refdb-users — List for RefDB users

Re: [Refdb-users] make error

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

Following up on the libdbi problem:

Has anybody successfully managed the make on a current debian system? I
did a fresh install of Ubuntu 6.06 to make sure there was no legacy
data, and have tried loading from the libdbi.sourceforge site as well as
from the dapper.ubuntu site and simply cannot get through make. I get
the wrong pointers error even with make dist-clean.

I'm wondering if there is not a way of checking that the correct perl
and other packages are installed and installing if not? I simply can't
get a source install to work.

I'd appreciate any experiences in debian: while I have no programming
experience, I'm not an inexperienced linux user and it is unusual for me
to get as stumped as I currently am.

-d

On Fri, 2006-16-06 at 08:17 +0200, Markus Hoenicka wrote:
> Hi,
> 
> Daniel O'Donnell <dan...@ul...> was heard to say:
> 
> > refdbdref.c: In function ‘read_ris_data’:
> > refdbdref.c:667: warning: passing argument 2 of ‘iconv’ from
> > incompatible pointer type
> 
> This is nothing to really worry about. There is an inconsistency about the type
> of an argument between the *BSDs and other OSes like Linux. In one case there'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* is 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 ‘is_journal’:
> > refdbdref.c:2370: error: ‘DBI_ROW_ERROR’ undeclared (first 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 previous
> 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
> 
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

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

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

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

>    I have to take complete ownership of the lost trailing space "bug;" it's
> not Markus' fault in any way. As a new RefDB user, it did not occur to me to
> use the "like" selector instead of the "exactly" selector. Mea culpa! All my
> ignorance.
>

I'm glad it turned out as a fairly simple accident. Who would have thought a
space can hunt you for days. Weird "bugs" like these always make me nervous,
especially when I'm about to finish a new release.

regards,
Markus

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

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

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

On Mon, 19 Jun 2006, Markus Hoenicka wrote:

> I haven't seen anything as weird as this (except maybe the duplicate
> keyword/trailing slash bug repoted by Rich).

All,

   I have to take complete ownership of the lost trailing space "bug;" it's
not Markus' fault in any way. As a new RefDB user, it did not occur to me to
use the "like" selector instead of the "exactly" selector. Mea culpa! All my
ignorance.

Rich

-- 
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Applied Ecosystem Services, Inc.(TM)    |            Accelerator
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Re: [Refdb-users] One last question

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

On Mon, 19 Jun 2006, Markus Hoenicka wrote:

> This solves one part of the puzzle. I'm still at a loss why the datasets
> are returned without empty lines inbetween. As you can see in the output
> above, your data work just fine on my system.

Markus,

   I can tell you why we see the different results, but not what causes it. Up
until now, the references database was encoded UTF8. No space between records
in the .ris dump. When I extracted the 'shortnose' records (all three of 'em
this time) to fix the trailing space in the last one, the encoding was
Latin1, and there was a space between records.

Whew!

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] One last question

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

On Mon, 19 Jun 2006, Markus Hoenicka wrote:

> The first two entries (desj00 and coen01) use the spaceless shortnose,
> whereas cunn01 uses the shortnose with a trailing space. While you ran
> your tests, you probably queried for :KW:=shortnose (without a
> space). This will return only the first two entries that match
> exactly. It will not return the third entry as the keyword differs by
> one space. In order to get that one too, you need to query for
> :KW:~shortnose or something similar. I reckon you added the "shortnose
> " accidentally and never found that entry again.

Markus,

   Exactly. I saw the two entries and did an exact match search. Thank you for
the lesson.

> This solves one part of the puzzle. I'm still at a loss why the datasets
> are returned without empty lines inbetween. As you can see in the output
> above, your data work just fine on my system.

   I cannot explain it, either. I'll just live with it since I don't expect
this to be a major concern since it's so easily fixed in an editor.

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] One last question

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

On Mon, 19 Jun 2006, Markus Hoenicka wrote:

> How did you check the encoding? I just ran the following on my box:

Markus,

   Well, I thought I used the -E option, but I must have done something
incorrectly. I just re-did it and it worked as expected. Unknown user error;
I could not reproduce the failure.

