[Babase] Fwd: babase update and conf call
Jeanne Altmann
altj at Princeton.EDU
Thu Sep 14 07:21:36 EDT 2006
I realize that would be better for me as well,
j
-----Original Message-----
From: babase-bounces at eeblistserv.princeton.edu
[mailto:babase-bounces at eeblistserv.princeton.edu] On Behalf Of Susan
Alberts
Sent: Wednesday, September 13, 2006 12:57 PM
To: The Baboon Database Project
Subject: RE: [Babase] Fwd: babase update and conf call
No worries, we knew you were in transit. I believe that Karl has a call
with Jun tomorrow morning so perhaps we should do 2:30.
Susan
>Sorry, you have probably been waiting on me, Just got into Princeton
>and found loads of messages, Either time is ok for me also, jeanne
>
>-----Original Message-----
>From: babase-bounces at eeblistserv.princeton.edu
>[mailto:babase-bounces at eeblistserv.princeton.edu] On Behalf Of
>Catherine Markham
>Sent: Tuesday, September 12, 2006 6:46 PM
>To: The Baboon Database Project
>Subject: Re: [Babase] Fwd: babase update and conf call
>
>Hi all,
>
>Wow - that's fantastic news about progress with the system!
>
>Unless something comes up with my schedule at the last minute (there
>are still a few TBA things that I'm on hold for), count me in for the
>conference call on Thursday. Either of the times Susan mentioned (10
>am or between 2:30 and 3:30) should work great.
>
>Thanks,
>Catherine
>
>
>
>Susan Alberts wrote:
>> Sorry, I don't know why I didn't send that the mailing list! Here is
>> it again.
>>
>> Susan
>>
>> Begin forwarded message:
>>
>>> *From: *Susan Alberts <alberts at duke.edu <mailto:alberts at duke.edu>>
>>> *Date: *September 12, 2006 5:24:13 PM EDT
>>> *To: *"Karl O. Pinc" <kop at meme.com <mailto:kop at meme.com>>, Jeanne
>>> Altmann <altj at Princeton.EDU <mailto:altj at Princeton.EDU>>, KETHERINE
>>> FENN <kfenn at Princeton.EDU <mailto:kfenn at Princeton.EDU>>, Leah Gerber
>>> <lgerber at duke.edu <mailto:lgerber at duke.edu>>, Catherine_Markham
>>> Markham <amarkham at princeton.edu <mailto:amarkham at princeton.edu>>
>>> *Subject: **babase update and conf call*
>>>
>>> Dear all,
>>>
>>> Karl is about to reach a solid end point and we are excited about
>>> this. There are some loose ends that will need to be tied up, and we
>>> think that a babase conference call for Thursday would be a good
>>> thing. We would really love Catherine to be involved if at all
>>> possible becuase of her relatively long history with babase (and as
>>> a
>
>>> future user), but I realize her schedule is now quite different.
>>>
>>> Jeanne and I have a different conf call at 11. We could do our
>>> babase
>
>>> conf call before that, at 10 am, or we could do it bewtween 2:30
>>> and 3:30. That is about all the time that I have free that day. If
>>> that can't work out then let me know and we will discuss another
>>> time after Karl is back in Chi, but it seems like it would be good
>>> to do it before he leaves here (but not absolutely necessary).
>>>
>>> Here is the update and agenda for our call:
>>>
>>> Here are the things that still need to be done before Karl leaves.
>>>
>>>
>>> 1. Cycgaps validation and assigning cycles.series AND automatic
>>> cycgaps updateing. This is in progress now.
>>> 2. Reconversion using the new automatic updates.
>>> 3. Update Ranks documentation (is this the last table for which
>the
>>> documentation reflects the old foxpro system?)
>>>
>>>
>>> At that point, the conversion is done, except for then debugging to
>>> deal with conversion errors that are programming errors (if any).
>>>
>>> After this final conversion, there are some things that we will
>>> need to do and decisions we need to make that affect how we use the
>>> database (I am NOT including in this list the things that we all
>>> know
>
>>> are outstanding, such a developing the data entry procedures,
>>> adding new tables, creating new ranker, and fixing the front end).
