registration('55829').sequences.values.first.iksnr.
Must fix errors like
Error: RuntimeError Message: undefined method `bsv_dossier' for nil:NilClass package ean code=7680580380018 Backtrace: /var/www/oddb.org/src/view/drugs/csv_result.rb:96:in `rescue in bsv_dossier' /var/www/oddb.org/src/view/drugs/csv_result.rb:93:in `bsv_dossier' /var/www/oddb.org/src/view/drugs/csv_result.rb:451:in `block (3 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:449:in `collect' /var/www/oddb.org/src/view/drugs/csv_result.rb:449:in `block (2 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:434:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:434:in `block in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:427:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:427:in `to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:472:in `block in to_csv_file' /var/www/oddb.org/src/view/drugs/csv_result.rb:471:in `open' /var/www/oddb.org/src/view/drugs/csv_result.rb:471:in `to_csv_file' /var/www/oddb.org/src/plugin/csv_export.rb:63:in `_export_drugs' /var/www/oddb.org/src/plugin/csv_export.rb:30:in `export_drugs' /var/www/oddb.org/src/util/exporter.rb:102:in `block in export_csv' /var/www/oddb.org/src/util/exporter.rb:343:in `call' /var/www/oddb.org/src/util/exporter.rb:343:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:101:in `export_csv' /var/www/oddb.org/src/util/exporter.rb:71:in `run' jobs/export_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/export_daily:12:in `<module:Util>' jobs/export_daily:11:in `<module:ODDB>' jobs/export_daily:10:in `<main>'
of
Error: ArgumentError Message: comparison of NilClass with ODDB::Ean13 failed Backtrace: /var/www/oddb.org/src/plugin/csv_export.rb:161:in `sort_by' /var/www/oddb.org/src/plugin/csv_export.rb:161:in `export_index_therapeuticus' /var/www/oddb.org/src/util/exporter.rb:168:in `block in export_index_therapeuticus_csv' /var/www/oddb.org/src/util/exporter.rb:343:in `call' /var/www/oddb.org/src/util/exporter.rb:343:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:166:in `export_index_therapeuticus_csv' /var/www/oddb.org/src/util/exporter.rb:73:in `run' jobs/export_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/export_daily:12:in `<module:Util>' jobs/export_daily:11:in `<module:ODDB>' jobs/export_daily:10:in `<main>'
or
Error: RuntimeError Message: undefined method `bsv_dossier' for nil:NilClass package ean code=7680580380018 Backtrace: /var/www/oddb.org/src/view/drugs/csv_result.rb:96:in `rescue in bsv_dossier' /var/www/oddb.org/src/view/drugs/csv_result.rb:93:in `bsv_dossier' /var/www/oddb.org/src/view/drugs/csv_result.rb:451:in `block (3 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:449:in `collect' /var/www/oddb.org/src/view/drugs/csv_result.rb:449:in `block (2 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:434:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:434:in `block in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:427:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:427:in `to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:472:in `block in to_csv_file' /var/www/oddb.org/src/view/drugs/csv_result.rb:471:in `open' /var/www/oddb.org/src/view/drugs/csv_result.rb:471:in `to_csv_file' /var/www/oddb.org/src/plugin/csv_export.rb:63:in `_export_drugs' /var/www/oddb.org/src/plugin/csv_export.rb:42:in `export_drugs_extended' /var/www/oddb.org/src/util/exporter.rb:105:in `block in export_csv' /var/www/oddb.org/src/util/exporter.rb:343:in `call' /var/www/oddb.org/src/util/exporter.rb:343:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:104:in `export_csv' /var/www/oddb.org/src/util/exporter.rb:71:in `run' jobs/export_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/export_daily:12:in `<module:Util>' jobs/export_daily:11:in `<module:ODDB>' jobs/export_daily:10:in `<main>'
Created unit tests for the cases where a package can be nil. Fixing the errors. Running jobs/import_bsv_followers to verify that they work. Did not work the first time. Must test for missing sl with unless sl.nil? instead of unless sl
Looking via at the registration 58038 Myozyme, to see why we cannot get the package for GTIN 7680580380018 (package.ikscd is 001). The method introduction_date cannot be executed because the composing slentry is nil. Why? Looks like it is a package recently create as I found in the logs
2016-03-16 22:23:03 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:969:in `update_package': 58038/01/001 {}
2016-03-16 22:23:03 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:990:in `update_package': create 58038/01/001 ptr :!create,:!registration,58038!sequence,01!package,001.. package #<ODDB::Package:0x007f0dd6601180
I must check, why the sl_entries did not get updated correctly when running import_bsv.
