mx-database-discuss Mailing List for mx

Yes, those four should be fine.  If you run the unit tests after the
fact and you don't see an inordinate number of errors your setup
should be fine.

M

On Mon, Jul 18, 2011 at 4:41 PM, Sharon Banting
<Sha...@um...> wrote:
> The documentation I’ve read states that users should be given all privileges
> on the mx databases.  Our policy is to only grant select, insert, update,
> delete to users in production and create any objects they need for them via
> scripts.  Is this definitely required, or can they run with a reduced set of
> privileges?
>
>
>
> Sharon Banting
>
> Information Services &
>
> Technology
>
> 100 Administration Building
>
> University of Manitoba
>
> Winnipeg, MB R3T 2N2
>
> Phone:  (204)474-9957
>
> Fax: (204)474-7502
>
>
>
> ------------------------------------------------------------------------------
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> Research study explores the data loss prevention market. Includes in-depth
> analysis on the changes within the DLP market, and the criteria used to
> evaluate the strengths and weaknesses of these DLP solutions.
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> _______________________________________________
> Mx-database-discuss mailing list
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>

The documentation I've read states that users should be given all privileges
on the mx databases.  Our policy is to only grant select, insert, update,
delete to users in production and create any objects they need for them via
scripts.  Is this definitely required, or can they run with a reduced set of
privileges?

 

Sharon Banting

Information Services &

Technology

100 Administration Building

University of Manitoba

Winnipeg, MB R3T 2N2

Phone:  (204)474-9957

Fax: (204)474-7502

 

That's a new one to me.  Googling I found this, which might help, or be related.

http://stackoverflow.com/questions/6199301/global-access-to-rake-dsl-methods-is-deprecated

cheers,
Matt

On Tue, Jun 28, 2011 at 5:51 PM, Carl Boettiger <cbo...@gm...> wrote:
> Hi list,
> I am having a simple problem with the install process at the rake step,
> wonder if anyone has any ideas?
>
>
> cboettig@wiglaf:~/.mx$ sudo rake gems:install
> (in /home/cboettig/.mx)
> rake aborted!
> uninitialized constant Rake::DSL
> /home/cboettig/.mx/Rakefile:7
> Thanks much,
> Carl
>
> --
> Carl Boettiger
> UC Davis
> http://www.carlboettiger.info/
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
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> Mx-database-discuss mailing list
> Mx-...@li...
> https://lists.sourceforge.net/lists/listinfo/mx-database-discuss
>
>

Hi list,

I am having a simple problem with the install process
<http://mx.phenomix.org/index.php/Installation>at the rake step, wonder if
anyone has any ideas?



cboettig@wiglaf:~/.mx$ sudo rake gems:install
(in /home/cboettig/.mx)
rake aborted!
uninitialized constant Rake::DSL
/home/cboettig/.mx/Rakefile:7

Thanks much,

Carl


-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/

Hi Chris,

> Hey, it's Chris Hamilton.  I've got a few questions regarding setting up my excel database in preparation for a batch upload.
>
> What column heading does a "collecting date" go under?

You'll need to break the date down into the the sd_d, sd_m, sd_y
columns, see http://mx.phenomix.org/index.php/App/specimen/batch_load#Valid_column_heads_on_batch_files.

>as well as the "collector/s" of the specimen?

Well that's a hell of a thing, that column isn't in there yet, I added
it now as 'collectors' (also adding 'micro_habitat' and
'micro_habitat'). Can you tell we've been using a verbatim approach?

> I think I have the column names correctly placed, but I don't have a collecting event "ce_id" designated.

A ce_id is a collecting event id that comes from mx, i.e. it's already
generated.  Use this only if you are referencing existing data (i.e.
in your case you don't need this column on initial imports).

> What is the collecting event going to represent, again?

A cumulative time/place/collectors/method/habitat record. I.e. the
who/where/when/how.

> Also, as for "elevation" of the GPS site...I don't have a "elev_min" and "elev_max", do I just duplicate the altitude I have into both columns or just put it in one? and which one?

You can put it in both if identical- to be more explicit, in some
cases were only min is included and max is required I duplicate to min
to max.

> So far, I've got "identifier", "otu_id", "sex", "latitude", "longitude", "elev_min", "elev_max", "locality", date, collectors, "notes"

Sounds good.

Matt

Matt,

Hey, it's Chris Hamilton.  I've got a few questions regarding setting up my excel database in preparation for a batch upload.

