20110202-debug-oddbdat-oddb_org
<< | Index | >>
- Check all the test-cases oddb.org
suspend - Debug oddbdat error
- Temporal solution (Skipping nil data)
- Dig into more deeper
- Update export_oddbdat with reporting
- Goal
- Update test-cases oddb.org / 70%
- Milestones
Check all the test-cases- Debug oddbdat error
Confirm the same error in local9:15Traceback error15:00- Update with report process
- Test-cases
- Commit
- Summary
- Commits
- ToDo Tomorrow
- Keep in Mind
- Also probably Dose error ch.ODDB.org Report - Error: Generikaliste - 02/2011 ch.ODDB.org Report - Error: oddb.csv - 02/2011
- Add my email address to SL-Update recipients
- Debug bsv_followers autorun
- oddb.org test-case 100%
- Some concerns about FI news job
- oddbbat error
- Check rdbi instead of dbi for ODBA
- Encoding woes (from Davatz-san)
- Feedback: This option indicates that the regular expression is parsed as 'UTF8' (from Davatz-san)
- pg on Ubuntu - see http://dev.ywesee.com/wiki.php/Gem/Pg (from Davatz-san)
- On Ice
- emerge --sync
Check all the test-cases oddb.org
masa@masa ~/ywesee/oddb.org $ ruby test/suite.rb ... 1006 tests, 2351 assertions, 7 failures, 43 errors
Note
- (7+43)/1006 = 95% success, but actually this does not become a validation
- since a test-case sometimes stops after an error
Debug oddbdat error
Error: NoMethodError Message: undefined method `qty' for nil:NilClass Backtrace: (druby://localhost:10005) /var/www/oddb.org/ext/export/src/oddbdat.rb:408:in `structure' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/oddbdat.rb:269:in `initialize' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/oddbdat.rb:292:in `initialize' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/oddbdat.rb:53:in `new' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/oddbdat.rb:53:in `lines' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:175:in `export_oddbdat' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:174:in `each' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:174:in `export_oddbdat' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:172:in `each' (druby://localhost:10005) /var/www/oddb.org/ext/export/src/odba_exporter.rb:172:in `export_oddbdat' /var/www/oddb.org/src/plugin/oddbdat_export.rb:51:in `export' /var/www/oddb.org/src/util/exporter.rb:152:in `export_oddbdat' /var/www/oddb.org/src/util/exporter.rb:289:in `call' /var/www/oddb.org/src/util/exporter.rb:289:in `safe_export' /var/www/oddb.org/src/util/exporter.rb:150:in `export_oddbdat' /var/www/oddb.org/src/util/exporter.rb:51:in `run' /var/www/oddb.org/jobs/export_daily:13 /var/www/oddb.org/src/util/job.rb:17:in `call' /var/www/oddb.org/src/util/job.rb:17:in `run' /var/www/oddb.org/jobs/export_daily:12
Confirm the same error in local
Run
- oddb.org/bin/oddbd
- currency/bin/currencyd
- oddb.org/ext/export/bin/exportd
Run export_oddbdat
masa@masa ~/ywesee/oddb.org $ bin/admin ch.oddb> Exporter.new(self).export_oddbdat
Result
Error: NoMethodError Message: undefined method `qty' for nil:NilClass Backtrace: (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:408:in `structure' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:269:in `initialize' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:292:in `initialize' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:53:in `new' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:53:in `lines' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:175:in `export_oddbdat' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:174:in `each' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:174:in `export_oddbdat' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:172:in `each' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:172:in `export_oddbdat' /home/masa/ywesee/oddb.org/src/plugin/oddbdat_export.rb:51:in `export' /home/masa/ywesee/oddb.org/src/util/exporter.rb:153:in `export_oddbdat' /home/masa/ywesee/oddb.org/src/util/exporter.rb:297:in `call' /home/masa/ywesee/oddb.org/src/util/exporter.rb:297:in `safe_export' /home/masa/ywesee/oddb.org/src/util/exporter.rb:149:in `export_oddbdat' (eval):1:in `_admin' /home/masa/ywesee/oddb.org/src/util/failsafe.rb:9:in `call' /home/masa/ywesee/oddb.org/src/util/failsafe.rb:9:in `failsafe' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1399:in `_admin' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `initialize' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `new' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `_admin' /usr/lib64/ruby/1.8/drb/drb.rb:1556:in `__send__' /usr/lib64/ruby/1.8/drb/drb.rb:1556:in `perform_without_block' /usr/lib64/ruby/1.8/drb/drb.rb:1516:in `perform' /usr/lib64/ruby/1.8/drb/drb.rb:1590:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1586:in `loop' /usr/lib64/ruby/1.8/drb/drb.rb:1586:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1582:in `start' /usr/lib64/ruby/1.8/drb/drb.rb:1582:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1431:in `run' /usr/lib64/ruby/1.8/drb/drb.rb:1428:in `start' /usr/lib64/ruby/1.8/drb/drb.rb:1428:in `run' /usr/lib64/ruby/1.8/drb/drb.rb:1348:in `initialize' /usr/lib64/ruby/1.8/drb/drb.rb:1628:in `new' /usr/lib64/ruby/1.8/drb/drb.rb:1628:in `start_service' bin/oddbd:38
Note
- It is the same error
Next
- Traceback the error message
Experiment
src/plugin/oddbdat_export.rb#export
def export
files = []
p "A"
# package tables
package_tables = [
AcTable, AccompTable, AcLimTable, AcmedTable, AcnamTable,
AcOddbTable, AcpricealgTable, AcscTable, LimitationTable,
LimTxtTable, EanTable
]
ids = []
@app.each_package { |pac| ids.push(pac.odba_id) }
p "A2"
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, package_tables)
p "B"
# codes table
ids = @app.atc_classes.values.collect { |atc| atc.odba_id }
p "B2"
@app.each_galenic_form { |galform| ids.push(galform.odba_id) }
p "B3"
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [CodesTable])
p "C"
# substances table
ids = @app.substances.collect { |subs| subs.odba_id }
p "C2"
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [ScTable])
p "D"
# companies table
ids = @app.companies.collect { |oid, comp| comp.odba_id }
p "D2"
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [CompTable])
p "E"
# readme
files += EXPORT_SERVER.export_oddbdat(nil, EXPORT_DIR, [Readme])
p "F"
# compress
EXPORT_SERVER.compress_many(EXPORT_DIR, 'oddbdat', files)
end
Run again
Result
"getin export_oddbdat" "1" "2" "A" "A2"
Note
- The following part does not run
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, package_tables)
Next
- Check EXPORT_SERVER.export_oddbdat
Experiment
ext/export/src/odba_exporter.rb#export_oddbdat
def OdbaExporter.export_oddbdat(odba_ids, dir, klasses)
FileUtils.mkdir_p(dir)
p "AA"
files = klasses.collect { |klass|
table = klass.new
file = Tempfile.new(table.filename, dir)
[file, table]
}
p "BB"
if(odba_ids.nil?)
p "CC"
files.each { |file, table|
file.puts table.lines
}
else
p "DD"
odba_ids.each { |odba_id|
item = ODBA.cache.fetch(odba_id, nil)
files.each { |file, table|
file.puts table.lines(item)
}
#ODBA.cache.clear
}
end
p "EE"
files.each { |file, table|
path = File.join(dir, table.filename)
FileUtils.mv(file.path, path)
}
p "FF"
files.collect { |file, table| table.filename }
ensure
if(files)
files.each { |file, table| file.close! }
end
end
Run again
Result
"AA" "BB" "DD"
Next ext/export/src/odba_exporter.rb#export_oddbdat
def OdbaExporter.export_oddbdat(odba_ids, dir, klasses)
FileUtils.mkdir_p(dir)
p "AA"
files = klasses.collect { |klass|
table = klass.new
file = Tempfile.new(table.filename, dir)
[file, table]
}
p "BB"
if(odba_ids.nil?)
