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201503124-oddb-org-wirkstoffe

Summary

  • oddb.org should import and display all components after a swissmedic-import as in oddb2xml

Commits

Index

Keep in Mind for work to do
  • Fix dojo error http://www.sitepen.com/blog/2012/10/31/debugging-dojo-common-error-messages/#forgot-dom-ready
  • I removed on May-27 tests for ix_registrationss, fix_sequences, fix_compositions, fix_packages from test/test_plugin/swissmedic.rb,as he could not find any references for them in the src code. Did I erroneously remove stuff when cleaning up the swissmedic import earlier?
  • The whole test for older/newer Packages must be adapted to xlsx. One must compare the rows (e.g. by creating csv files) and do the same stuff in xlsx!
  • creat gem: task: input=file with ean-codes, standard output show ean-codes + atc-code. Source is Swissmedic Packungen.xlsx or XML.
  • Import via data/medreg_companies.yaml

oddb.org should import and display all components after a swissmedic-import as in oddb2xml

Must fix problem shown by unit-test to discover chemical and units with '%'. Made additional unit-test pass under oddb2xml --calc. Looking now again at the unit-tests of oddb.org. Here I must make pass in test/test_plugin/swissmedic.rb the test_update_composition__chemical_form. This proved to be easy.

Now I must check why we run the update often, even when there are now changes. Running jobs/import_swissmedic_only update_compositions on oddb-ci2.

Pushed the following commits to oddb2xml

Waiting for import to finish. But log looks better and only makes an update if necessary. Log looks a lot better, but I rerun it again to see why I still got 286 deletions and 5351 creations. Report-Mail was

ODDB::SwissmedicPlugin - Report 24.03.2015
Total time to update: 130.00 [m]
Updated compositions: 21502
Deleted compositions: 228
Updated agents: 2775
New agents: 5351

Analysing what is happening with IKSNR 47657 seq 01 Nanocoll, Markierungsbesteck

2015-03-24 16:25:19 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent update 47657/01 from creator ptr :!create,:!registration,47657!sequence,01!composition,33022254!active_agent,Albuminum Humanum Colloidale 0%.5 Mg%, Stanni(ii) Chloridum Dihydricum.. label nil 2 args {:substance=>"Albuminum Humanum Colloidale 0.5 Mg, Stanni(ii) Chloridum Dihydricum", :dose=>Quanty(0.2,'mg')}
2015-03-24 16:25:19 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent update 47657/01 from creator ptr :!create,:!registration,47657!sequence,01!composition,33022254!active_agent,Poloxamerum.. label nil 2 args {:substance=>"Poloxamerum", :dose=>Quanty(238,'')}
2015-03-24 16:25:20 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent update 47657/01 from creator ptr :!create,:!registration,47657!sequence,01!composition,33032907!active_agent,I) Recenter Radioactivatum.. label "II" 4 args {:substance=>"I) Recenter Radioactivatum", :dose=>Quanty(99,''), :chemical_substance=>"Natrii Pertechnetas.", :chemical_dose=>nil}
2015-03-24 16:25:21 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:633 update_compositions delete1 1 atc_idx 0 :!registration,47657!sequence,01!composition,33022254!active_agent,Albuminum Humanum Colloidale 0%.5 Mg%, Stanni(ii) Chloridum Dihydricum. 0.2 mg
2015-03-24 16:25:21 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:633 update_compositions delete1 1 atc_idx 1 :!registration,47657!sequence,01!composition,33022254!active_agent,Poloxamerum. Poloxamerum 238 
2015-03-24 16:25:21 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:647 iksnr 47657 seqnr 01 comp_idx 2 delete :!registration,47657!sequence,01!composition,33032907. 99 
2015-03-24 16:36:31 +0100: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent update 53889/01 from active_agent ptr :!registration,53889!sequence,01!composition,9476577!active_agent,222849. label nil 0 args {}

via bin/admin

ch.oddb> registration('47657').sequence('01').compositions.last
-> Markierungsbesteck: 
ch.oddb> registration('47657').sequence('01').compositions.last.oid
-> 33022254
ch.oddb> registration('47657').sequence('01').compositions.first.oid
-> 9464580
ch.oddb> registration('47657').sequence('01').compositions.first
-> Markierungsbesteck: 
ch.oddb> registration('47657').sequence('01').compositions.first.substances.size
-> 0
ch.oddb> registration('47657').sequence('01').compositions.first.active_agents.size
-> 0
ch.oddb> registration('47657').sequence('01').compositions.last.active_agents.size
-> 0
ch.oddb> registration('47657').sequence('01').compositions.last.substances.size
-> 0
-> I): albuminum humanum colloidale 0.5 mg, stanni(II) chloridum dihydricum 0.2 mg, glucosum anhydricum, dinatrii phosphas monohydricus, natrii fytas (9:1), poloxamerum 238, q.s. ad pulverem pro vitro.
ch.oddb> registration('47657').sequence('01').compositions.last.source
-> I): albuminum humanum colloidale 0.5 mg, stanni(II) chloridum dihydricum 0.2 mg, glucosum anhydricum, dinatrii phosphas monohydricus, natrii fytas (9:1), poloxamerum 238, q.s. ad pulverem pro vitro.

May be I should use the method create_active_agent in model/composition. Does not work as expected. http://ch.oddb.org/de/gcc/drug/reg/47657/seq/01 shows the expected result whereas http://oddb-ci2.dyndns.org/de/gcc/drug/reg/47657/seq/01 still show two compositions without a galenic_form and without any substance.

IKSNR 00274 sequence 01 is getting upgraded each time, but it looks alright when visiting it via http://oddb-ci2.dyndns.org/de/gcc/drug/reg/00274/seq/01 and has the new "E 216" and "E 218" substances. Found the culprit. Comparision fails because sometimes of mixed case in substance name.

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Page last modified on March 24, 2015, at 07:45 PM