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20150401-oddb-org-wirkstoffe

Summary

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

Commits

• https://github.com/ngiger/oddb2xml/commit/810facb1ff960afbd6c4edf4cd3862de575a91c4 Various fixes for --calc. Adds is_active_agent flag
• https://github.com/ngiger/oddb.org/commit/e5c3e055d0a63fc85b2063bbfb393acd7ea53b96 Reworked parsing compositions in swissmedic
• https://github.com/ngiger/oddb.org/commit/b7426fe80b1bb11c87db84390cbe68d5f59e7cde Added parse_compositions

Index

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

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

improve oddb2xml

For Dr. Reckeweg R 51 Thyreosan IKSNR 45079 oddb2xml --calc produces a lot less substances. Adding an example for its atropa belladonna D30, iodum D30, lapis albus D12, lycopus virginicus D12, natrii chloridum D30 ana partes 0.1 ml, excipiens ad solutionem pro 1 ml, corresp. ethanolum 35 % V/V.

Pushed commit Various fixes for --calc. Adds is_active_agent flag

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 with NoMethodError undefined method `resolve' for nil:NilClass. Using pry to debug the problem. Added a work-around in src/util/persistence, which returns nil (and display class/oid of concerned element) when no pointer found. This leads to 4 lines like No pointer in ODDB::ActiveAgent 33039681 when displaying http://oddb-ci2.dyndns.org/de/gcc/drug/reg/00500/seq/04. I found this oid 33039681 in the logs of my imports. Dropping and reloading the database and running the import for 00500 to see, whether I still have the problem.

Must fix the rewritten handling of replacing compositions. We have often differences as we add a lot more substances and solvens as before. Somehow, when adding a new agent, no corresponding substance is set.

Fixing this problem. Now http://oddb-ci2.dyndns.org/de/gcc/drug/reg/00500/seq/04 looks okay after an import, but the changes do not show up in the e-mail message. Also no more nil pointers in active agents.

Pushed commits Reworked parsing compositions in swissmedic and Added parse_compositions

Import does some stuff it should not, but not too much. Takes about 2 hours.