20110518-update-active_agent-de_oddb
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- Error email import_gkv yesterday
- Check class structure, Sequence, Package, Active Agent
- Delete all the Wrikstoff but the first one
- Goal/Estimate/Evaluation
- Update active agent / 50% /
- Milestones
- Check the structure among sequence, package, active agent
- Think how to update the active agents
- Summary
- Commits
- Next
- Add PDF Producer and version in a report mail
Error email import_gkv yesterday
I got an error email from import_gkv with the updated rpdf2txt yesterday
Tue May 17 16:48:52 2011: de.oddb.org ODDB::Import::Gkv#import NoMethodError undefined method `value' for nil:NilClass ./lib/oddb/import/gkv.rb:361:in `postprocess' ./lib/oddb/import/gkv.rb:358:in `each' ./lib/oddb/import/gkv.rb:358:in `postprocess' ./lib/oddb/import/gkv.rb:101:in `import' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:96:in `reported_import' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:103:in `call' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:103:in `_reported_import' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:96:in `reported_import' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:58:in `import_gkv' /usr/lib64/ruby/1.8/open-uri.rb:32:in `open_uri_original_open' /usr/lib64/ruby/1.8/open-uri.rb:32:in `open' ./lib/oddb/import/gkv.rb:77:in `download_latest' /usr/lib64/ruby/site_ruby/1.8/oddb/util/updater.rb:57:in `import_gkv' jobs/import_gkv:16 ./lib/oddb/util/job.rb:16:in `call' ./lib/oddb/util/job.rb:16:in `run' jobs/import_gkv:15 Imported 6510 Zubef-Entries on 17.05.2011: Visited 6217 existing Zubef-Entries Visited 6501 existing Companies Visited 1136 existing Substances Created 293 new Zubef-Entries Created 0 new Products Created 8 new Sequences Created 9 new Companies Created 1 new Substances Assigned 0 Chemical Equivalences Assigned 0 Companies Created 5 Incomplete Packages: http://de.oddb.org/de/drugs/package/pzn/9075301 http://de.oddb.org/de/drugs/package/pzn/9075347 http://de.oddb.org/de/drugs/package/pzn/9075330 http://de.oddb.org/de/drugs/package/pzn/9075324 http://de.oddb.org/de/drugs/package/pzn/7755606 Created 0 Product(s) without a name (missing product name):
Note
- But the company names were correctly updated
- I have also done the import_gkv on the server
Check class structure, Sequence, Package, Active Agent
Sequence
1
ActiveAgent *--1 Composition *-------+-------* Package
Experiment
masa@masa ~/ywesee/de.oddb.org $ bin/admin de.oddb> ODDB::Drugs::Package.all[0].active_agents[0].to_s -> Omeprazol 20 mg
Experiment (check 'Zuzahlungsbefreit', which means if it is true the package data is on Zubef PDF file)
de.oddb> ODDB::Drugs::Package.find_by_name('Jodid 500 Tabletten').code(:zuzahlungsbefreit)
->
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').code(:zuzahlungsbefreit)
-> true
Note
- It looks possible to directly access to the active_agent instance from an package instance
Experiment (check all the 'Zuzahlungsbefreit')
de.oddb> open('/home/masa/work/zuzahl_all.dat','w'){|f| i=0; ODDB::Drugs::Package.all.each{|x| f.print i+=1,"\t", x.code(:cid), "\t", x.code(:zuzahlungsbefreit), "\t", x.cascading_name('de'), "\n"}}
Result
1 3799162 nil Jodid 500 Tabletten 2 3799156 nil Jodid 500 Tabletten 3 4169664 false Amisulprid dura 200 mg Tabletten 4 7356935 nil Omnic Ocas Mg 5 5116078 nil Formatris Ug Inhedp 6 1607715 true Akineton retard Tabletten 7 3816601 nil Antagonil 20 Kapseln 8 6308325 nil Omnic Ocas 0,4 mg Retardtabletten 9 3816624 nil Antagonil 20 Kapseln ... 42886 nil nil Verasal 240 mg retard Tabletten 42887 nil nil Zanipress 10mg/10mg 42888 nil nil Zurcal S Mg 42889 nil nil Zurcal S Mg 42890 nil nil Zurcal S Mg 42891 nil nil Zurcal S Mg 42892 nil nil Zurcal S Mg 42893 nil nil Zurcal S Mg
Check on browser
Delete all the Wrikstoff but the first one
Plan
- Delete all the Wirkstoff but the first one if the 'Zuzahlungsbefreit' flag of the package is true
- from bin/admin command
Refer to lib/oddb/html/state/drugs/admin/sequence.rb#ajax_delete_active_agent
def ajax_delete_active_agent
check_model
keys = [:uid, :active_agent, :composition]
