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Data too long for column error in `EltonTraits` on Python 3 #672

Closed ethanwhite closed 7 years ago

ethanwhite commented 8 years ago
ethan@gandalf:~$ retriever install postgres EltonTraits
=> Installing Mammal and Bird foraging attributes -- Wilman, et al., 2014
Creating database EltonTraits...
Couldn't create database (schema "eltontraits" already exists
). Trying to continue anyway.
Creating table EltonTraits.BirdCitations...
Progress: 58 / 58 rows inserted into EltonTraits.BirdCitations: 

Creating table EltonTraits.MammFuncDat...
Progress: 5400 / 5400 rows inserted into EltonTraits.MammFuncDat: 

Creating table EltonTraits.MammCitations...
INSERT INTO EltonTraits.MammCitations (ref_id, full_reference) VALUES  ('Ref_1', 'Nowak R.M. (1999). Walker''s mammals of the world. Sixth edition edn. The Johns Hopkins University Press, Baltimore, Maryland'), ('Ref_2', 'Genus Average'), ('Ref_3', 'Family Average'), ('Ref_4', 'Afrotheria Specialist Group (Tenrec Section), Jenkins, P. & Goodman, S. (2008). Hemicentetes nigriceps. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 29 December 2008'), ('Ref_5', 'Kirkpatrick, R. C., Long, Y. C., Zhong, T., and Xiao, L. (1998). \"Social organization and range use in the Yunnan snub-nosed monkey Rhinopithecus bieti\". International Journal of Primatology 19: 13–51'), ('Ref_6', 'Macdonald, D.W. (2006) The Encyclopedia of Mammals. Oxford University Press, Oxford.'), ('Ref_7', 'Martin, J. K., Handasyde K.A. et al. (2004). \"Aspects of the ecology of the bobuck T. caninus in the Strathbogie Ranges, Victoria\". in R. L. Goldingay and S. M. 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value too long for type character varying(255)
henrykironde commented 8 years ago

I suggest writing to the authors http://esapubs.org/archive/ecol/E095/178/#authors and informing them about the errors in the data.

The authors are using tab delimiters and end of line as "\t\t\t" making it hard to handle the data because they also use \n to mark a continuing line as shown in the fig below.

When the retriever tries to detect for incomplete lines, it will fail in this case since the line has an \n and has the correct required number of fields(2) yet the second field is incomplete 'Ref_34', 'Emmons L.H. & F. Feer. 1997. Neotropical Rain Forest Mammals, a Field Guide. 2da ed. The \n'

eltontraits_errors

ethanwhite commented 8 years ago

Ah, OK. So was this failing on Python 2 as well? I thought it was working there.

henrykironde commented 8 years ago

On Python 2, It does not fail but it install the wrong data. We need to add a check for such errors. Sample installed using able data installed

Installed rows / do not match the total number of rows in the raw data cmd

ethanwhite commented 7 years ago

Fixed by #740.