[Babase] Validating ALLMISCS.Txt
Karl O. Pinc
kop at meme.com
Mon Jul 9 22:44:31 EDT 2007
On 07/09/2007 07:39:53 AM, Lacey Maryott wrote:
> 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?
You'd delete the ALLMISCS and put in a POINTS row with
the right Sid. Or maybe just bump the SAMPLES.mins column.
That's probably it. I can write more when I get back Fri.
Is 'OS' a legal in ALLMISCS.Txt?
>
> 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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>
Karl <kop at meme.com>
Free Software: "You don't pay back, you pay forward."
-- Robert A. Heinlein
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