p "CC"
files.each { |file, table|
file.puts table.lines
}
else
p "DD"
odba_ids.each { |odba_id|
print "odba_id="
p odba_id
item = ODBA.cache.fetch(odba_id, nil)
files.each { |file, table|
print "file="
p file
print "table.class="
p table.class
file.puts table.lines(item)
}
#ODBA.cache.clear
}
end
p "EE"
files.each { |file, table|
path = File.join(dir, table.filename)
FileUtils.mv(file.path, path)
}
p "FF"
files.collect { |file, table| table.filename }
ensure
if(files)
files.each { |file, table| file.close! }
end
end
Result
... odba_id=218092 file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s01x.4036.0> table.class=ODDB::OdbaExporter::AcTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s19x.4036.0> table.class=ODDB::OdbaExporter::AccompTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s09x.4036.0> table.class=ODDB::OdbaExporter::AcLimTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s02x.4036.0> table.class=ODDB::OdbaExporter::AcmedTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s03x.4036.0> table.class=ODDB::OdbaExporter::AcnamTable
Keep in mind
- 'odba_id=218092'
Next
- Check ODDB::OdbaExporter::AcnamTable
class AcnamTable < Table
FILENAME = 's03x'
def lines(package)
[AcnamLine.new(package)]
end
end
Note
- The argument looks 'Package' class
Next
- Check AcnamLine.new
class AcnamLine < PackageLine
...
Next
- Check PackageLine.new
class PackageLine < Line
def initialize(package, *args)
@package = package
super
end
end
Next
- Check Line.new
class Line
def initialize(*args)
@date = Date.today.strftime("%Y%m%d%H%M%S")
@structure = structure
end
Next
- AcnamLine#structure
ext/export/src/oddbdat.rb::AcnamLine#structure
class AcnamLine < PackageLine
LENGTH = 26
def structure
seq = @package.sequence
galform = if(gf = seq.galenic_forms.first)
gf.to_s
end
conc, unit = if((dose = seq.dose) && dose.is_a?(Quanty))
[dose.qty, dose.unit]
end
measures = @package.parts.collect { |part| part.measure }.compact
measure, munit = unless(measures.empty?)
ms = measures.inject { |a, b| a + b }
[ms.qty, ms.unit] if ms.is_a?(Quanty)
end
comform = @package.commercial_forms.first
qty, qty_unit = if(munit && !munit.empty?)
[measure, munit]
else
[@package.comparable_size.qty, comform] # <= HERE
end
Note
- @package probably comes from ODBA.cache.fetch(218092)
Experiment ext/export/src/oddbdat.rb::AcnamLine#structure
class AcnamLine < PackageLine
LENGTH = 26
def structure
seq = @package.sequence
galform = if(gf = seq.galenic_forms.first)
gf.to_s
end
conc, unit = if((dose = seq.dose) && dose.is_a?(Quanty))
[dose.qty, dose.unit]
end
measures = @package.parts.collect { |part| part.measure }.compact
measure, munit = unless(measures.empty?)
ms = measures.inject { |a, b| a + b }
[ms.qty, ms.unit] if ms.is_a?(Quanty)
end
comform = @package.commercial_forms.first
qty, qty_unit = if(munit && !munit.empty?)
[measure, munit]
else
[@package.comparable_size.qty, comform] # <= HERE
end
Experiment
class AcnamLine < PackageLine
LENGTH = 26
def structure
seq = @package.sequence
galform = if(gf = seq.galenic_forms.first)
gf.to_s
end
conc, unit = if((dose = seq.dose) && dose.is_a?(Quanty))
[dose.qty, dose.unit]
end
measures = @package.parts.collect { |part| part.measure }.compact
measure, munit = unless(measures.empty?)
ms = measures.inject { |a, b| a + b }
[ms.qty, ms.unit] if ms.is_a?(Quanty)
end
comform = @package.commercial_forms.first
qty, qty_unit = if(munit && !munit.empty?)
