---
Got the following error message in import_daily
Plugin: ODDB::SwissmedicPlugin Error: NoMethodError Message: undefined method `to_i' for #<DateTime:0x000000cbb801c0> Backtrace: /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/compatibility.rb:29:in `date_cell' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:274:in `_comparable' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:220:in `block in rows_diff' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:218:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:218:in `each_with_index' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:218:in `rows_diff' /var/www/oddb.org/src/plugin/swissmedic.rb:422:in `rows_diff' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:136:in `block in diff' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:312:in `block in each_valid_row' /usr/local/lib/ruby/gems/1.9.1/gems/rubyXL-1.2.10/lib/rubyXL/worksheet.rb:31:in `block in each' /usr/local/lib/ruby/gems/1.9.1/gems/rubyXL-1.2.10/lib/rubyXL/worksheet.rb:31:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/rubyXL-1.2.10/lib/rubyXL/worksheet.rb:31:in `each' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:300:in `each_valid_row' /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/swissmedic-diff.rb:110:in `diff' /var/www/oddb.org/src/plugin/swissmedic.rb:63:in `update' /var/www/oddb.org/src/util/updater.rb:399:in `block in update_swissmedic' /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:397:in `update_swissmedic' /var/www/oddb.org/src/util/updater.rb:197: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>'
In log/oddb/debug/2014/07.log found
2014-07-07 07:21:10 CESTlog notify Fach- und Patienteninfo Updates (swissmedicinfo.ch): sent mail 2014-07-07 07:21:10 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb: 276 updated download.size is 2678294./var/www/oddb.org/data/xls/Packungen-2014.07.07.xlsx now 2678294 bytes != /var/www/oddb.org/data/xls/Packungen-latest.xlsx 2672682 2014-07-07 07:21:10 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb: 53 update target "/var/www/oddb.org/data/xls/Packungen-2014.07.07.xlsx"2678294 bytes. Latest /var/www/oddb.org/data/xls/Packungen-latest.xlsx 2672682 bytes 2014-07-07 07:21:11 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb: 281 skip writing /var/www/oddb.org/data/xls/Präparateliste-2014.07.07.xlsx as /var/www/oddb.org/data/xls/Präparateliste-latest.xlsx is 2228737 bytes. Returning latest 2014-07-07 07:28:32 CESTlog notify Error: swissmedic: start outgoing process ["log"] 2014-07-07 07:28:32 CESTUtil.send_mail list_and_recipients ["log"] 2014-07-07 07:28:32 CEST Util.log_and_deliver_mail to=["ngiger@ywesee.com", "zdavatz@ywesee.com"] subject ch.ODDB.org Report - Error: swissmedic - 07/2014 size Plugin: ODDB::Swiss
Reproduced the error locally. Tried changing /usr/local/lib/ruby/gems/1.9.1/gems/swissmedic-diff-0.1.7/lib/compatibility.rb:29 to
if data.value.class.to_s == 'DateTime'
puts "data is_a RubyXL::Cell and value #{data.value.class} is_a? Date #{data.value.is_a?(Date)} DateTime #{data.value.is_a?(DateTime)}"
return Date.new(1899,12,30)+data.to_date.value.to_i
else
return Date.new(1899,12,30)+data.value.to_i if data.is_a?(RubyXL::Cell)
end
Now we get further, but have the following error
Plugin: ODDB::SwissmedicPlugin Error: TypeError Message: '2014-06-06'(DateTime) should be NilClass or Date Backtrace: /var/www/oddb.org/src/util/persistence.rb:121:in `block (2 levels) in define_check_class_methods' /var/www/oddb.org/src/util/persistence.rb:87:in `block in update_values' /var/www/oddb.org/src/util/persistence.rb:84:in `each' /var/www/oddb.org/src/util/persistence.rb:84:in `update_values' /var/www/oddb.org/src/util/persistence.rb:260:in `issue_update' /var/www/oddb.org/src/util/oddbapp.rb:133:in `block in update' /var/www/oddb.org/src/util/failsafe.rb:10:in `call' /var/www/oddb.org/src/util/failsafe.rb:10:in `failsafe' /var/www/oddb.org/src/util/oddbapp.rb:131:in `update' /var/www/oddb.org/src/util/oddbapp.rb:1575:in `update' /var/www/oddb.org/src/plugin/swissmedic.rb:830:in `update_sequence' /var/www/oddb.org/src/plugin/swissmedic.rb:764:in `block in update_registrations' /var/www/oddb.org/src/plugin/swissmedic.rb:760:in `each' /var/www/oddb.org/src/plugin/swissmedic.rb:760:in `update_registrations' /var/www/oddb.org/src/plugin/swissmedic.rb:70:in `update' /var/www/oddb.org/src/util/updater.rb:406:in `block in update_swissmedic' /var/www/oddb.org/src/util/updater.rb:508:in `call' /var/www/oddb.org/src/util/updater.rb:508:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:404:in `update_swissmedic' /var/www/oddb.org/src/util/updater.rb:188:in `run' jobs/import_daily:34: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>'
One of the problem is that a DateTime object is also a Date.object. Rerunning import and debugging, which accessor has problems dealing with the DateTime. I think it might be easier to relax the model to accept a DateTime, too like in src/model/registration.rb: :registration_date => ["DateTime","Date"]. Adding a dump of each row and restarting import_swissmedic again.