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] One last question

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

Rich Shepard writes:
 >    I just checked again with both joe and emacs. When I press ctrl-e (to move
 > to the end of the line), the cursor immediately follows the final 'e' in both
 > cases. I cannot find a trailing space. In both editors, if I press 'ctrl-d'
 > to delete the character to the right of the point (in both editors), the
 > newline is removed. I cannot find a trailing space after either of them. I
 > _thought_ that I had checked for that before asking for help.
 > 

No matter what I do, the space is there. I've checked the SQL dump you
sent me off-list. The "shortnose" keyword has the ID 222, the
"shortnose " (note the trailing space) has the ID 308. I managed to
create a scirefs database in PostgreSQL with exactly these data. I ran
the following query:

refdbc: getref -t ris :KW:~shortnose -o rich.ris
932 byte written to /usr/home/markus/rich.ris
999:3 retrieved:0 failed

rich.ris looks like this:


TY  - RPRT
ID  - desj00
AU  - Desjardins,M.
AU  - Markle,D.F.
KW  - fish
KW  - lakes
KW  - Klamath Basin
KW  - distribution
KW  - shortnose
KW  - Lost River
KW  - sucker
RP  - NOT IN FILE
BT  - Distribution and biology of suckers in Lower Klamath Reservoirs
CY  - Portland, Oregon
PY  - 2000///
ER  - 

TY  - RPRT
ID  - coen01
AU  - Coen,M.A.
AU  - Shively,R.
KW  - fish
KW  - Oregon
KW  - lakes
KW  - spawning
KW  - Klamath Basin
KW  - shortnose
KW  - Lost River
KW  - sucker
RP  - NOT IN FILE
BT  - Sampling of suckers in Upper Klamath Lake, Oregon to identify shoreline spawning sites
PY  - 2001///
ER  - 

TY  - RPRT
ID  - cunn01
AU  - Cunningham,M.E.
AU  - Shively,R.
TI  - Monitoring report of Lost River and Shortnose suckers in the lower Williamson River, Oregon
KW  - fish
KW  - Oregon
KW  - monitoring
KW  - rivers
KW  - Klamath Basin
KW  - Lost River
KW  - sucker
KW  - shortnose 
RP  - NOT IN FILE
PY  - 2001///
ER  - 

The first two entries (desj00 and coen01) use the spaceless shortnose,
whereas cunn01 uses the shortnose with a trailing space. While you ran
your tests, you probably queried for :KW:=shortnose (without a
space). This will return only the first two entries that match
exactly. It will not return the third entry as the keyword differs by
one space. In order to get that one too, you need to query for
:KW:~shortnose or something similar. I reckon you added the "shortnose
" accidentally and never found that entry again.

This solves one part of the puzzle. I'm still at a loss why the
datasets are returned without empty lines inbetween. As you can see in
the output above, your data work just fine on my system.

regards,
Markus

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

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

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

J.I...@uv... writes:
 > Yes I do. I get an error in the xterm running refdba. It says "error"
 > when I run viewstat or listuser. But if I insert the command listdb, the
 > pager displays an empty document. Does it tell you something? I have
 > also asked refdba for a .log file during a simple session, and it
 > doesn't add much information:
 > 
 > 7:pid=5034:Mon Jun 19 15:43:39 2006:viewstat
 > 7:pid=5034:Mon Jun 19 15:43:46 2006:quit
 > 

I haven't seen anything as weird as this (except maybe the duplicate
keyword/trailing slash bug repoted by Rich). The funny thing is that
the sources do not contain a single line that would issue the message
"error". The message is defined in statgen.pl which creates the header
file that holds the messages, but the corresponding error number (001)
is not referenced anywhere in the code. All other errors cause a
different, usually more verbose, error message. Is that "error"
message sent to stderr or to stdout? In the latter case, it should be
within the pager (which is less according to your config files), in
the former case it should appear only if you leave the pager. Is there
any chance that the "error" message is generated by a different
program (the pager, the shell that invokes the pager etc)?

As a last resort, would it be possible for me to either remotely
access refdbd or to get a temporary shell account on your box for
further debugging? I'm really stymied here.

regards,
Markus

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

Re: [Refdb-users] One last question

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

Rich Shepard writes:
 >    I tried dumping all the records, deleting the db and recreating it before
 > restoring the records. Postgres still sees both refdb and scirefs as UTF8.


How did you check the encoding? I just ran the following on my box:

refdba: createdb -E ISO-8859-1 latin
235:latin
999:1 created:0 failed
refdba: adduser -d latin markus
238:markus@:latin
999:1 added:0 failed
refdba: createdb -E UTF-8 utf
235:utf
999:1 created:0 failed
refdba: adduser -d utf markus
238:markus@:utf
999:1 added:0 failed


That is, now I've got two databases, the first one intended to use
Latin-1 and the second one UTF-8.