>>>
>>>
>>> 1. *Non-trigger error checks.* There are a set of error checks
>that
>>> we can run to check the integrity and accuracy of the
database.
>>> The errors that this would find are not errors that could or
>>> should be coded as automatic triggers, hence we will describe
>>> these as non-trigger error checks. They are things like
>checking
>>> that every animal present in the group has a rank assigned
(as
>>> opposed to checking that no one is assigned a rank unless
they
>>> are in the group - this latter one is a trigger, the former
> >> cannot be because before ranks are assigned, no one has a
>>> rank). Karl notes that we have always had these non-trigger
>>> error checks available to run in foxpro, but that no one has
>>> every really run them or used them to identify and correct
>>> errors. Hence, they are effectively optional error checks.
The
>>> code has been written for these error checks, but not
debugged
>>> and hence not run before. Our options are:
>>> 1. Take the error checks that Karl has written and debug
and
>>> run them ourselves, one by one as needed. They are sql
>>> queries, so this is highly feasible but laborious.
>>> 2. Have Karl debug and concatenate them into a single
>program
>>> that would be run whenever we wanted it to be, probably
>>> automatically on a regular basis.
>>> 3. Outsource this project to someone else - i.e., hire
>>> someone to concatenate and debug these programs into a
>>> single program that would be run automatically.
>>> 2. *Testing and pushing the system.* Karl's concern as a
>>> professional programmer is that we find the worst bugs early
on
>>> and fix them. He points out that of course there will be
bugs.
>>> To find them, we need to push the system - do a lot of
>>> manipulation of the tables using babase_test. Update rows,
>>> delete rows, make illegal and legal changes and see how the
>>> system performs. Ideally this should be done for all tables,
>all
>>> columns. The sexual cycles tables should have special
attention
>>> here because there are so many "analyzed" tables. This kind
of
>>> testing will also reveal performance issues that might come
up
>>> that we haven't anticipated or found yet. One approach would
>be
>>> to just devote a certain amount of time in Leah's and Tabby's
>>> week, some week, to doing this. Another option would be
>>> contracting Karl or someone else to do this. It might be a
>>> couple of days work, hard for me to say.
>>> 3. *Dealing with warnings and unwanted error messages.* Every
>>> night, the program will run the triggers, and these automatic
>>> checks will produce a list of error messages and warnings
>>> related to data "errors" in the database. Specifically,
anytime
>>> a rule is violated (rules outlined in the documentation) a
>>> message will appear. Some of these we will want to ignore
>>> forever or for the time being, and we will not want to be
>>> revisited with them every day. So, Karl proposes a program
that
>>> will defer or eliminate unwanted error messages and warnings.
>>> This is optional, but would be a great convenience. It is not
>>> really something that I think is feasible for us to do
without
>>> professional help, unless Leah or Tabby have insight into
this.
>>> What to do?
>>> 4. *Checking cycle ids?* Karl points out that in creating the
new
>>> cycle files in the new babase system, cycles have different
>cids
>>> in many cases than they did in the old babase system. He
wants
>>> to know whether we want a program that maps old onto new, so
>>> that we can find particular cycles that we analyzed in
foxpro.
>>>
>>>
>>> -----------------------------------------------
>>> Susan Alberts, Dept. Biology, Duke University, Durham NC 27708.
>>> Phone
>
>>> 919-660-7272, Fax 919-660-7293. alberts at duke.edu
>>> <mailto:alberts at duke.edu>
>>>
>>>
>>>
>>
>> -----------------------------------------------
>> Susan Alberts, Dept. Biology, Duke University, Durham NC 27708.
>> Phone 919-660-7272, Fax 919-660-7293. alberts at duke.edu
>> <mailto:alberts at duke.edu>
>>
>>
>>
>>
>>
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--
------------------------------------------------------------------------
--------------------------------------------------------------
Susan Alberts, Department of Biology, Duke University, Box 90338, Durham
NC 27708
919-660-7272 (phone), 919-660-7293 (FAX)
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