Now I get the error Message: sequence_date= '2014-06-02'(DateTime) should be NilClass or Datex
Copied downloads Packungen.xlsx to test/data/Packungen_2014_small.xlsx in swissmedic-diff. Now the unit tests take almost 10 minutes to complete, but show the error. Adding a workaroung and some debugging output to catch the failing rows. Now I see output like
Rescue in Spreadsheet.date_cell for idx 7 ["00274", "01", (4,2): Cardio-Pulmo-Rénal Sérocytol, suppositoire, datatype = s, style_index = 6, (4,3): Sérolab, société anonyme, datatype = s, style_index = 4, (4,4): 08.07., datatype = s, style_index = 4, (4,5): J06AA, datatype = s, style_index = 4, (4,6): Blutprodukte, datatype = s, style_index = 4, (4,7): 40294, datatype = , style_index = 23, (4,8): 40294, datatype = , style_index = 23, (4,9): 42119, datatype = , style_index = 23, "001", (4,11): 3, datatype = s, style_index = 4, (4,12): Suppositorien, datatype = s, style_index = 5, (4,13): B, datatype = s, style_index = 6, (4,14): globulina equina (immunisé avec coeur, tissu pulmonaire, reins de porcins), datatype = s, style_index = 6, (4,15): globulina equina (immunisé avec coeur, tissu pulmonaire, reins de porcins) 8 mg, propylenglycolum, conserv.: E 216, E 218, excipiens pro suppositorio., datatype = s, style_index = 6, (4,16): Traitement immunomodulant selon le Dr Thomas
Now when looking at the field "Erstzul.datum Präp." of row 7 00277 Coeur-Vaisseaux Sérocytol, suppositoire I had before in the unit-tests "26.04.2010" whereas now it displays "26.04.10" and has as "40294" as value to edit. Trying to copy a few lines from the new Packungen.xlsx resulted in RuntimeError: invalid file when running rake test. Trying to generate the small file from the current xlsx resulted in the same error. Therefore it triggered an error either in the RubyXL
Error comes with
Updating 61249 02 sequence_date Imnovid 2mg Hartkapseln -> #<DateTime: 2014-06-02T00:00:00+00:00 ((2456811j,0s,0n),+0s,2299161j)> todate #<Date: 2014-06-02 ((2456811j,0s,0n),+0s,2299161j)> DateTime -> Date
Fixed and added unit test with commits:
Trying to load rubyXL when running sudo -u apache /usr/local/bin/ruby bin/oddbd resulted in
/usr/local/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- rubyXL (LoadError)
from /usr/local/lib/ruby/site_ruby/1.9.1/rubygems/core_ext/kernel_require.rb:55:in `require'
from bin/oddbd:7:in `<main>'
Tried a long time till I figured out that I could provoke the same error when running as local user if I move the $HOME/.gem directory to $HOME/.gem.unused. Using gem env to analyse the difference.
Calling
sudo chown -R apache:apache /usr/local/lib/ruby/gems/1.9.1 sudo -u apache /usr/local/bin/gem install rubyXL sudo -u apache /usr/local/bin/gem content rubyXLfixed the problem.
Pushed commit Updated to use rubyzip >= 1.0.0. Now I am able to start oddbd without problem.
Reloading DB dump of last week and restarting import_daily.
Got the following error [# Opened /var/www/oddb.org/log/oddb/debug/2014/07.log
WARNING: RubyXL::Worksheet is not aware what to do with RubyXL::GenericStorageObject
WARNING: RubyXL::Worksheet is not aware what to do with RubyXL::GenericStorageObject /var/www/oddb.org/src/util/mail.rb: Configured email using /var/www/oddb.org/etc/oddb.yml @cfg is now "smtp.gmail.com" 587 "ngiger@ywesee.com" Util.log_and_deliver_mail to=["ngiger@ywesee.com"] subject ch.ODDB.org Report - Error: swissmedic - 07/2014 size Plugin: ODDB::SwissmedicPlugin Error: NoMethodError Message: undefined method `at' for #<RubyXL::Row:0x0000001aee03f8> Backtrace: /var/www/oddb.org/src/plugin/swissmedic.rb:442:in `block in source_row'
Fixed this error, too. Reloading db and restarting import_daily too. After a successfull import of the fachinfo my cablecom had a network error (around 19:04) and I had to restart the import_daily again. Now I received the emails from FI and PI. Update BSV still running. Pushing Update to use swissmedic-diff 0.1.8 to fix to_i-error.
I see (again) several errors like this
NoMethodError: undefined method `fachinfo' for nil:NilClass when updating index 'interactions_index_de' with a ODDB::Sequence ["(eval):2:in `block in proc_instance_origin'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:202:in `call'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:202:in `update_target'", "/usr/local/lib/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:161:in `update'"] [...]
After running emerge --umerge ruby I was unable to emerge ruby18!!
Zeno remarked that the print button in Rezeptansicht did not work in oddb.org