Running whichdb on these databases gives:

refdbc: whichdb
Current database: latin
Number of references: 0
Highest reference ID: 0
Number of notes: 0
Highest note ID: 0
Encoding: ISO-8859-1
Database type: risx
Database version: 2
Database server: pgsql
Created: 2006-06-19 19:41:19 UTC
Using refdb version: 0.9.7-pre7
Last modified: 2006-06-19 19:41:19 UTC

refdbc: whichdb
Current database: utf
Number of references: 0
Highest reference ID: 0
Number of notes: 0
Highest note ID: 0
Encoding: UTF-8
Database type: risx
Database version: 2
Database server: pgsql
Created: 2006-06-19 19:43:00 UTC
Using refdb version: 0.9.7-pre7
Last modified: 2006-06-19 19:43:00 UTC

I also checked the databases using the PostgreSQL command line client with
the following queries:

latin=> select encoding from pg_database where datname='latin';
 encoding 
----------
        8
(1 row)

latin=> select encoding from pg_database where datname='utf';
 encoding 
----------
        6
(1 row)


I'd have to look up in the headers what '8' and '6' stand for, but at
least they're different.

So unfortunately I can't reproduce this problem on my box. Did anyone
else try?

regards,
Markus

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

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

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

Hi,

this is interesting. There is no indication of an error on the server side. Do
you still get the error message in the refdba client?

regards,
Markus

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

> 7:pid=5021:Mon Jun 19 14:40:02 2006:dbi_driver_dir went to:
> 7:pid=5021:Mon Jun 19 14:40:02 2006:
> 7:pid=5021:Mon Jun 19 14:40:02 2006:dbi is up using default driver dir
> 6:pid=5021:Mon Jun 19 14:40:02 2006:Available libdbi database drivers:
> 6:pid=5021:Mon Jun 19 14:40:02 2006:sqlite
> 6:pid=5021:Mon Jun 19 14:40:02 2006:Requested libdbi driver found
> 6:pid=5021:Mon Jun 19 14:40:02 2006:Database directory:
> 6:pid=5021:Mon Jun 19 14:40:02 2006:/usr/local/var/lib/refdb/db
> 6:pid=5021:Mon Jun 19 14:40:02 2006:application server started
> 6:pid=5021:Mon Jun 19 14:40:02 2006:share extended notes by default
> 7:pid=5021:Mon Jun 19 14:40:02 2006:use /tmp/refdbd_fifo5021 as fifo
> 6:pid=5021:Mon Jun 19 14:40:02 2006:server waiting n_max_fd=5
> 6:pid=5021:Mon Jun 19 14:40:29 2006:adding client 127.0.0.1 on fd 6
> 6:pid=5021:Mon Jun 19 14:40:29 2006:server waiting n_max_fd=6
> 6:pid=5021:Mon Jun 19 14:40:29 2006:parent removing client on fd 6
> 6:pid=5021:Mon Jun 19 14:40:29 2006:server waiting n_max_fd=5
> 6:pid=5021:Mon Jun 19 14:40:29 2006:child exited with code 0
> 6:pid=5021:Mon Jun 19 14:40:29 2006:server waiting n_max_fd=5
> 6:pid=5021:Mon Jun 19 14:40:53 2006:server exited gracefully
>
>
>
>


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

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

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

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

> I pasted the refdb-bug output below.
>

I could not see anything unusual in your setup. Could you please send me the
refdb database file (according to your config in /usr/local/var/lib/refdb/db)
off-list? I'd like to have a look at it and test it on my system.

regards,
Markus

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

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

[<J.I...@uv...>]

Hi,

> In order to check this, could you run the refdb-bug script and send
the output
> to the list?=20

I pasted the refdb-bug output below.=20

> What are the permissions of the refdb database file?

First only root could access the database file, but I have changed
permissions to allow all users (myself only) to read, write and execute.
The "main database is too old or corrupt" error still appears when I use
refdba. I'll be very happy if you can help me. Thank you.

Ignasi.


refdb-bug output:

Linux arsmagna 2.6.15-23-386 #1 PREEMPT Tue May 23 13:49:40 UTC 2006
i686 GNU/Linux
RefDB binaries and scripts in the path:
/usr/local/bin/refdbd
/usr/local/bin/refdba
/usr/local/bin/refdbc
/usr/local/bin/refdbib
/usr/local/bin/nmed2ris
/usr/local/bin/bib2ris
and their version numbers:
refdbd 0.9.6
refdba 0.9.6
refdbc 0.9.6
refdbib 0.9.6
nmed2ris 0.9.6
nmed2ris is
bib2ris 0.9.6
DSSSL engines in the path:
/usr/bin/openjade
and their version numbers:
openjade:I: "openjade" version "1.3.2"
openjade:I: "OpenSP" version "1.5.2"

