[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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> 
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