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201503131-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
  • Fix problem with radioactivatum 99m-technetio when parsing Wirkstoffe

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

Some IKSNR, eg. 00500 sequence 01 show up after the import under http://oddb-ci2.dyndns.org/de/gcc/drug/reg/00500/seq/04 having an empty substance. In the import I find 2015-03-30 23:22:11 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:590 update_active_agent update 00500/04 from creator 2 substances '' ptr :!create,:!registration,00500!sequence,04!composition,25004884!active_agent,Natrii Chloridi Solutio 9 G/l.. label nil 2 args {:dose=>Quanty(33,'ml'), :substance=>33020339} chemical_dose

Using pry to debug the problem.

Displaying 00615/seq/01 leads still to NoMethodError undefined method `resolve' for nil:NilClass. May be I must exclude lines starting with "Solvens" too.

Also I see superfluos updates like this 

2015-03-31 08:35:18 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:590 update_active_agent update 38471/01 from active_agent 9 substances 'Calcii Chloridum' ptr :!registration,38471!sequence,01!composition,9468552!active_agent,219761. label nil 1 args {:substance=>531} chemical_dose

bin/admin show 

ch.oddb> substance(513).oid
-> 513
ch.oddb> substance(513)
-> Quinaprilatum Monohydricum
ch.oddb> substance('Calciumchlorid')
-> Calcii Chloridum
ch.oddb> substance('Calciumchlorid').oid
-> 531
ch.oddb> substance('Calciumchlorid').names
-> ["Calciumchlorid", "Calcium Chloride", "Calcium Chlorure", "Calcii Chloridum", "Chlorure de Calcium", "Calcii Chloridum Dihydr.", "Calcii Chloridum Dihydricum", "Calcium", "Kalzium", "Kalcium"]

Which means, that I must check all possible names of a substance before doing an update. Changes seem to work for IKSNR 38471.

Now looking at the lines 2015-03-31 10:44:46 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent 15322/01 chemical_dose 3.5-4.2 == chemical_substance sennosidum b == nil and 2015-03-31 10:44:46 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:590 update_active_agent update 15322/01 from creator 3 substances ptr :!create,:!registration,15322!sequence,01!composition,9458026!active_agent,Sennae Folii Pulvis.. label nil 4 args {:dose=>Quanty(145,'mg'), :substance=>4821, :chemical_dose=>Quanty(3.85,), :chemical_substance=>4056} chemical_dose 3.5-4.2 mg

The http://oddb-ci2.dyndns.org/de/gcc/drug/reg/15322/seq/01 has Resolve nil errors. Some as IKNSR 00500. Looking via bin/admin at 00500. 

-> Redimune 1 g, Trockensubstanz mit Solvens
ch.oddb> registration('00500').sequence('04').compositions.size
-> 1
ch.oddb> registration('00500').sequence('04').compositions.first
-> Trockensubstanz mit Solvens: Immunoglobulinum Humanum Normale 1 g, 
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.size
-> 2
ch.oddb> registration('00500').sequence('04').compositions.first.substances.size
-> 2
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.first.oid
-> 25004887
ch.oddb> registration('00500').sequence('04').compositions.first.substances.first.oid
-> 24362289
ch.oddb> registration('00500').sequence('04').compositions.first.substances.first
-> Immunoglobulinum Humanum Normale
ch.oddb> registration('00500').sequence('04').compositions.first.substances.first
-> Immunoglobulinum Humanum Normale
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.first.substance.oid
-> 24362289
ch.oddb> registration('00500').sequence('04').compositions.first.substances.last
-> 
ch.oddb> registration('00500').sequence('04').compositions.first.substances.last.class
-> NilClass
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.last.class
-> ODDB::ActiveAgent
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.last.oid
-> 33037805
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.last.pointer
-> :!create,:!registration,00500!sequence,04!composition,25004884!active_agent,Natrii Chloridi Solutio 9 G/l..
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.last.dose.class
-> NilClass
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.last.to_a
-> [nil, nil]

