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connotea-code-devel — Discussion and devlopment of the core Connotea code and plug-ins.
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From: Martin F. <ma...@ne...> - 2007-12-18 22:29:20
|
Christopher Townson wrote: > How does the throttling work for the Connotea server? > > I'm wondering because API calls that get refused receive HTML (rather than > RDF or XML, which is not ideal to have to handle as a client). > > Would it be possible to get the server to return an RDF message when API > calls are refused? This could also make the reasoning clear by providing a > human-readable error message. Hi Chris, We may do this at some point. Throttling just happens earlier in the process. What we actually advise is to first refer to the HTTP status code. For 503 as the return code you can stop and loop for a retry after a pause. For API access, you should say "WWW::Connotea" in your outbound User-Agent header, which will be recognized on our end for a bit of extra help. (The Perl API wrapper, if not all of them, should do this for you.) This page describes the throttling algorithm: http://www.connotea.org/wiki/Throttling Regards, Martin Flack |
|
From: Benjamin G. <go...@in...> - 2007-12-18 21:41:51
|
Is there anything wrong with this request for any two bookmarks ? http://www.connotea.org/data/bookmarks?num=2&start=0 Why does it time out? thanks -Ben |
|
From: Benjamin G. <go...@in...> - 2007-12-17 21:57:02
|
Hi, For many queries to the api (like http://www.connotea.org/data/ bookmarks/tag/ontology?num=5) it returns an empty element for the postCount field <postCount></postCount> (the java api really doesn't like this) I haven't managed to find any queries that actually return anything in this field. Bug? Does nothing in this tag mean 1 post ? thanks -Ben |
|
From: Christopher T. <c.t...@na...> - 2007-12-14 10:56:55
|
Hi, How does the throttling work for the Connotea server? I'm wondering because API calls that get refused receive HTML (rather than RDF or XML, which is not ideal to have to handle as a client). Would it be possible to get the server to return an RDF message when API calls are refused? This could also make the reasoning clear by providing a human-readable error message. Cheers, Chris |
|
From: Martin F. <ma...@ne...> - 2007-12-05 20:21:50
|
Ah - I've figured it out. Follow the README that came in the tarball which will help you setup a CGI::Wiki database. Wiki::Toolkit is the newer version, and the www.connotea.org/code page has already been updated to mention it, but the 1.8 beta tarball code is not updated to use it, so you'll have to use CGI::Wiki for now. Martin Ganguly, Arindam wrote: > Hey Martin, > Wiki-toolkit version 0.74 > And no fulltext indexing in the search tables. > > > -arindam > -----Original Message----- > From: Martin Flack [mailto:ma...@ne...] > Sent: Tuesday, December 04, 2007 3:26 PM > To: Ganguly, Arindam > Cc: con...@li... > Subject: Re: [Connotea-code-devel] FW: connotea install complete...but > still some errors > > Ganguly, Arindam wrote: >> undef error - DBD::mysql::st execute failed: Unknown column 'node' in >> 'where clause' [for Statement "SELECT metadata_type, metadata_value > FROM >> metadata WHERE node='User:aganguly' AND version='0'"] at >> /usr/local/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52. >> >> Issue with the wiki-tookkit? > > Yes, what version do you have? This should tell you: > perl -MWiki::Toolkit -e 'print $Wiki::Toolkit::VERSION, "\n"' > > Note that we don't use CGI::Wiki anymore. > >> user aganguly (1) requests /search?q=tag bringing load to with db at >> 1196729034 >> >> undef error - DBD::mysql::st execute failed: Can't find FULLTEXT index >> matching the column list [for Statement "SELECT ub.user_bookmark_id, > [snip] > > I think this might be a bug in the schema in that particular tarball. > > You should have a main database with InnoDB tables, and if you want > search to work, a secondary database with MyISAM tables replicating from > > the first one. DBI_SEARCH in the config indicates the secondary one. > > The schema for the secondary database should be created from the schema > for the primary