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sudo -u apache ruby jobs/export_oddb2tdat 2>&1| tee /vagrant/export_oddb2tdat.txt failed as file /var/www/oddb.org/data/downloads/oddb.csv was missing
sudo -u apache ruby jobs/export_oddb2_csv. Creates ./data/csv/oddb2.2013-06-01.csv
ch.oddb> patinfos.size
-> 5295
ch.oddb> patinfos.values.find_all{|info| /ebi.pharm/i.match(info.company_name)}.size
-> 172
Looking at http://www.swissmedicinfo.ch/ I however find 205 patient infos for Ebi-Pharm AG.
ruby jobs/update_textinfo_swissmedicinfo --target=pi --reparse EbiPharm Novartis Pfizer
niklaus@ng-tr:/opt/src/oddb.org$ ruby test/test_util/updater.rb
/home/niklaus/.rvm/rubies/ruby-1.9.3-p392/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead.
racc/parser.rb:33: warning: already initialized constant Racc_Runtime_Version
racc/parser.rb:34: warning: already initialized constant Racc_Runtime_Revision
racc/parser.rb:36: warning: already initialized constant Racc_Runtime_Core_Version_R
racc/parser.rb:37: warning: already initialized constant Racc_Runtime_Core_Revision_R
racc/parser.rb:41: warning: already initialized constant Racc_Runtime_Core_Revision_C
racc/parser.rb:49: warning: already initialized constant Racc_Main_Parsing_Routine
racc/parser.rb:50: warning: already initialized constant Racc_YY_Parse_Method
racc/parser.rb:51: warning: already initialized constant Racc_Runtime_Core_Version
racc/parser.rb:52: warning: already initialized constant Racc_Runtime_Core_Revision
racc/parser.rb:53: warning: already initialized constant Racc_Runtime_Type
[DEPRECATED] By requiring 'spreadsheet/excel' you are loading a Compatibility
layer which provides a drop-in replacement for Spreadsheet::Excel
versions <= 0.3.5.1. This code will be removed in Spreadsheet
version 1.0.0
could not find htmlgrid.so, falling back to pure-ruby class
/opt/src/oddb.org/src/view/changelog.rb:27: warning: already initialized constant SORT_DEFAULT
Run options:
# Running tests:
..................EFE.E...F.......E.............
Finished tests in 141.287055s, 0.3397 tests/s, 0.3114 assertions/s.
1) Error:
test_run(ODDB::TestUpdater):
NoMethodError: undefined method `export_oddb2tdat' for <FlexMock:exp>:FlexMock
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:136:in `block in method_missing'
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:266:in `flexmock_wrap'
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:128:in `method_missing'
/opt/src/oddb.org/src/util/updater.rb:107:in `export_oddb2tdat'
/opt/src/oddb.org/src/util/updater.rb:265:in `update_bsv_followers'
/opt/src/oddb.org/src/util/updater.rb:202:in `run'
test/test_util/updater.rb:541:in `block in test_run'
test/test_util/updater.rb:247:in `setup_logfile_stats'
test/test_util/updater.rb:534:in `test_run'
2) Failure:
test_run_random(ODDB::TestUpdater) [test/test_util/updater.rb:395]:
<"notify"> expected but was
<nil>.
3) Error:
test_update_analysis(ODDB::TestUpdater):
ArgumentError: wrong number of arguments (2 for 0)
/opt/src/oddb.org/src/util/updater.rb:211:in `update_analysis'
test/test_util/updater.rb:305:in `test_update_analysis'
4) Error:
test_update_bsv_followers(ODDB::TestUpdater):
NoMethodError: undefined method `export_oddb2tdat' for <FlexMock:exp>:FlexMock
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:136:in `block in method_missing'
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:266:in `flexmock_wrap'
/home/niklaus/.rvm/gems/ruby-1.9.3-p392/gems/flexmock-1.3.1/lib/flexmock/core.rb:128:in `method_missing'
/opt/src/oddb.org/src/util/updater.rb:107:in `export_oddb2tdat'
/opt/src/oddb.org/src/util/updater.rb:265:in `update_bsv_followers'
test/test_util/updater.rb:498:in `test_update_bsv_followers'
5) Failure:
test_update_fachinfo(ODDB::TestUpdater) [test/test_util/updater.rb:387]:
<"notify"> expected but was
<nil>.
6) Error:
test_update_migel(ODDB::TestUpdater):
NameError: uninitialized constant ODDB::TestUpdater::MiGeLPlugin
test/test_util/updater.rb:430:in `test_update_migel'
48 tests, 44 assertions, 2 failures, 4 errors, 0 skips
ruby jobs/update_patinfo_only 'Ebi-Pharm AG'. But got an E-Mail back with
Plugin: ODDB::TextInfoPlugin Error: NoMethodError Message: undefined method `radiobutton_with' for nil:NilClass Backtrace: /var/www/oddb.org/src/plugin/text_info.rb:345:in `search' /var/www/oddb.org/src/plugin/text_info.rb:460:in `search_company' /var/www/oddb.org/src/plugin/text_info.rb:544:in `block in import_company' /var/www/oddb.org/src/plugin/text_info.rb:541:in `each' /var/www/oddb.org/src/plugin/text_info.rb:541:in `import_company' /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:314:in `update_patinfo_only' jobs/update_patinfo_only: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/update_patinfo_only:12:in `<module:Util>' jobs/update_patinfo_only:11:in `<module:ODDB>' jobs/update_patinfo_only:10:in `<main>'
#!/usr/bin/env ruby
$: << File.dirname(__FILE__)
$: << File.expand_path("../src", File.dirname(__FILE__))
require 'util/updater'
require 'util/log'
require 'plugin/text_info'
require 'pp'
opts = {
:target => :pi,
:reparse => true,
:iksnrs => [],
:companies => ['Ebi', 'Novartis Consumer'],
:download => true,
}
ti = ODDB::TextInfoPlugin.new(:import_swissmedicinfo, opts)
ODDB.config.text_info_searchform = 'http://www.swissmedicinfo.ch/'
res = ti.import_swissmedicinfo_by_companies(opts[:companies], :target => :pi)
pp res
import_swissmedicinfo_by_companies method. Seems to work. Testing it on the funtoo system.
ruby jobs/update_textinfo_swissmedicinfo --target=pi --reparse Ebi 'Novartis Consu'.