refdb-users — List for RefDB users

Re: [Refdb-users] Password for Access

[Rich S. <rsh...@ap...>]

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> I hardly dare to ask, but did you remove the leading hash in the
> relevant line? The example config file has

   Yup. The only hash is for the comment at the top of the file that
identifies the contents.

Rich

-- 
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[Refdb-users] RIS Tags By Type

[Markus H. <mar...@mh...>]

Rich Shepard writes:
 > refdbc: getref :ID:=15
 > ID*:15 (1999)
 > Key: albr1999
 > Albrect,J., Guesgen,H.
 > A combinatorial fuzzy set-theoretic approach to the mapping between
 > quantitative
 >   and qualitative data
 > 
 > :8
 > 
 >    This means that a lot of these tags are not appropriate for a conference
 > proceeding article. Is there an available guide that instructs me what tags
 > to use for various types? There is for BibTeX, how about RIS?
 > 

First of all, your data are not lost. The getref command returns a
fairly compact format by default which is convenient if you browse the
results for particular hits. In order to keep the output clean, many
tags are suppressed by default. To make sure all of the tags were
imported properly, run a command like

getref -t ris :ID:=15

to display the results using the input format.

In order to display more details in the default screen format, use the
-s switch, e.g.:

getref -s ALL :ID:=15

to display all available fields, or

getref -s N1AVRP

to display your notes, the availability, and the reprint status in
addition to the default fields. Needless to say that you can edit the
fields variable in ~/.refdbcrc to have additional fields displayed by
default.

Now for the RIS "style guide". The closest thing to such a guide is
the Reference Manager manual which is freely available as a PDF:

http://www.referencemanager.com/support/docs/ReferenceManager11.pdf

It contains a chapter on the RIS types and which fields they use.

regards,
Markus

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Re: [Refdb-users] Database Type

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard writes:
 >    Thank you. I read in the tutorial last evening that the RIS format requires
 > an explicit encoding, too, while risx has that as the first line of the data
 > file. I see that both refdb and the main reference database are encoded UTF8,
 > but that's not the default encoding on my system. Regardless, it works.
 > 

As long as refdbd can determine the encoding of the input data, there
is no problem as it will convert the data on the fly. refdbdrc sets
the input encoding of RIS files to ISO-8859-1 by default as this
covers both US and most European needs.

regards,
Markus

-- 
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mar...@ca...
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[Refdb-users] Password for Access

[Markus H. <mar...@mh...>]

Hi,

I hardly dare to ask, but did you remove the leading hash in the
relevant line? The example config file has

#passwd *

You should change this to

passwd abc

regards,
Markus

Rich Shepard writes:
 >    I put my RefDB password into ~/.refdbcrc, yet I'm still asked for it when I
 > start the client. Is there something I missed in doing it correctly?
 > 
 > TIA,
 > 
 > Rich
 > 
 > -- 
 > Richard B. Shepard, Ph.D.               |    The Environmental Permitting
 > Applied Ecosystem Services, Inc.(TM)    |            Accelerator
 > <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863
 > 
 > 
 > 
 > _______________________________________________
 > Refdb-users mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users
 > 

-- 
Markus Hoenicka
mar...@ca...
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http://www.mhoenicka.de

Re: [Refdb-users] RIS Tags By Type

[Rich S. <rsh...@ap...>]

On Fri, 16 Jun 2006, Z F wrote:

> I do not know which fields are appropriate and which are not, but
> you are forgetting that getref may not display all information
> available.

Lazar,

   I discovered this later while puttering around the entries.

> To display information in addition to default ask getref for more fields
> with -c option to getref or "fields" field in refdbcrc

   Thanks.