[measure, munit]
else
print "@package="
p @package
[@package.comparable_size.qty, comform] # <= HERE
end
Result
... odba_id=218092 file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s01x.4811.0> table.class=ODDB::OdbaExporter::AcTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s19x.4811.0> table.class=ODDB::OdbaExporter::AccompTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s09x.4811.0> table.class=ODDB::OdbaExporter::AcLimTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s02x.4811.0> table.class=ODDB::OdbaExporter::AcmedTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s03x.4811.0> table.class=ODDB::OdbaExporter::AcnamTable @package.class=ODDB::Package
Next
- Check ODDB::Package#comparable_size method
Experiment
src/model/package.rb#comparable_size
def comparable_size
print "@parts="
p @parts
@parts.collect { |part| part.comparable_size }.inject { |a, b| a + b }
rescue RuntimeError
@parts.inject(Dose.new(0)) { |comp, part|
ODDB::Dose.new(comp.qty + part.comparable_size.qty)
} rescue nil
end
Note
- 'ODDB::Package#comparable_size' means the sum of its @parts comparable_sizes
- But ODDB::Package#comparable_size should have 'qty' method too
Result
... odba_id=218092 file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s01x.5495.0> table.class=ODDB::OdbaExporter::AcTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s19x.5495.0> table.class=ODDB::OdbaExporter::AccompTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s09x.5495.0> table.class=ODDB::OdbaExporter::AcLimTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s02x.5495.0> table.class=ODDB::OdbaExporter::AcmedTable file=#<File:/home/masa/ywesee/oddb.org/data/downloads/s03x.5495.0> table.class=ODDB::OdbaExporter::AcnamTable @package.class=ODDB::Package @parts=[]
Note
- There is no @parts element
Next
- Check ODDB::Package@parts
src/model/package.rb#create_part
def create_part
part = Part.new
part.package = self
@parts.push part
part
end
Note
- @parts is an Array of Part instance
Next
- Check Part class
class Part
include Persistence
include SizeParser
Next
- Module SizeParser
src/model/package.rb::SizeParser#comparable_size
def comparable_size
ODDB::Dose.from_quanty(@comparable_size)
end
Note
- Namely, ODDB::Package#comparable_size comes from ODDB::SizeParser#comparable_size
- But this comes from ODDB::Dose#from_quanty method (and ODDB::SizeParser@comparable_size)
- The ODDB::SizeParser@comparable_size is set in the following ODDB::SizeParser#set_comparable_size!
src/model/package.rb::SizeParser#set_comparable_size!
def set_comparable_size!
measure = (@measure.nil? || @measure == UNIT) \
? _composition_scale \
: @measure
measure ||= UNIT
scale = @scale || UNIT
@comparable_size = multiplier * measure / scale
end
Note
- ODDB::SizeParser@comparable_size should be float variable (probably not an integer)
Experiment
ext/export/src/oddbdat.rb::AcnamLine#structure
class AcnamLine < PackageLine
LENGTH = 26
def structure
seq = @package.sequence
galform = if(gf = seq.galenic_forms.first)
gf.to_s
end
conc, unit = if((dose = seq.dose) && dose.is_a?(Quanty))
[dose.qty, dose.unit]
end
measures = @package.parts.collect { |part| part.measure }.compact
measure, munit = unless(measures.empty?)
ms = measures.inject { |a, b| a + b }
[ms.qty, ms.unit] if ms.is_a?(Quanty)
end
comform = @package.commercial_forms.first
qty, qty_unit = if(munit && !munit.empty?)
[measure, munit]
else
print "@package.class="
p @package.class
if sss = @package.comparable_size
print "@package.comparable_size.class="
p @package.comparable_size.class
end
[@package.comparable_size.qty, comform] # <= HERE
end
Result
... @package.comparable_size.class=ODDB::Dose ...
