[Babase] Fwd: babase update and conf call
Catherine Markham
amarkham at princeton.edu
Thu Sep 14 07:25:16 EDT 2006
Sounds good to me - I'll be in Jeanne's lab by 2:30 to get in on the
call as well.
Catherine
Jeanne Altmann wrote:
> 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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