Rich

-- 
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Applied Ecosystem Services, Inc.(TM)    |            Accelerator
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Re: [Refdb-users] RIS Tags By Type

[Z F <mai...@ya...>]

--- Rich Shepard <rsh...@ap...> wrote:

>    I've found a description of the RIS standard, and the available
> tags are
> also listed in the client tutorial. What I need, however, is a guide
> to the
> appropriate tags for each reference type.
> 
>    One of my references was entered with TY  - CONF, but I did not
> use the
> ris.el template for that one because I had changed the type from
> JOUR. The
> full record is this:
> 
> TY  - CONF
> ID  - albr1999
> AU  - Albrect,J.
> AU  - Guesgen,H.
> TI  - A combinatorial fuzzy set-theoretic approach to the mapping
> between quantitative and qualitative data
> JO  - GeoComputation98:.Proc. 3rd.Internat. Conf. on.GeoComp.
> KW  - fuzzy sets
> KW  - fuzzy logic
> KW  - qualitative data
> KW  - data
> SP  - 1
> EP  - 8
> RP  - IN FILE
> AV  - 115
> PB  - Univ. of Bristol, U.K.
> PY  - 1999///
> ER  -
> 
>    However, when I view it in refdbc, most of these fields are not
> displayed:
> 
> refdbc: getref :ID:=15
> ID*:15 (1999)
> Key: albr1999
> Albrect,J., Guesgen,H.
> A combinatorial fuzzy set-theoretic approach to the mapping between
> quantitative
>   and qualitative data
> 
> :8
> 
>    This means that a lot of these tags are not appropriate for a
> conference
> proceeding article. Is there an available guide that instructs me
> what tags
> to use for various types? There is for BibTeX, how about RIS?

I do not know which fields are appropriate and which are not, but
you are forgetting that getref may not display all information
available.
To display information in addition to default ask getref for more
fields with -c option to getref or "fields" field in refdbcrc

Lazar

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Re: [Refdb-users] Prompt Not Returned in Clients -- SOLVED

[Z F <mai...@ya...>]

Hello Richard,

Change the pager in refdbcrc to something else, if you do not like
"less"

for example

pager more
or
pager stdout

Lazar 
--- Rich Shepard <rsh...@ap...> wrote:

> On Thu, 15 Jun 2006, Rich Shepard wrote:
> 
> >   Any idea what I broke here? More importantly, how can I fix it?
> 
>    Trial-and-error to the rescue. Pressing the 'q' key did the trick.
> 
> Rich
> 
> -- 
> Richard B. Shepard, Ph.D.               |    The Environmental
> Permitting
> Applied Ecosystem Services, Inc.(TM)    |            Accelerator
> <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax:
> 503-667-8863
> 
> 
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users
> 


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Re: [Refdb-users] make error

[Dan O'D. <dan...@ul...>]

Thanks Markus,

-d

On Fri, 2006-16-06 at 08:17 +0200, Markus Hoenicka wrote:
> Hi,
>=20
> Daniel O'Donnell <dan...@ul...> was heard to say:
>=20
> > refdbdref.c: In function =C3=A2=E2=82=AC=CB=9Cread_ris_data=C3=A2=E2=82=
=AC=E2=84=A2:
> > refdbdref.c:667: warning: passing argument 2 of =C3=A2=E2=82=AC=CB=9Cic=
onv=C3=A2=E2=82=AC=E2=84=A2 from
> > incompatible pointer type
>=20
> This is nothing to really worry about. There is an inconsistency about th=
e type
> of an argument between the *BSDs and other OSes like Linux. In one case t=
here's
> a char*, in the other case there'sa const char*. If I fix this on Linux, =
I'll
> get a warning on BSD and vice versa. However, the char* vs. const char* i=
s a
> compile-time warning which will not cause a runtime error as the sizes of=
 both
> pointers are identical. Unfortunately the iconv header file does not use =
a
> typedef which would allow to work around this issue.
>=20
> > refdbdref.c: In function =C3=A2=E2=82=AC=CB=9Cis_journal=C3=A2=E2=82=AC=
=E2=84=A2:
> > refdbdref.c:2370: error: =C3=A2=E2=82=AC=CB=9CDBI_ROW_ERROR=C3=A2=E2=82=
=AC=E2=84=A2 undeclared (first use in this
> > function)refdbdref.c:2370: error: (Each undeclared identifier is
> > reported only once
>=20
> This points to a libdbi version issue. DBI_ROW_ERROR is declared in
> <prefix>/include/dbi/dbi.h in libdbi versions 0.8.0 and later. If you use=
 an
> older version of libdbi, you'll simply have to upgrade. If you do have 0.=
8.0 or
> later installed, you may have stale header files lying around from a prev=
ious
> installation of an older version. E.g. if you had installed 0.7.x in /usr=
 and
> later installed 0.8.0 in /usr/local, the older headers will pop up first =
when
> the compiler looks for the include files.
>=20
> regards,
> Markus
>=20