Note
- So, the 'qty' is a method of ODDB::Dose
Consideration
- The problem is [].inject becomes nil
- I guess the following modification will resolve the error
- but this is not fundamental understanding of mine
src/model/package.rb#comparable_size
def comparable_size
# @parts.collect { |part| part.comparable_size }.inject { |a, b| a + b }
@parts.collect { |part| part.comparable_size }.inject { |a, b| a + b } or raise RuntimeError
rescue RuntimeError
@parts.inject(Dose.new(0)) { |comp, part|
ODDB::Dose.new(comp.qty + part.comparable_size.qty)
} rescue nil
end
Result
masa@masa ~/ywesee/oddb.org $ bin/admin
ch.oddb> ODBA.cache.fetch('218092', nil).name
-> Phytomed Knoblauch/Weissdorn, Kapseln
ch.oddb> ODBA.cache.fetch('218092', nil).comparable_size
-> 0
Test
Reboot
- oddb.org/bin/oddbd
- oddb.org/ext/export/bin/exportd
Run
- currency/bin/currencyd
Run export_oddbdat
masa@masa ~/ywesee/oddb.org $ bin/admin ch.oddb> Exporter.new(self).export_oddbdat
Result
Error: NoMethodError Message: undefined method `multi' for nil:NilClass Backtrace: (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:423:in `structure' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:269:in `initialize' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:292:in `initialize' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:53:in `new' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/oddbdat.rb:53:in `lines' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:189:in `export_oddbdat' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:184:in `each' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:184:in `export_oddbdat' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:176:in `each' (druby://localhost:10005) /home/masa/ywesee/oddb.org/ext/export/src/odba_exporter.rb:176:in `export_oddbdat' /home/masa/ywesee/oddb.org/src/plugin/oddbdat_export.rb:52:in `export' /home/masa/ywesee/oddb.org/src/util/exporter.rb:153:in `export_oddbdat' /home/masa/ywesee/oddb.org/src/util/exporter.rb:297:in `call' /home/masa/ywesee/oddb.org/src/util/exporter.rb:297:in `safe_export' /home/masa/ywesee/oddb.org/src/util/exporter.rb:149:in `export_oddbdat' (eval):1:in `_admin' /home/masa/ywesee/oddb.org/src/util/failsafe.rb:9:in `call' /home/masa/ywesee/oddb.org/src/util/failsafe.rb:9:in `failsafe' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1399:in `_admin' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `initialize' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `new' /home/masa/ywesee/oddb.org/src/util/oddbapp.rb:1397:in `_admin' /usr/lib64/ruby/1.8/drb/drb.rb:1556:in `__send__' /usr/lib64/ruby/1.8/drb/drb.rb:1556:in `perform_without_block' /usr/lib64/ruby/1.8/drb/drb.rb:1516:in `perform' /usr/lib64/ruby/1.8/drb/drb.rb:1590:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1586:in `loop' /usr/lib64/ruby/1.8/drb/drb.rb:1586:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1582:in `start' /usr/lib64/ruby/1.8/drb/drb.rb:1582:in `main_loop' /usr/lib64/ruby/1.8/drb/drb.rb:1431:in `run' /usr/lib64/ruby/1.8/drb/drb.rb:1428:in `start' /usr/lib64/ruby/1.8/drb/drb.rb:1428:in `run' /usr/lib64/ruby/1.8/drb/drb.rb:1348:in `initialize' /usr/lib64/ruby/1.8/drb/drb.rb:1628:in `new' /usr/lib64/ruby/1.8/drb/drb.rb:1628:in `start_service' bin/oddbd:38
Note
- This is a different error but it looks coming from the similar part
- This error comes from
class AcnamLine < PackageLine
LENGTH = 26
def structure
seq = @package.sequence
galform = if(gf = seq.galenic_forms.first)
gf.to_s
end
conc, unit = if((dose = seq.dose) && dose.is_a?(Quanty))
[dose.qty, dose.unit]
end
measures = @package.parts.collect { |part| part.measure }.compact
measure, munit = unless(measures.empty?)
ms = measures.inject { |a, b| a + b }
[ms.qty, ms.unit] if ms.is_a?(Quanty)
end
comform = @package.commercial_forms.first
qty, qty_unit = if(munit && !munit.empty?)
[measure, munit]
else
[@package.comparable_size.qty, comform]
end
{
1 => '03',
2 => @date,
3 => '1',
4 => @package.oid,
5 => 'D',
6 => '4',
7 => seq.name,
8 => seq.name_base,
9 => seq.name_descr,
11 => galform,
12 => conc,
13 => unit,
16 => @package.parts.first.multi, #<= HERE
17 => comform,
18 => qty,
19 => qty_unit,
}
end
end
Note
- This coding indicates that
- it seems that ODDB::Package instance should have @parts (an Array of Part instances) elements, at least one.