$REFDBLIB is /usr/local/share/refdb
global refdbd config file:
refdblib /usr/local/share/refdb
serverip=09localhost
dbsport=09=09
dbserver=09sqlite
dbpath=09=09/usr/local/var/lib/refdb/db
port=099734
logfile /var/log/refdbd.log
logdest file
loglevel info
pidfile=09=09/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan t
db_encoding=09
in_encoding=09ISO-8859-1

global refdba config file:
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
logdest file
loglevel info
logfile /var/log/refdba.log

global refdbc config file:
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/local/share/refdb/css/refdb.css
fromencoding ISO-8859-1

global refdbc config file (cgi):
refdblib /usr/local/share/refdb
serverip=09127.0.0.1
port=099734
logfile /var/log/refdbcgi.log
logdest file
loglevel info
autokill 1800

global refdbib config file:
refdblib /usr/local/share/refdb
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
outtype=09bibtex
logfile /var/log/refdbib.log
logdest file
loglevel info
stylespecdir=09.
ignore_missing=09f

global nmed2ris config file:
medsource=09PUBMED
outappend=09t
ignoretag=09t
logfile /var/log/nmed2ris.log
logdest file
loglevel info

global bib2ris config file:
refdblib /usr/local/share/refdb
logfile /var/log/bib2ris.log
logdest file
loglevel info
abbrevfirst=09t
forcejabbrev=09t
listsep ;

$HOME is /home/josep
user refdba config file:

user refdba config file (hidden):
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
logfile /var/log/refdba.log

user refdbc config file:

user refdbc config file (hidden):
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
logfile /var/log/refdbc.log
cssurl /usr/local/share/refdb/css/refdb.css
fromencoding ISO-8859-1

user refdbib config file:

user refdbib config file (hidden):
refdblib /usr/local/share/refdb
serverip=09127.0.0.1
port=099734
pager=09less
passwd=09<protected>
outtype=09bibtex
logfile /var/log/refdbib.log
logdest file
loglevel info
stylespecdir=09.
ignore_missing=09f

user nmed2ris config file:

user nmed2ris config file (hidden):
medsource=09PUBMED
outappend=09t
ignoretag=09t
logfile /var/log/nmed2ris.log
logdest file
loglevel info

user bib2ris config file:

user bib2ris config file (hidden):
refdblib /usr/local/share/refdb
logfile /var/log/bib2ris.log
logdest file
loglevel info
abbrevfirst=09t
forcejabbrev=09t
listsep ;

Re: [Refdb-users] One last question

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

Hi,

Rich Shepard writes:
 >    I really don't try to break things that work for others; sometimes it just
 > happens. Attached is the output of:
 > 
 > refdbc: getref -t ris -o editme.ris :KW:=shortnose
 > 
 > that shows the entries that produce two records in the keyword list. That's
 > also attached.
 > 

 > shortnose
 > shortnose 

These entries differ by a trailing space at the end of the second one
(users with graphical mail clients may have to view the raw data of
the email message to see the difference). This explains why the
shortnose appears twice in the keyword list.

It does not explain why the two references are not separated by a
space when you retrieve them. The relevant lines in backend-ris.c look
like this:

if (print_field_ris(item, ptr_rendinfo, "\nTY  - ") == NULL) {
[...] 
if ((new_ref = mstrcat(*(ptr_rendinfo->ptr_ref), "\nER  - \n", ptr_rendinfo->ptr_ref_len, 0)) == NULL) {

That is, a newline is inserted in front of each type tag. As each end
of reference tag is closed with a newline as well, two
consecutive references are always separated by an empty line. You
don't, by any chance, use a filter or an editor that skips empty
lines?


As I'm more or less stuck here, I think it is best to have a look at
your original data. Are you sufficiently familiar with PostgreSQL to
create a SQL dump of your reference database? Something like:

pg_dump -C -O -U username dbname > dumpfile.txt

I'll then try to restore the database here and see if your data are
broke or something else.

regards,
Markus


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

[Refdb-users] One last question

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

Hi,

Rich Shepard writes:
 >    Why are records not separated by a space when I output them with 'getref -t
 > ris -o output.ris :ID:>0' or some other selector? While editing multiple
 > records (e.g., to get keywords consistent), I add the space following the ER
 > - tag.
 > 

Here they are separated by an empty line, and they always have
been. Could you send me an example output file off-list for further
analysis?

regards,
Markus

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

[Refdb-users] Same Keyword Listed Twice

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

Hi,

Rich Shepard writes:
 >    I have two references that discuss the shortnose sucker. For each one there
 > is a separate line with 'KW  - shortnose'. Since that's the only instance of
 > the keyword in each of the two records, I expect it to appear in the keyword
 > list (getkw) only once. But, it appears twice, sequentially.
 > 
 >    The spelling is the same, there is not an extra space after one word. I'm
 > curious why it would appear twice in the list of keywords.
 > 