[Refdb-users] RIS Tags By Type

[Rich S. <rsh...@ap...>]

   I've found a description of the RIS standard, and the available tags are
also listed in the client tutorial. What I need, however, is a guide to the
appropriate tags for each reference type.

   One of my references was entered with TY  - CONF, but I did not use the
ris.el template for that one because I had changed the type from JOUR. The
full record is this:

TY  - CONF
ID  - albr1999
AU  - Albrect,J.
AU  - Guesgen,H.
TI  - A combinatorial fuzzy set-theoretic approach to the mapping between quantitative and qualitative data
JO  - GeoComputation98:.Proc. 3rd.Internat. Conf. on.GeoComp.
KW  - fuzzy sets
KW  - fuzzy logic
KW  - qualitative data
KW  - data
SP  - 1
EP  - 8
RP  - IN FILE
AV  - 115
PB  - Univ. of Bristol, U.K.
PY  - 1999///
ER  -

   However, when I view it in refdbc, most of these fields are not displayed:

refdbc: getref :ID:=15
ID*:15 (1999)
Key: albr1999
Albrect,J., Guesgen,H.
A combinatorial fuzzy set-theoretic approach to the mapping between
quantitative
  and qualitative data

:8

   This means that a lot of these tags are not appropriate for a conference
proceeding article. Is there an available guide that instructs me what tags
to use for various types? There is for BibTeX, how about RIS?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Password for Access

[Rich S. <rsh...@ap...>]

   I put my RefDB password into ~/.refdbcrc, yet I'm still asked for it when I
start the client. Is there something I missed in doing it correctly?

TIA,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Prompt Not Returned in Clients -- SOLVED

[Rich S. <rsh...@ap...>]

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> By default, the clients pipe the output through "less" to allow you to page
> through longer output. However, you can choose any other pager or even
> stdout in the config file instead.

   I was so wrapped up in details that I had completely forgotten this. Too
many things going on simultaneously.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] refdb-init.sh update

[Rich S. <rsh...@ap...>]

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> I'm afraid you're mistaken here. The reference database is created with the
> following command in refdb-init.sh:

   Oh. Missed that.

> I don't know how you ran into this problem though.

   Me, neither. But, it's all working now.

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Database Type

[Rich S. <rsh...@ap...>]

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> RefDB supports two input formats, RIS and risx, but they both end up in the
> same database type. RIS has no means to store user-specific data (like AV,
> RP, N1) for more than one user, whereas risx does. Therefore risx is a more
> appropriate name for the database type. The database has a type tag only
> for future compatibility with RefDB versions which may support other
> reference database types.

Hi Markus,

   Thank you. I read in the tutorial last evening that the RIS format requires
an explicit encoding, too, while risx has that as the first line of the data
file. I see that both refdb and the main reference database are encoded UTF8,
but that's not the default encoding on my system. Regardless, it works.