What column heading does a "collecting date" go under? as well as the "collector/s" of the specimen?  I think I have the column names correctly placed, but I don't have a collecting event "ce_id" designated.  What is the collecting event going to represent, again?

Also, as for "elevation" of the GPS site...I don't have a "elev_min" and "elev_max", do I just duplicate the altitude I have into both columns or just put it in one? and which one?

So far, I've got "identifier", "otu_id", "sex", "latitude", "longitude", "elev_min", "elev_max", "locality", date, collectors, "notes"

thanks,
Chris

------------------------------------------------------------
"The mystery of the beginning of all things is insoluble by us; and I for one must be content to remain an agnostic" - Charles Darwin

Chris Hamilton
PhD student
The Bond Lab
http://core.ecu.edu/biol/bondja/Bond_Lab_Website/Home.html
Department of Biology
East Carolina University
ch...@8l...
ham...@st...
www.8legs2fangs.com

We're still finding the odd bugs to resolve in the migration to
2.3.10.  If you are running an instance in production you should
*immediately* update to the latest migration and truncate your
sessions table.

Cheers,
Matt

Just a note to point out that we've updated mx to use Rails 2.3.10.
You'll have to update some gems and run a migration, but other than
that things are straightforward and as before.  If you're running a
production server you'll note that we're now using a database store
for sessions, so you'll *definitely* need to setup a cron to clear
that table relatively frequently.

cheers,
Matt

Yes, it likely is, we haven't used that in production.  I'll take a
stab a fixing it but we also need to double check this model is what
you want.  Will it be useful to you as you interpret it now?

Matt

On Wed, May 12, 2010 at 5:37 AM, Andreas Wallberg
<and...@gm...> wrote:
> This is what I get:
>
> =====
>
> ActiveRecord::StatementInvalid in Chromatogram#new
>
> Showing app/views/chromatogram/_form.html.erb where line #51 raised:
>
> Mysql::Error: You have an error in your SQL syntax; check the manual
> that corresponds to your MySQL server version for the right syntax to
> use near '))' at line 1: SELECT count(*) AS count_all FROM `seqs`
> INNER JOIN pcrs ON seqs.pcr_id = pcrs.id    WHERE ((`pcrs`.id = ))
>
> Extracted source (around line #51):
>
> 48:
> Attached to these seqs:
>
> 49:
> 50: <% if params[:commit] != "Create"  %>
> 51:   <% if @seqs.size == 0 %>
> 52:      none
>
>
> 53:   <% else %>
> 54:     <% @seqs.each do |seq| %>
>
> Trace of template inclusion: app/views/chromatogram/new.html.erb
>
> RAILS_ROOT: /home/est/mx
>
> =====
>
> /Andreas
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Mx-database-discuss mailing list
> Mx-...@li...
> https://lists.sourceforge.net/lists/listinfo/mx-database-discuss
>

This is what I get:

=====

ActiveRecord::StatementInvalid in Chromatogram#new

Showing app/views/chromatogram/_form.html.erb where line #51 raised:

Mysql::Error: You have an error in your SQL syntax; check the manual
that corresponds to your MySQL server version for the right syntax to
use near '))' at line 1: SELECT count(*) AS count_all FROM `seqs`
INNER JOIN pcrs ON seqs.pcr_id = pcrs.id    WHERE ((`pcrs`.id = ))

Extracted source (around line #51):

48:
Attached to these seqs:

49:
50: <% if params[:commit] != "Create"  %>
51:   <% if @seqs.size == 0 %>
52:      none


53:   <% else %>
54:     <% @seqs.each do |seq| %>

Trace of template inclusion: app/views/chromatogram/new.html.erb

RAILS_ROOT: /home/est/mx

=====

/Andreas

Just a heads up that I'm going to be doing some serious code
cleanup/changes in the next 2-3 weeks.  It may or may not affect your
code, which you may or may not be using. In brief, I'm formalizing a
lot of the ontology related stuff that was largely hacked on to start.
 I don't anticipate this affecting people except if you have custom code
that references the Part or Isa models, which will be
deprecated/renamed.  Best thing to do would be to make a note that the
current SF commit (418, edge branch) is quite stable, and you should
first update your your to that commit then wait for an all clear
before updating again.

I *may* lump all the database migrations up to
that 418 as well into a single migration, so this would make your
migration path tricky (very) if you don't update to 418 first. In
other words, please update to edge 418 if you plan to keep using mx.

cheers,
Matt