database with this command: > perl sql/mkschema_search < sql/schema.sql > > If that output does not contain FULLTEXT lines like this, then there is > a problem, and I'll have to help: > perl sql/mkschema_search < sql/schema.sql | grep FULLTEXT > ,FULLTEXT INDEX `name_ft` (`firstname`, `forename`, `lastname`) > ,FULLTEXT INDEX `url_ft` (`url`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `entry_ft` (`entry`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `description_ft` (`description`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `medline_ta_ft` (`medline_ta`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `description_ft` (`description`) > > Martin |
|
From: Martin F. <ma...@ne...> - 2007-12-05 15:53:18
|
Hello Huw, Huw Jones wrote: > The good news is I now have no error messages. The bad news is...I have > no error messages. I'm not sure whether the installation worked or not > since I don't know what a good test is. Simply typing > http://www.mydomain.com/bibliotech returns a Not Found page. I was > hoping there would be some index.html file within site/default. Am I > going about this the wrong way? Do I need to create my own > webpages/applications with the templates provided or should the connotea > front end much like that viewable on the web be available in the source > tarball? I guess also a good test would be to check apache can now > recognise perl scripts as I am suspicious that the connotea-code.conf > file was actually read by the http daemon on startup? First, create a syntax error in connotea-code.conf and restart Apache to see if it is loading it or not. If it is, it should complain about the syntax error. If not, you need to check your vendor docs for Apache and make sure it is going to be loaded. Just copy and paste to httpd.conf if necessary. Second, you can see if the 404 is from Connotea Code by setting this in the /etc/bibliotech.conf file and restarting Apache: EXPLAIN_HTTP_CODES = true Now, if Connotea Code is giving the 404 you will get an explanation page in text instead. There is no index.html because most of the web site is dynamic, but hitting /bibliotech should produce a home page with home.tt. If you want to try a static file, try hitting /bibliotech/design.css which the Connotea Code handler should decline back to the Apache normal file handler. The templates in the 1.8 beta tarball should give you a little web site that could be a basis for your own site. You should be able to register and add a few bookmarks without making any edits to start with. Martin |
|
From: Martin F. <ma...@ne...> - 2007-12-05 00:49:59
|
Arindam, Please use the attached schema.sql as a replacement for the one that came in the 1.8 beta tarball. You can just generate a schema_search.sql as I indicated previously by running sql/mksearch_schema on it: perl sql/mksearch_schema sql/schema.sql > sql/schema_search.sql In your case, assuming nothing important is in your database at this early stage, you can run, in mysql, "source sql/wipe.sql" in the main database, which will wipe it and propagate that wipe to the search database, assuming replication is live, and then you can "use bibliotech_search" (or whatever you named the search database, i.e. the MyISAM one) and run "source sql/schema_search.sql" to rebuild it with FULLTEXT keys. Martin Ganguly, Arindam wrote: > Hey Martin, > Wiki-toolkit version 0.74 > And no fulltext indexing in the search tables. > > > -arindam > -----Original Message----- > From: Martin Flack [mailto:ma...@ne...] > Sent: Tuesday, December 04, 2007 3:26 PM > To: Ganguly, Arindam > Cc: con...