Thanks for all you've done -- and continue to do -- with RefDB,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Database Type

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard <rsh...@ap...> was heard to say:

>    I just added the first 65 records to RefDB from a .ris file. However, when
> I ran the command, 'whichdb,' I see 'Database type: risx'.
>

RefDB supports two input formats, RIS and risx, but they both end up in the same
database type. RIS has no means to store user-specific data (like AV, RP, N1)
for more than one user, whereas risx does. Therefore risx is a more appropriate
name for the database type. The database has a type tag only for future
compatibility with RefDB versions which may support other reference database
types.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Prompt Not Returned in Clients -- SOLVED

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard <rsh...@ap...> was heard to say:

> On Thu, 15 Jun 2006, Rich Shepard wrote:
>
> >   Any idea what I broke here? More importantly, how can I fix it?
>
>    Trial-and-error to the rescue. Pressing the 'q' key did the trick.
>

By default, the clients pipe the output through "less" to allow you to page
through longer output. However, you can choose any other pager or even stdout
in the config file instead.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] refdb-init.sh update

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard <rsh...@ap...> was heard to say:

>    When the refdb-init.sh script is run, the database command 'createdb
> <name>' is run. RefDB does not see this as a valid RefDB databse because it
> was not created within the client, refdba.
>
>    When the script gets to this last stage, it would need to invoke refdba --
> as the database user -- ask for the password, then run 'createdb <name>' from
> within the administrative client.
>

I'm afraid you're mistaken here. The reference database is created with the
following command in refdb-init.sh:

# create a reference database
if [ "${referencedb_name}" ]; then
    echo ""
    echo "==="
    echo "Create ${referencedb_name} as reference database"
    <prefix>/bin/refdba -c stdout -C createdb ${referencedb_name}
fi

The only time the script uses the Postgres command createdb is when the system
database refdb is created. I don't know how you ran into this problem though.

regards,
Markus



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mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Toward a Working Reference Database

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard <rsh...@ap...>:

>    Page 51: Section 5.5 (Add, edit, or delete bibliographic styles).
> Currently
> there are:
>
> refdba: liststyle
> Eur.J.Pharmacol.
> J.Biol.Chem.
> bibtex-abbrev
> bibtex-full
> 999:4 retrieved:0 failed
> refdba:
>
> and the manual tells me to use 'addstyle' for more. Where are these located
> and described? The above are what I find in

The new (and not so shiny yet) refdb-init.sh script has already loaded all
available styles for you, so there is nothing left for you to do. The manual
assumes that you do everything manually.

regards,
Markus

-- 
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mar...@ca...
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http://www.mhoenicka.de

Re: [Refdb-users] main database is too old or corrupt

[Markus H. <mar...@mh...>]

Hi,

J.I...@uv... was heard to say:

> My name is Ignasi. I am new here. I'd like to be a new user of refdb. I
> have installed it in my box. The OS is Ubuntu 6.0.6., and the database
> engine will be sqlite. The "main database is too old or corrupt" error
> appears each time I type "viewstat" (or any other command) in the refdba
> prompt. I know you have been discussing about that error, and it seems
> that Dan O'Donell could solve the problem by changing the default
> database and user name in the config files. It didn'n work for me. I'm

In order to check this, could you run the refdb-bug script and send the output
to the list? The script creates a file refdb-bug.txt in the current working
directory and lists all configuration details and such.

> - As I don't know which directory should contain the HTML files, I
> specified that simple URL direction (file:///refdb), that my browser may
> understand. I'm not sure if it is correct.
>

This is nothing to worry about unless you use the web interface (which is still
a bit shaky at the moment).

> - I created the database successfully and run refdbd and refdba without
> problems. And then the error appeared.
>

What are the permissions of the refdb database file?

regards,
Markus

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mar...@ca...
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http://www.mhoenicka.de

Re: [Refdb-users] make error

[Markus H. <mar...@mh...>]

Hi,

Daniel O'Donnell <dan...@ul...> was heard to say:

> refdbdref.c: In function =E2=80=98read_ris_data=E2=80=99:
> refdbdref.c:667: warning: passing argument 2 of =E2=80=98iconv=E2=80=99=
 from
> incompatible pointer type

This is nothing to really worry about. There is an inconsistency about th=
e type
of an argument between the *BSDs and other OSes like Linux. In one case t=
here's
a char*, in the other case there'sa const char*. If I fix this on Linux, =
I'll
get a warning on BSD and vice versa. However, the char* vs. const char* i=
s a
compile-time warning which will not cause a runtime error as the sizes of=
 both
pointers are identical. Unfortunately the iconv header file does not use =
a
typedef which would allow to work around this issue.