Temporal solution (Skipping nil data)
Experiment (Skip nil data)
src/model/package.rb#comparable_size
def comparable_size
# @parts.collect { |part| part.comparable_size }.inject { |a, b| a + b }
@parts.collect { |part| part.comparable_size }.inject { |a, b| a + b } or raise RuntimeError
rescue RuntimeError
@parts.inject(Dose.new(0)) { |comp, part|
ODDB::Dose.new(comp.qty + part.comparable_size.qty)
} rescue nil
end
ext/export/src/oddbdat.rb::AcnamLine#structure
...
{
1 => '03',
2 => @date,
3 => '1',
4 => @package.oid,
5 => 'D',
6 => '4',
7 => seq.name,
8 => seq.name_base,
9 => seq.name_descr,
11 => galform,
12 => conc,
13 => unit,
#16 => @package.parts.first.multi,
16 => @package.parts.first ? @package.parts.first.multi : 'masa',
17 => comform,
18 => qty,
19 => qty_unit,
}
end
Run
- oddb.org/bin/oddbd
- currency/bin/currencyd
- oddb.org/ext/export/bin/exportd
Run export_oddbdat
masa@masa ~/ywesee/oddb.org $ bin/admin ch.oddb> Exporter.new(self).export_oddbdat
Result
- No email comes
- New files are created
masa@masa ~/ywesee/oddb.org $ ls data/downloads/ -al insgesamt 19000 drwxr-xr-x 2 masa masa 4096 2. Feb 13:55 . drwxr-xr-x 8 masa masa 64 2. Feb 13:47 .. -rw-r--r-- 1 masa masa 2129601 2. Feb 13:55 oddbdat.tar.gz -rw-r--r-- 1 masa masa 2114956 2. Feb 13:55 oddbdat.zip -rw------- 1 masa masa 1564 2. Feb 13:55 README -rw------- 1 masa masa 2267400 2. Feb 13:54 s01x -rw------- 1 masa masa 1490904 2. Feb 13:54 s02x -rw------- 1 masa masa 3723469 2. Feb 13:54 s03x -rw------- 1 masa masa 1094490 2. Feb 13:54 s06x -rw------- 1 masa masa 905903 2. Feb 13:54 s07x -rw------- 1 masa masa 111740 2. Feb 13:54 s09x -rw------- 1 masa masa 1430231 2. Feb 13:54 s10x -rw------- 1 masa masa 416422 2. Feb 13:55 s11x -rw------- 1 masa masa 73769 2. Feb 13:55 s12x -rw------- 1 masa masa 105999 2. Feb 13:54 s16x -rw------- 1 masa masa 827293 2. Feb 13:54 s19x -rw------- 1 masa masa 484995 2. Feb 13:55 s40x -rw------- 1 masa masa 2023634 2. Feb 13:54 s41x -rw------- 1 masa masa 208172 2. Feb 13:54 s99x
Note
- This is not fundamental solution, since I do not understand why ODDB::Package@parts becomes empty
- This is just skipping the nil data that raises an error
Dig into more deeper
Question
- Why (How) does ODDB::Package@parts becomes [] (emptiy)?
- This is the cause of the error above
Next
- When is the Package@parts set?
src/model/package.rb#create_parts
def create_part
part = Part.new
part.package = self
@parts.push part
part
end
Note
- But 'parts' is an Array and is set as 'attr_reader', this indicates that @parts might be changed outside of the class
Memo
- The ODDB::Package.parts (Dose instances) are corresponding to the following interface
Note
- That is why ODDB::Package@parts (Array) is empty
Solution
- Skipping the empty (nil) data but reporting the data
Update export_oddbdat with reporting
Question
- Where should I catch and throw the error?
Candidates
- src/model/package.rb (Package#comparable_size) (core part, this is related to many objects)
- ext/export/src/odba_exporter.rb (OdbaExporter.export_oddbdat, checking it with odba_id) (middle, only for export_oddbdat job)
- ext/export/src/oddbdat.rb (AcnamLine#structure, package.comparable_size is nil) (surface, there may be many other places regarding qty)
Conditions
- We do not want to stop the export_oddbdat job
- We want an report mail when the Dose data is missing
Consideration
- 1. is the best position to be caught, but it is difficult to send an report
- 2. is better than 3., but still difficult to report an email and at the same time to resume the process
Memo
- The link to a package will be as follows
http://ch.oddb.org/de/gcc/resolve/pointer/%3A!registration%2C(reg.no.)!sequence%2C(seq.no.)!package%2C(pac.no.).
