www/oddb.org/src/util/updater.rb:508:in `block in update_notify_simple' /var/www/oddb.org/src/util/updater.rb:488:in `call' /var/www/oddb.org/src/util/updater.rb:488:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:506:in `update_notify_simple' /var/www/oddb.org/src/util/updater.rb:423:in `update_package_trade_status_by_swissindex' /var/www/oddb.org/src/util/updater.rb:398:in `update_swissmedic_followers' /var/www/oddb.org/src/util/updater.rb:196:in `run' /var/www/oddb.org/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' /var/www/oddb.org/jobs/import_daily:12:in `<module:Util>' /var/www/oddb.org/jobs/import_daily:11:in `<module:ODDB>' /var/www/oddb.org/jobs/import_daily:10:in `<main>'
Added some changes in src/util/updater.rb and src/plugin/plugin.rb to avoid this error. Running import_daily in a console to see whether everything is okay. Seems to be okay. Pushed commit Fix option handling for import_daily