I thought I had implemented the behaviour that you expect. I did not
manage to reproduce this on my system. I switched to PostgreSQL for
this test to be as close to your system as possible. No matter what I
did, the only way to store the keyword twice in a reference is to add
two identical lines to the same RIS reference. It is a matter of taste
whether this behaviour makes sense. There is also an automatic keyword
scan which is turned on by default. It scans the titles and abstracts
of new or updated references for keywords already known to the
database. However, refdbd checks whether the reference has already
specified the keyword before adding it to that reference, so
duplicates are not possible.

I have no idea how you managed to get duplicate keyword entries in a
single reference without specifying the keyword twice. Do you still
have the input files handy?

regards,
Markus

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

[Refdb-users] Same Keyword Listed Twice

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

   I have two references that discuss the shortnose sucker. For each one there
is a separate line with 'KW  - shortnose'. Since that's the only instance of
the keyword in each of the two records, I expect it to appear in the keyword
list (getkw) only once. But, it appears twice, sequentially.

   The spelling is the same, there is not an extra space after one word. I'm
curious why it would appear twice in the list of keywords.

Carpe weekend,

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] One last question

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

   Having found answers to all but one question in the handbook, I'll ask it
here.

   Why are records not separated by a space when I output them with 'getref -t
ris -o output.ris :ID:>0' or some other selector? While editing multiple
records (e.g., to get keywords consistent), I add the space following the ER
- tag.

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] Password for Access

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

Rich Shepard writes:
 > On Fri, 16 Jun 2006, Markus Hoenicka wrote:
 > 
 > > this should read
 > > passwd <removed_by_design>
 > 
 >    Sonofagun! I use tabs to line up the values for the options, and of course
 > it's looking for only a single space. Sigh.
 > 

Actually no, you just had "passwd" misspelled as "password". The
variable name and value can be separated by any combination of one or
more tabs or spaces.

regards,
Markus

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

Re: [Refdb-users] Password for Access

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

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> this should read
> passwd <removed_by_design>

   Sonofagun! I use tabs to line up the values for the options, and of course
it's looking for only a single space. Sigh.

Many thanks, Markus,

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] Password for Access

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

Rich Shepard writes:
 > password      <removed_by_design>

this should read 

passwd <removed_by_design>

regards,
Markus

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

Re: [Refdb-users] Password for Access

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

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> Weird.

   It's Friday.

> Are you sure there is no leftover "passwd *" entry below the one you're
> looking at in your config file? Do you attempt to use an empty password or
> a password consisting of spaces?

   Yes:

serverip	    127.0.0.1
username      rshepard
password      <removed_by_design>
defaultdb     scirefs
pager         less
toencoding    ISO-8859-1
fromencoding  ISO-8859-1

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] Password for Access

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

Rich Shepard writes:
 > On Fri, 16 Jun 2006, Markus Hoenicka wrote:
 > 
 > > Does it work if you pass the password on the command line, like in refdbc
 > > -w abc?
 > 
 > Markus,
 > 
 >    Yes, it does.
 > 
 > > Are you sure refdbc picks up your other settings (check with the "set"
 > > command in refdbc)?
 > 
 >    Yes, it does.
 > 

Weird. Are you sure there is no leftover "passwd *" entry below the
one you're looking at in your config file? Do you attempt to use an
empty password or a password consisting of spaces?

regards,
Markus

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

Re: [Refdb-users] Password for Access

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

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> Does it work if you pass the password on the command line, like in refdbc
> -w abc?

Markus,

   Yes, it does.

> Are you sure refdbc picks up your other settings (check with the "set"
> command in refdbc)?

   Yes, it does.

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] Password for Access

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

Rich Shepard writes:
 > 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.
 > 

The logic of the startup code is pretty simple. If there is a passwd
line in one of the config files and the password is non-empty, refdbc
should not ask again. Does it work if you pass the password on the
command line, like in refdbc -w abc? Are you sure refdbc picks up your
other settings (check with the "set" command in refdbc)?


regards,
Markus

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

Re: [Refdb-users] RIS Tags By Type

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

On Fri, 16 Jun 2006, Markus Hoenicka wrote:

> First of all, your data are not lost.

Markus,

   This I knew.

> 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.

   Thank you.

> 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.

   That's good to know. I'll grab a copy. And it certainly is boring entering
references, even when it's cleaning up an existing .ris database exported
from EndNotes (thanks to a free 30-day trial I installed in VMware).

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