Experiment
src/model/package.rb#comparable_size
def comparable_size
@parts.collect { |part| part.comparable_size }.inject{ |a, b| a + b } or raise RuntimeError
rescue RuntimeError
@parts.inject(Dose.new(0)) { |comp, part|
ODDB::Dose.new(comp.qty + part.comparable_size.qty)
} rescue nil
end
ext/export/src/oddbdat.rb::AcnamLine#structure
{
1 => '03',
2 => @date,
3 => '1',
4 => @package.oid,
5 => 'D',
6 => '4',
7 => seq.name,
8 => seq.name_base,
9 => seq.name_descr,
11 => galform,
12 => conc,
13 => unit,
#16 => @package.parts.first.multi,
16 => @package.parts.first ? @package.parts.first.multi : '',
17 => comform,
18 => qty,
19 => qty_unit,
}
end
src/plugin/oddbdat_export.rb#export
def export
files = []
# package tables
package_tables = [
AcTable, AccompTable, AcLimTable, AcmedTable, AcnamTable,
AcOddbTable, AcpricealgTable, AcscTable, LimitationTable,
LimTxtTable, EanTable
]
ids = []
dose_missing_list = []
@app.each_package { |pac|
ids.push(pac.odba_id)
if pac.parts.empty?
dose_missing_list.push([pac.basename, pac.iksnr, pac.sequence.seqnr, pac.ikscd])
end
}
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, package_tables)
# codes table
ids = @app.atc_classes.values.collect { |atc| atc.odba_id }
@app.each_galenic_form { |galform| ids.push(galform.odba_id) }
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [CodesTable])
# substances table
ids = @app.substances.collect { |subs| subs.odba_id }
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [ScTable])
# companies table
ids = @app.companies.collect { |oid, comp| comp.odba_id }
files += EXPORT_SERVER.export_oddbdat(ids, EXPORT_DIR, [CompTable])
# readme
files += EXPORT_SERVER.export_oddbdat(nil, EXPORT_DIR, [Readme])
# compress
EXPORT_SERVER.compress_many(EXPORT_DIR, 'oddbdat', files)
# warning
return dose_missing_list
end
src/util/exporter.rb#export_oddbdat
def export_oddbdat
dose_missing_list = []
safe_export 'oddbdat' do
exporter = OdbaExporter::OddbDatExport.new(@app)
dose_missing_list = exporter.export
EXPORT_SERVER.clear
sleep(30)
run_on_weekday(1) {
exporter.export_fachinfos
EXPORT_SERVER.clear
sleep(30)
}
# here to raise warning if package.parts is empty
if !dose_missing_list.empty?
log = Log.new(@@today)
log.report = [
"Warning: Dose data is missing",
"Message: export_oddbdat succeeded but the following package(s) do not have Dose data",
"Package(s):",
dose_missing_list.collect do |list|
list[0].to_s + ", " + \
"http://ch.oddb.org/de/gcc/resolve/pointer/%3A!registration%2C" + list[1].to_s + \
"!sequence%2C" + list[2].to_s + "!package%2C" + list[3].to_s + ".\n"
end
].join("\n")
log.notify("Warning Export: oddbdat")
end
end
Run
- oddb.org/bin/oddbd
- currency/bin/currencyd
- oddb.org/export/bin/exportd
Run export_oddbdat
masa@masa ~/ywesee/oddb.org $ bin/admin ch.oddb> Exporter.new(self).export_oddbdat
- It took about 10 minutes to run
- Email ch.ODDB.org Report - Warning Export: oddbdat - 02/2011
Warning: Dose data (ODDB::Package.parts, Array of ODDB::Dose instances) is empty. Message: export_oddbdat succeeded but the following package(s) do not have Dose data. Package(s): Phytomed Knoblauch/Weissdorn, http://oddb.masa.org/de/gcc/resolve/pointer/%3A!registration%2C46799!sequence%2C02!package%2C011.
Note
Commit