input = user_input(keys, keys)
agents = []
if(!error? \
&& (composition = @model.compositions.at(input[:composition].to_i)))
if(agent = composition.active_agents.at(input[:active_agent].to_i))
agent.delete
composition.remove_active_agent(agent)
composition.save
end
agents = composition.active_agents
end
AjaxActiveAgents.new(@session, agents)
end
Test (delete an active agent on bin/admin)
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents.length
-> 8
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').code(:cid)
-> 459810
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> hpidinolydrochloridiTc 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> Ticidrohlcorlyhpidinod 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> clopidindiTidryohlcorh 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> riTclidohlcoroyhpidind 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> cTidrohlordyhpidinilco 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[2].delete
-> chlordidrTiclopidinhyo 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents[1].delete
-> dTiidrohlcocyhpidinolr 250 mg
de.oddb> ODDB::Drugs::Package.find_by_name('Ticlopidin- Ct 250 mg Filmtabletten').active_agents.length
-> 1
Note
- I have checked this is reflected to the database after the rebooting
Just in case (backup database)
masa@masa ~/ywesee/de.oddb.org $ sudo pg_dump -U postgres oddb > oddb_bak_after_import_gkv.sql
Experiment (lib/oddb/util/server.rb#delete_all_active_agent_but_first)
def delete_all_active_agent_but_first
ODDB::Drugs::Package.all.each do |pack|
if pack.code(:zuzahlungsbefreit)
while pack.active_agents[1]
pack.active_agents[1].delete
end
end
end
end
Run
- Reboot de.oddb/bin/oddbd
masa@masa ~/ywesee/de.oddb.org $ bin/admin de.oddb> delete_all_active_agent_but_first -> Array
- Before
- After
Note
- But some Zuzahlungsbefreit flags are not checked even if it is found in the PDF
Example
- On the pdf
- On the web
Commit
Check how the Zuzahlungsbefreit flag is set in import_gkv
Refer to
lib/oddb/import/gkv.rb#postprocess
def postprocess
Drugs::Package.search_by_code(:type => 'zuzahlungsbefreit',
:value => 'true',
:country => 'DE').each { |package|
pzn = package.code(:cid).value
unless(@confirmed_pzns.include?(pzn))
@deleted += 1
package.code(:zuzahlungsbefreit).value = false
save package
end
...
lib/oddb/import/gkv.rb#import_row
def import_row(row)
if row == :doubtful
@doubtful_pzns.push @created_pzn if @created_pzn
@created_pzn = nil
return
end
@count += 1
package = import_package(row)
return if package.nil?
@confirmed_pzns.store(package.code(:cid).value, true)
if(code = package.code(:zuzahlungsbefreit))
if(code.value)
@existing += 1
else
@created += 1
end
code.value = true
else
@created += 1
code = Util::Code.new(:zuzahlungsbefreit, true, 'DE')
package.add_code(code)
end
...
Note
- This code says, the package.code(:zuzahlungsbefreit) definitely becomes true when the importing of a package
Experiment (lib/oddb/import/gkv.rb#import_row)
def import_row(row)
if row == :doubtful
@doubtful_pzns.push @created_pzn if @created_pzn
@created_pzn = nil
return
end
@count += 1
package = import_package(row)
return if package.nil?
@confirmed_pzns.store(package.code(:cid).value, true)
if row.to_s =~ /3867225/
p "import_row"
p package.code(:zuzahlungsbefreit)
end
if(code = package.code(:zuzahlungsbefreit))
if(code.value)
@existing += 1
else
@created += 1
end
code.value = true
else
@created += 1
code = Util::Code.new(:zuzahlungsbefreit, true, 'DE')
package.add_code(code)
end
if row.to_s =~ /3867225/
p "import_row"
p package.code(:zuzahlungsbefreit)
end
Result
"import_row"
#<ODDB::Util::Code:0x7f24096f1358 @country="DE", @values={Thu, 13 Dec 2007=>false, Thu, 20 Dec 2007=>true, Tue, 03 Jul 2007=>true}, @type="zuzahlungsbefreit">
"import_row"
#<ODDB::Util::Code:0x7f24096f1358 @country="DE", @values={Thu, 13 Dec 2007=>false, Thu, 20 Dec 2007=>true, Tue, 03 Jul 2007=>true}, @type="zuzahlungsbefreit">
Note
- The package.code(:zuzahlungsbefreit) is not false
- It looks true, and it should be shown on the browser, but the Zubef flag check box is not checked on the web interface