[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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