[Babase] Validating ALLMISCS.Txt

Lacey Maryott lacey.maryott at duke.edu
Mon Jul 9 08:39:53 EDT 2007


I made notes below about each sample,

Karl O. Pinc wrote:
> Hi,
>
> Looks like there are some "OS" type ALLMISCS rows.  Are these valid?
>
>
> (Lacey, note that the following SQL is, unlike what we did yesterday,
> SQL standards compliant.)
>
> babase=> select substring(allmiscs.txt from 1 for position(',' in 
> allmiscs.txt) - 1) as col1, count(*), max(samples.date) from allmiscs, 
> samples where samples.sid = allmiscs.sid group by col1;
>  col1 | count |    max
> ------+-------+------------
>  OS   |     3 | 2006-01-23
>  C    |   563 | 2006-12-15
>  U    |   990 | 2005-11-10
>  O    |   573 | 2006-06-13
> (4 rows)
>
> babase=> select * from samples, allmiscs where samples.sid = 
> allmiscs.sid and substring(allmiscs.txt from 1 for position(',' in 
> allmiscs.txt) - 1) = 'OS' order by samples.date;
>   sid  |    date    | stime | observer | stype | grp  | sname | mins | 
> minsis | programid | setupid | palmtop | almid |  sid  |  atime   |  txt
> -------+------------+-------+----------+-------+------+-------+------+--------+-----------+---------+---------+-------+-------+----------+-------- 
>
>  13254 | 2002-02-16 |       | JKW      | J     | 1.21 | OIL   |    5 
> |      3 |         1 |       1 |       4 |  1084 | 13254 | 14:41:46 | 
> OS,,,,
    OIL's sample for 02-02-16 P4 should be OS as in out of sight... she 
had a few valid points within the sample too. it looks as though the ADL 
was an error and should have been <PNT>
<HDR>,0202161433OIL,PTSAMPLR_AUG01,SETUP_AUG01,4,16 Feb 2002,OMO,JKW,OIL,JUV
<PNT>,0202161433OIL,14:35:21,R2,OMO,OZO,XXX,
<PNT>,0202161433OIL,14:36:22,R2,OZO,OMO,XXX,
<PNT>,0202161433OIL,14:37:18,OS,,,,
<PNT>,0202161433OIL,14:38:50,F3,OMO,DUI,XXX,UNK
<PNT>,0202161433OIL,14:41:37,OS,,,,
*<ADL>,0202161433OIL,14:41:46,OS,,,,*
>  34732 | 2006-01-23 |       | RSM      | F     | 2.10 | LIW   |   10 
> |      9 |         1 |       2 |       1 |  1981 | 34732 | 15:30:57 | OS,
> 34732 | 2006-01-23 |       | RSM      | F     | 2.10 | LIW   |   10 
> |      9 |         1 |       2 |       1 |  1982 | 34732 | 15:31:20 | OS,
> (3 rows)
>
>
the same seems to be the case with this LIW sample.

<HDR>,0601231530LIW,PTSAMPLR_JUL03,SETUP_JUL03,1,23 Jan 2006,LIN,RSM,LIW,FEM
<PNT>,0601231530LIW,15:30:49,OS,
*<ADL>,0601231530LIW,15:30:57,OS,
<ADL>,0601231530LIW,15:31:20,OS,*
<PNT>,0601231530LIW,15:31:50,W1VS,WIP,WIP,XXX,
<PNT>,0601231530LIW,15:32:42,W1VS,WIP,WIP,XXX,
<PNT>,0601231530LIW,15:33:40,W1VS,WIP,WIP,XXX,
<PNT>,0601231530LIW,15:34:41,W1VS,WIP,WIP,XXX,

what is the next step in fixing these?

Lacey
> Karl <kop at meme.com>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
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-- 
Lacey Maryott
Alberts Lab
Department of Biology
Duke University
ph: 919-660-7306
fax: 919-660-7293
Lacey.Maryott at duke.edu 



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