[Babase] Fwd: babase update and conf call

Jeanne Altmann altj at Princeton.EDU
Wed Sep 13 18:29:14 EDT 2006


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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