Here active_agents.last does not have a substance. This seems to happen a few times. Trying to resolve the problem via bin/admin 

ch.oddb> delete registration('00500').sequence('04').compositions.first.active_agents.find { |x| x.substance == nil}.pointer
-> 
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents.find { |x| x.substance == nil}.pointer
-> :!create,:!registration,00500!sequence,04!composition,25004884!active_agent,Natrii Chloridi Solutio 9 G/l..
ch.oddb> registration('00500').sequence('04').compositions.first.delete_active_agent(33037805)
-> 
ch.oddb> registration('00500').sequence('04').compositions.first.active_agents
-> [#<ODBA::Stub:83292400#25004887 @odba_class= @odba_container=83762120#25004886>]

And now http://oddb-ci2.dyndns.org/de/gcc/drug/reg/00500/seq/04 works without problems. Adding a check to delete all such occurrences in plugin/swissmedic.rb.

Trying to find out why I have problems displaying http://oddb-ci2.dyndns.org/de/gcc/drug/reg/57875/seq/01. Using bin/admin shows 

ch.oddb> registration('57875').sequence('01').compositions.first.source
-> dextromethorphani hydrobromidum 8.5 mg corresp. dextromethorphanum 6.25 mg, arom.: natrii cyclamas, vanillinum et alia, color.: E 150, conserv.: E 218, E 216, excipiens ad solutionem pro 5 ml.
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].substance
-> Dextromethorphani Hydrobromidum
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].chemical_substance
-> Dextromethorphanum
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].chemical_dose
-> 6.25 
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].chemical_substance.oid
-> 5929
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].substance.oid
-> 5250
ch.oddb> registration('57875').sequence('01').compositions.first.active_agents[0].dose
-> 8.5mg / 5ml

In the import log I find the lines 

2015-03-31 11:46:49 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:582 update_active_agent 57875/01 chemical_dose 6.25  ==  chemical_substance dextromethorphanum == nil
2015-03-31 11:46:49 +0200: /var/www/oddb.org/src/plugin/swissmedic.rb:590 update_active_agent update 57875/01 from creator 6 substances '' ptr :!create,:!registration,57875!sequence,01!composition,12791603!active_agent,Dextromethorphani Hydrobromidum.. label nil 4 args {:dose=>Quanty(1.7,'mg/ml'), :substance=>5250, :chemical_dose=>Quanty(6.25,''), :chemical_substance=>5929} chemical_dose 6.25 mg

Here it does not find the correct active agent. Don't understand why the args contain :dose => "1.7 mg/ml". Also substance.oid and chemical_substance.oid match.

After a discussion with Zeno we decided to use in oddb_calc.xml also the concept of active_agents and trying to make it similar to the datastructure in ch.oddb.org. But we do drop the requirement, that all substances are listed. After looking at the code in ch.oddb.org (and de.oddb.org) I resume the situation

  • A composition has many active_agents
  • a active_agent has many substance
  • a substance has many names
  • a substance may contain a chemical_substance and dose

http://ch.oddb.org/de/gcc/drug/reg/55491/seq/01 we take sennae folii extractum methanolicum siccum 78-104 mg corresp. sennosidum B 12.5 mg, DER: 18:1, excipiens pro compresso. and set the name to sennae folii extractum methanolicum siccum which a chemical substance sennosidum B

Whereas for Ecodurec http://ch.oddb.org/de/gcc/drug/reg/47837/seq/01 Zeno would like to interpret the Zusammensetzung of amiloridi hydrochloridum dihydricum 5.67 mg corresp. amiloridi hydrochloridum anhydricum 5 mg, hydrochlorothiazidum 50 mg, excipiens pro compresso. as

  • SUBSTANCE Amiloridi Hydrochloridum Anhydricum
  • CHEMICAL Amiloridi Hydrochloridum Dihydricum

It looks like I must discover at run time whether the active_agent is on the left or the right side of the corresp.

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Page last modified on April 01, 2015, at 01:52 PM