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20130730-fi-table-format

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Summary

  • fix formatting of tables in fachinfo
  • reparse must update all links

Commits

Index

reparse must update all links

Running jobs/update_textinfo_swissmedicinfo --reparse --target=pi "Mepha" does not correctly update all links. But running jobs/update_textinfo_swissmedicinfo --reparse --target=pi 52557 52558 46535 46852 46519 46851 updates the links.

Investigating the difference between these two commands!

  • import_swissmedicinfo_by_iksnrs ["32917", "45138", "58267", "60916", "62184"]@@ calls for each id
    • import_swissmedicinfo_by_iksnrs iksnr "26453" {}
  • import by name calls search first for id by calling
    • textinfo_swissmedicinfo_company_index
    • import_swissmedicinfo_by_iksnrs
    • import_swissmedicinfo_by_iksnrs iksnr "26453" {}

Comparing the output of a an import by name I remarked lots of line like extract_matched_name could not find 55184.

Changed the search for ID belonging to company to use the Aips_download_latest.xml. Found curious ID there, eg. 

  <medicalInformation type="fi" version="3" lang="de" safetyRelevant="false">
    <title>Lukair®</title>
    <authHolder>MSD Merck Sharp &amp;#038; Dohme AG</authHolder>
    <atcCode>R03DC03</atcCode>
    <substances>Montelukast</substances>
    <authNrs>59341 (comprimés filmés), 59342 (comprimés à mâcher), 59343 (granulé oral)</authNrs>
    <remark>Warnhinweise und Vorsichtsmassnahmen; Unerwünschte Wirkungen</remark>

What a horrible XML file!

Here I found my mistake. extract_matched_name worked only, when the XML-authNrs had the numbers without any additional formatting like 55'184, 55'186. Added test-cases and fixed the xpath handling.

Added a log entry IKSNR-not foundwhen extract_matched_name could not find a FI or PI.

While running the import again, got the following error 

Plugin: ODDB::TextInfoPlugin
Error: DBI::ProgrammingError
Message: ERROR:  duplicate key value violates unique constraint "object_connection_pkey"

Restarted all services and rerun the import again.

Pushed commit All availabe FI/PI are now handled correctly when import by company Attention: Has probably an error

After a restart of my VM and redoing the import I got quite at the end the following error 

Plugin: ODDB::TextInfoPlugin
Error: NotImplementedError
Message: method `method_missing' called on terminated object (0x0000002a8c0300 flags=0x0 klass=0x0)
Backtrace:
(eval):3:in `block in proc_resolve_search_term'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:146:in `call'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:146:in `search_term'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:149:in `search_terms'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:278:in `search_terms'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:206:in `block in update_target'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:204:in `each'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:204:in `update_target'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/index.rb:161:in `update'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/stub.rb:112:in `method_missing'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:590:in `block in update_indices'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:589:in `each'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:589:in `update_indices'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/cache.rb:515:in `store'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:274:in `odba_isolated_store'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:395:in `block in odba_store_unsaved'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `each'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:392:in `odba_store_unsaved'
/usr/local/lib64/ruby/gems/1.9.1/gems/odba-1.1.0/lib/odba/persistable.rb:380:in `odba_store'
/var/www/oddb.org/src/util/persistence.rb:261:in `issue_update'
/var/www/oddb.org/src/util/oddbapp.rb:127: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:126:in `update'
/var/www/oddb.org/src/util/oddbapp.rb:1532:in `update'
/var/www/oddb.org/src/plugin/text_info.rb:114:in `store_fachinfo'
/var/www/oddb.org/src/plugin/text_info.rb:156:in `block in update_fachinfo'
/var/www/oddb.org/src/plugin/text_info.rb:150:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:150:in `update_fachinfo'
/var/www/oddb.org/src/plugin/text_info.rb:1120:in `parse_and_update'
/var/www/oddb.org/src/plugin/text_info.rb:1132:in `block (3 levels) in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1131:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:1131:in `block (2 levels) in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1130:in `each_pair'
/var/www/oddb.org/src/plugin/text_info.rb:1130:in `block in import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1127:in `each_pair'
/var/www/oddb.org/src/plugin/text_info.rb:1127:in `import_info'
/var/www/oddb.org/src/plugin/text_info.rb:1205:in `block in import_swissmedicinfo_by_iksnrs'
/var/www/oddb.org/src/plugin/text_info.rb:1197:in `each'
/var/www/oddb.org/src/plugin/text_info.rb:1197:in `import_swissmedicinfo_by_iksnrs'
/var/www/oddb.org/src/plugin/text_info.rb:1216:in `import_swissmedicinfo_by_companies'
/var/www/oddb.org/src/plugin/text_info.rb:1229:in `import_swissmedicinfo'
/var/www/oddb.org/src/util/updater.rb:500:in `block in update_notify_simple'
/var/www/oddb.org/src/util/updater.rb:476:in `call'
/var/www/oddb.org/src/util/updater.rb:476:in `wrap_update'
/var/www/oddb.org/src/util/updater.rb:494:in `update_notify_simple'
/var/www/oddb.org/src/util/updater.rb:303:in `update_textinfo_swissmedicinfo'
/var/www/oddb.org/jobs/update_textinfo_swissmedicinfo:39: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'
/var/www/oddb.org/jobs/update_textinfo_swissmedicinfo:12:in `<module:Util>'
/var/www/oddb.org/jobs/update_textinfo_swissmedicinfo:11:in `<module:ODDB>'
/var/www/oddb.org/jobs/update_textinfo_swissmedicinfo:10:in `<main>'

Fixed the error with commit fixed wrong handling of xpath in last commit. Cleaner log messages

The report mail now lists all FI/PI, which could not be found (seems to occur quite frequently). E.g. 

Not found FI/PI in swissmedicXML
  IKSNR-not found "26660" : Patinfo - DE -

fix formatting of tables in fachinfo

  • Cleanup the handling of spaces for patinfo
  • Updated the patinfo unit-test to the actual XML-data

Pushed commit Updated nasivin unit tests

  • Corrected the formatting of table cells by not generating new paragraphs if the HTML class is a span.

Running the import manually. The isentress tables look a lot better (there is quite some space around, but that is probably just a problem of the used style). See

Pushed commit Fixed handling line-break in tables

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Page last modified on July 30, 2013, at 06:58 PM