@li... > Subject: Re: [Connotea-code-devel] FW: connotea install complete...but > still some errors > > Ganguly, Arindam wrote: >> undef error - DBD::mysql::st execute failed: Unknown column 'node' in >> 'where clause' [for Statement "SELECT metadata_type, metadata_value > FROM >> metadata WHERE node='User:aganguly' AND version='0'"] at >> /usr/local/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52. >> >> Issue with the wiki-tookkit? > > Yes, what version do you have? This should tell you: > perl -MWiki::Toolkit -e 'print $Wiki::Toolkit::VERSION, "\n"' > > Note that we don't use CGI::Wiki anymore. > >> user aganguly (1) requests /search?q=tag bringing load to with db at >> 1196729034 >> >> undef error - DBD::mysql::st execute failed: Can't find FULLTEXT index >> matching the column list [for Statement "SELECT ub.user_bookmark_id, > [snip] > > I think this might be a bug in the schema in that particular tarball. > > You should have a main database with InnoDB tables, and if you want > search to work, a secondary database with MyISAM tables replicating from > > the first one. DBI_SEARCH in the config indicates the secondary one. > > The schema for the secondary database should be created from the schema > for the primary database with this command: > perl sql/mkschema_search < sql/schema.sql > > If that output does not contain FULLTEXT lines like this, then there is > a problem, and I'll have to help: > perl sql/mkschema_search < sql/schema.sql | grep FULLTEXT > ,FULLTEXT INDEX `name_ft` (`firstname`, `forename`, `lastname`) > ,FULLTEXT INDEX `url_ft` (`url`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `entry_ft` (`entry`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `description_ft` (`description`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `medline_ta_ft` (`medline_ta`) > ,FULLTEXT INDEX `name_ft` (`name`) > ,FULLTEXT INDEX `title_ft` (`title`) > ,FULLTEXT INDEX `description_ft` (`description`) > > Martin |
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From: Martin F. <ma...@ne...> - 2007-12-04 23:26:11
|
Ganguly, Arindam wrote: > undef error - DBD::mysql::st execute failed: Unknown column 'node' in > 'where clause' [for Statement "SELECT metadata_type, metadata_value FROM > metadata WHERE node='User:aganguly' AND version='0'"] at > /usr/local/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52. > > Issue with the wiki-tookkit? Yes, what version do you have? This should tell you: perl -MWiki::Toolkit -e 'print $Wiki::Toolkit::VERSION, "\n"' Note that we don't use CGI::Wiki anymore. > user aganguly (1) requests /search?q=tag bringing load to with db at > 1196729034 > > undef error - DBD::mysql::st execute failed: Can't find FULLTEXT index > matching the column list [for Statement "SELECT ub.user_bookmark_id, [snip] I think this might be a bug in the schema in that particular tarball. You should have a main database with InnoDB tables, and if you want search to work, a secondary database with MyISAM tables replicating from the first one. DBI_SEARCH in the config indicates the secondary one. The schema for the secondary database should be created from the schema for the primary database with this command: perl sql/mkschema_search < sql/schema.sql If that output does not contain FULLTEXT lines like this, then there is a problem, and I'll have to help: perl sql/mkschema_search < sql/schema.sql | grep FULLTEXT ,FULLTEXT INDEX `name_ft` (`firstname`, `forename`, `lastname`) ,FULLTEXT INDEX `url_ft` (`url`) ,FULLTEXT INDEX `title_ft` (`title`) ,FULLTEXT INDEX `title_ft` (`title`) ,FULLTEXT INDEX `entry_ft` (`entry`) ,FULLTEXT INDEX `name_ft` (`name`) ,FULLTEXT INDEX `description_ft` (`description`) ,FULLTEXT INDEX `name_ft` (`name`) ,FULLTEXT INDEX `medline_ta_ft` (`medline_ta`) ,FULLTEXT INDEX `name_ft` (`name`) ,FULLTEXT INDEX `title_ft` (`title`) ,FULLTEXT INDEX `description_ft` (`description`) Martin |
|
From: Martin F. <ma...@ne...> - 2007-12-04 20:36:41
|
Hello Huw,
I hope you don't mind I'm cc'ing my answer to the connotea-code-devel
list to get the text out on the web, as some of your questions have just
been brought to my attention by another user as points that need
updating in the docs from a prior version.
Huw Jones wrote:
> 9.Added a Bibliotech webdirectory to /usr/local/apach2/htdocs/.
You'd be better off making this a symlink to site/default that came in
the source code tarball.
> 10.Added the config file provided from the source download
> as /etc/bibliotech.cnf .
Good, but make sure it is .conf not .cnf.
Make sure you change the secrets and setup basic info like your site
name, email, etc. The comments are helpful.
A couple more fixes to the 1.8-beta example config:
- Remove the block that starts "CITATION {" - it is the one citation
block lacking a name before the opening brace.
