[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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