Fixing via bin/admin
registration('58038').package('001').create_sl_entry
ch.oddb> registration('58038').package('001').sl_entry.valid_from = Date.new(2011,11,1)
-> 2011-11-01
ch.oddb> registration('58038').package('001').sl_entry.introduction_date = Date.new(2011,11,1)
-> 2011-11-01
ch.oddb> registration('58038').package('001').sl_entry.valid_until = Date.new(9999,12,31)
-> 9999-12-31
registration('58038').package('001').odba_store
Now http://ch.oddb.org/de/gcc/show/reg/58038/seq/01/pack/001 displays correctly again. But we cannot edit it as admin user, because the sl_entry.pointer is wrong. Fixing by comparing to another pointer and setting it to the correct value
ch.oddb> registration('53662').sequence('01').package('013').sl_entry.pointer
-> :!registration,53662!sequence,01!package,013!sl_entry.
h.oddb> registration('53662').sequence('01').package('013').sl_entry.pointer == registration('53662').sequence('01').package('013').pointer + :sl_entry
-> true
registration('58038').package('001').sl_entry.pointer = registration('58038').package('001').pointer + :sl_entry
registration('58038').package('001').odba_store
Now http://ch.oddb.org/de/gcc/sl_entry/reg/58038/seq/01/pack/001 loads correctly again.
As expected by myself this did not fix the problem when exporting oddb.csv, as their are others errors of the same type. Changing the code to insert into the generated CSV values like "missing_sl_entry package ean code=" instead of raising a Runtime Error.
Trying to iterate over all bad sl_entries. Resetting my database to state of yesterday. Adding a breakpoint at line 245 of src/view/admin/package where it displays either "Bearbeiten" or "Erstellen".
Did see the following output of oddbd ODBA::Stub was unable to replace #27558508 from ODDB::Package:#9848279. Model.oid 9848279 at the breakpoint. Model.pointer is :!registration,58038!sequence,01!package,001.. In the pry session we see a difference:
[13] pry(#<ODDB::View::Admin::PackageForm>)> puts 99 unless model.sl_entry => nil [14] pry(#<ODDB::View::Admin::PackageForm>)> puts 99 unless model.sl_entry.nil? 99 => nil [16] pry(#<ODDB::View::Admin::PackageForm>)> model.sl_entry.class => NilClass
Therefore the admin-interface incorrectly assumes, that there is a SL-Entry even when there is none. Could not continue as pry did throw an exception.
Comparing output of de/gcc/drug/reg/58038/seq/01/pack/001 and /de/gcc/drug/reg/39036/seq/01/pack/001. Here I get
[1] pry(#<ODDB::View::Admin::PackageForm>)> model.oid => 34443561 [2] pry(#<ODDB::View::Admin::PackageForm>)> model.pointer => :!registration,39036!sequence,01!package,001. [3] pry(#<ODDB::View::Admin::PackageForm>)> model.sl_entry.class => NilClass [4] pry(#<ODDB::View::Admin::PackageForm>)> model.sl_entry.pointer NoMethodError: undefined method `pointer' for nil:NilClass [5] pry(#<ODDB::View::Admin::PackageForm>)> model.sl_entry.nil? => [6] pry(#<ODDB::View::Admin::PackageForm>)> puts model.oid unless model.sl_entry 34443561 => nil [7] pry(#<ODDB::View::Admin::PackageForm>)> puts model.oid unless model.sl_entry.nil? => nil
I enter a second time into the statement and see
[11] pry(#<ODDB::View::Admin::PackageForm>)> @session.request_path => "/de/gcc/drug/reg/58038/seq/01/pack/001" [12] pry(#<ODDB::View::Admin::PackageForm>)> model.oid => 9848279 [13] pry(#<ODDB::View::Admin::PackageForm>)> model.iksnr => "58038" [14] pry(#<ODDB::View::Admin::PackageForm>)> model.class => ODDB::Package [15] pry(#<ODDB::View::Admin::PackageForm>)> model.sl_entry.class => NilClass "/var/www/oddb.org/src/view/admin/package.rb:246:in `sl_entry'", [17] pry(#<ODDB::View::Admin::PackageForm>)> continue ODBA::Stub was unable to replace NilClass#27558508 from ODDB::Package:#9848279
It looks as if we have two stubs (packages) for this. Why? I go therefore into bearbeiten. I get the error about the parent being nil.