> refdbdref.c: In function =E2=80=98is_journal=E2=80=99:
> refdbdref.c:2370: error: =E2=80=98DBI_ROW_ERROR=E2=80=99 undeclared (fi=
rst use in this
> function)refdbdref.c:2370: error: (Each undeclared identifier is
> reported only once

This points to a libdbi version issue. DBI_ROW_ERROR is declared in
<prefix>/include/dbi/dbi.h in libdbi versions 0.8.0 and later. If you use=
 an
older version of libdbi, you'll simply have to upgrade. If you do have 0.=
8.0 or
later installed, you may have stale header files lying around from a prev=
ious
installation of an older version. E.g. if you had installed 0.7.x in /usr=
 and
later installed 0.8.0 in /usr/local, the older headers will pop up first =
when
the compiler looks for the include files.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Database Type

[Rich S. <rsh...@ap...>]

   I just added the first 65 records to RefDB from a .ris file. However, when
I ran the command, 'whichdb,' I see 'Database type: risx'.

   Why is that?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Prompt Not Returned in Clients -- SOLVED

[Rich S. <rsh...@ap...>]

On Thu, 15 Jun 2006, Rich Shepard wrote:

>   Any idea what I broke here? More importantly, how can I fix it?

   Trial-and-error to the rescue. Pressing the 'q' key did the trick.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] refdb-init.sh update

[Rich S. <rsh...@ap...>]

On Wed, 14 Jun 2006, Markus Hoenicka wrote:

> This doesn't look like a user error. Could you send me some debug info?
> Please check whether /var/log/refdbd.log contains something useful, and
> maybe you can get hold of a PostgreSQL log file (or the relevant entries in
> /var/log/messages) as well.

Markus,

   Having gone through the process manually (and following the manual, plus
experimenting), I think that I understand the source of the error.

   When the refdb-init.sh script is run, the database command 'createdb
<name>' is run. RefDB does not see this as a valid RefDB databse because it
was not created within the client, refdba.

   When the script gets to this last stage, it would need to invoke refdba --
as the database user -- ask for the password, then run 'createdb <name>' from
within the administrative client.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Prompt Not Returned in Clients

[Rich S. <rsh...@ap...>]

   I have been trying to add the example database as I work my way through the
tutorial. When I run refdbc I cannot get the prompt to return:

[rshepard@salmo ~]$ refdbc
Please enter your password: 
240:scirefs
lines 1-1/1 (END)

   If I press [Enter] or [Tab], the speaker beeps at me. If I press ctrl-c the
same lines 1-1/1 (END) is shown with 'aborting' after it.

   Any idea what I broke here? More importantly, how can I fix it?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Not a RefDB database -- SOLVED

[Rich S. <rsh...@ap...>]

On Thu, 15 Jun 2006, Rich Shepard wrote:

>   What am I still missing?

   Nailed that one down.

   I used the postgres 'dropdb scirefs' to remove it, then logged onto the
refdba client. When I create the scirefs database here, it works. And, now
when I run the refdbc client, I'm automatically connected to scirefs.

Excelsior,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Not a RefDB database

[Rich S. <rsh...@ap...>]

   I must still be missing something crucial here. After creating refdb and
populating it according to instructions, and setting up both ~/.refdbcrc and
~/.refdbibrc to specify the defaultdb as 'scirefs', I created that database
with postgres' createdb command.

   However, when I try to access that db from the client tool, refdbc, I'm
told that it's not a RefDB database. It has no schema, because I did not see
where in the handbook I was told to load a schema.

   What am I still missing?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
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