emulating read and readline methods

MRAB google at mrabarnett.plus.com
Thu Sep 11 00:01:28 CEST 2008


On Sep 10, 6:59 pm, Sean Davis <seand... at gmail.com> wrote:
> I have a large file that I would like to transform and then feed to a
> function (psycopg2 copy_from) that expects a file-like object (needs
> read and readline methods).
>
> I have a class like so:
>
> class GeneInfo():
>     def __init__(self):
>         #urllib.urlretrieve('ftp://ftp.ncbi.nih.gov/gene/DATA/
> gene_info.gz',"/tmp/gene_info.gz")
>         self.fh = gzip.open("/tmp/gene_info.gz")
>         self.fh.readline() #deal with header line
>
>     def _read(self,n=1):
>         for line in self.fh:
>             if line=='':
>                 break
>             line=line.strip()
>             line=re.sub("\t-","\t",line)
>             rowvals = line.split("\t")
>             yield "\t".join([rowvals[i] for i in
> [0,1,2,3,6,7,8,9,10,11,12,14]]) + "\n"
>
>     def readline(self,n=1):
>         return self._read().next()
>
>     def read(self,n=1):
>         return self._read().next()
>
Each time readline() and read() call self._read() they are creating a
new generator. They then get one value from the newly-created
generator and then discard that generator. What you should do is
create the generator in __init__ and then use it in readline() and
read().

>     def close(self):
>         self.fh.close()
>
> and I use it like so:
>
> a=GeneInfo()
> cur.copy_from(a,"gene_info")
> a.close()
>
> It works well except that the end of file is not caught by copy_from.
> I get errors like:
>
> psycopg2.extensions.QueryCanceledError: COPY from stdin failed: error
> during .read() call
> CONTEXT:  COPY gene_info, line 1000: ""
>
> for a 1000 line test file.  Any ideas what is going on?
>
I wonder whether it's expecting readline() and read() to return an
empty string at the end of the file instead of raising StopIteration.



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