I think this problem stems from the fact that when running bsv-xml importer this package got replaced and the sl_entry was not correctly replaced.
Something got really confused. Output of bin/admin
ch.oddb> registration('39036').sequence('01').package('001').sl_entry.nil?
-> true
ch.oddb> registration('58038').sequence('01').package('001').sl_entry.nil?
-> false
ch.oddb> registration('58038').sequence('01').package('001').sl_entry.class
-> NilClass
-> NilClass
ch.oddb> nil.object_id
-> 4
ch.oddb> registration('58038').sequence('01').package('001').sl_entry.object_id
-> 70321544656780
ch.oddb> registration('39036').sequence('01').package('001').sl_entry.object_id
-> 4
Okay. I have an object which pretends to be of class nil, but has a different object_id than nil. Very Ruby!
Finding all of them
ch.oddb> $x = packages.find_all{|pack| pack.sl_entry.kind_of?(NilClass) && pack.sl_entry.object_id != 4}
-> Array
ch.oddb> $x.size
-> 35
$x.each{ |pack| puts "Correcting #{pack.iksnr}/#{pack.seqnr}/#{pack.ikscd}"; pack.sl_entry= nil; pack.odba_store}
Outputs on oddbdd
Correcting 56235/01/014 Correcting 56235/01/016 Correcting 56235/02/018 Correcting 56235/02/020 Correcting 56235/03/022 Correcting 56235/03/024 Correcting 58038/01/001 Correcting 52110/01/130 Correcting 52110/01/149 Correcting 52110/02/041 Correcting 52110/02/076 Correcting 52110/03/084 Correcting 52110/03/106 Correcting 52110/04/157 Correcting 52110/04/165 Correcting 51079/01/028 Correcting 51079/02/029 Correcting 39893/01/053 Correcting 39893/01/061 Correcting 50583/01/023 Correcting 50583/05/112 Correcting 50583/05/120 Correcting 50583/06/147 Correcting 44140/01/012 Correcting 44140/02/020 Correcting 44140/02/039 Correcting 44140/02/047 Correcting 44140/02/225 Correcting 44140/02/249 Correcting 44140/03/071 Correcting 44140/03/101 Correcting 44140/03/233 Correcting 44140/03/241 Correcting 44140/04/209 Correcting 29789/02/045
Okay. It looks as if in the import of the March 16, 35 of the newly created 89 Re-Created missing Packages, the update of the fields from swissmedic_source created the disaster. This item is also a bit special as it is done using a Hash. But now these packages display "Erstellen" for "Sl Eintrag", which is correct, as the bsv_xml-import did not run again.
When looking at http://ch.oddb.org/de/gcc/fachinfo/reg/56235 it display correctly only "Vollst. Fachinformation", "DDD". Rerunning import_bsv_follower another time.
Now seening the following error
Plugin: ODDB::CsvExportPlugin Error: NoMethodError Message: undefined method `active?' for #<Array:0x0000000580a1b0> Backtrace: /var/www/oddb.org/src/model/package.rb:442:in `public?' /usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing' /var/www/oddb.org/src/view/drugs/csv_result.rb:291:in `out_of_trade' /var/www/oddb.org/src/view/drugs/csv_result.rb:470:in `block (3 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:468:in `collect' /var/www/oddb.org/src/view/drugs/csv_result.rb:468:in `block (2 levels) in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:452:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:452:in `block in to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:445:in `each' /var/www/oddb.org/src/view/drugs/csv_result.rb:445:in `to_csv' /var/www/oddb.org/src/view/drugs/csv_result.rb:493:in `block in to_csv_file' /var/www/oddb.org/src/view/drugs/csv_result.rb:492:in `open' /var/www/oddb.org/src/view/drugs/csv_result.rb:492:in `to_csv_file' /var/www/oddb.org/src/plugin/csv_export.rb:63:in `_export_drugs' /var/www/oddb.org/src/plugin/csv_export.rb:30:in `export_drugs' /var/www/oddb.org/src/util/updater.rb:97:in `block in export_oddb_csv' /var/www/oddb.org/src/util/updater.rb:530:in `call' /var/www/oddb.org/src/util/updater.rb:530:in `wrap_update' /var/www/oddb.org/src/util/updater.rb:95:in `export_oddb_csv' /var/www/oddb.org/src/util/updater.rb:301:in `update_bsv_followers' jobs/import_bsv_followers:14: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_bsv_followers:12:in `<module:Util>' jobs/import_bsv_followers:11:in `<module:ODDB>' jobs/import_bsv_followers:10:in `<main>'