- Add this CLICKS block somewhere, and edit with a user and password for
the clicks database:
CLICKS {
# options regarding click tracking
# database connection details
DBI_CONNECT = 'dbi:mysql:clicks'
DBI_USERNAME = 'user'
DBI_PASSWORD = 'secret'
}
> (a) It isn't apparent nor clear to me where to insert the lines:
>
> PerlOptions +Parent
> PerlSwitches -I/usr/local/apache2/htdocs/perl/...
> PerlModule Bibliotech::Apache
> PerlModule Bibliotech::AuthCookie
> <Location /bibliotech>
> SetHandler perl-script
> PerlHandler Bibliotech::Apache
> PerlAuthenHandler Bibliotech::AuthCookie::authen_handler
> AuthName Bibliotech
> AuthType basic
> require valid-user
> #ErrorDocument 503 /paused.html
> ErrorDocument 503 /unavailable.html
> </Location>
>
> in my httpd.conf file (apache 2.2.6 has a slightly different httpd.conf
> file compared to apache 2.0.x) and attempts to insert the lines anywhere
> result in being unable to restart the http daemon.
If you have a conf.d directory you can add a file called
connotea-code.conf and put it in there.
If you still have problems, tell me the error message.
> (b) "Everything under the html subdirectory should be placed or linked
> into an Apache-accessible location". If I set up an html subdirectory
> such as /usr/local/apache2/htdocs/Bibliotech/ what am I meant to put in
> there? Am I meant to put the contents of the Bibliotech directory
> supplied in the download in there?
Yes, sorry about this, as I mentioned above, this has changed and the
docs were not updated in time. We now have to manage a couple web site
designs so we needed another layer of depth, so the "html" folder is now
the "site/default" folder in the tarball.
> (c) "Remember to populate the COMPONENT WIKI block of your configuration
> file with the wiki database details" This would be /etc/my.cnf
> or /etc/bibliotech.cnf?
/etc/bibliotech.conf
> (d) The other files/directories provided with the download:
>
> admin_util/
> Bibliotech.pm
> CGI-Wiki-0.63/
> CGI-Wiki-0.63.tar.gz
> deploy/
> doc_util/
> LICENSE
> site/
> t/
> test_util/
>
> these are meant to go where? I can find no installation script or
> makefile so I presume that I need to put some/all of the
> files/directories in the source download in areas where they can be
> accessed by the rest of the modules/software I downloaded and installed?
The PerlSwitches -I line in the Apache configuration block will instruct
Apache's Perl instance as to the path where it can load Bibliotech.pm
and see the Bibliotech folder at the same level.
> (e)If I wish to add a link to the locally installed connotea web
> application which perl module/script do I call to generate the frontpage
> or do I go about doing this some other way?
When properly setup, Apache will call the Perl handler for any URL under
the Connotea-handled namespace. So if you put the namespace at
/bibliotech on your domain then any link that starts with
/bibliotech.... will be handed to Bibliotech::Apache::handler() to take
care of.
This might sum up the steps more succinctly:
Untar the files to /var/www/perl/connotea_code.
In /etc/bibliotech.conf use these lines:
DOCROOT = '/var/www/perl/connotea_code/site/default'
LOCATION = 'http://mydomain.com/bibliotech/'
PREPATH = '/bibliotech'
TEMPLATE_ROOT = ''
BIBUTILS_PATH = '/var/www/perl/connotea_code/bibutils/'
Add this to Apache's configuration:
PerlOptions +Parent
PerlSwitches -I/var/www/perl/connotea_code
PerlModule Bibliotech::Apache
PerlModule Bibliotech::AuthCookie
<Location /bibliotech>
SetHandler perl-script
PerlHandler Bibliotech::Apache
PerlAuthenHandler Bibliotech::AuthCookie::authen_handler
AuthName Bibliotech
AuthType basic
require valid-user
#ErrorDocument 503 /paused.html
ErrorDocument 503 /unavailable.html
</Location>
Now, go in whatever folder is the DocumentRoot for this domain in
Apache, go and make a symbolic link called "bibliotech" that links to
/var/www/perl/connotea_code/site/default.
Remember to restart Apache after all this. (You have to restart Apache
for any changes to Apache or Connotea configurations.)
If you have any errors from this, post a message to connotea-code-devel
and we'll answer there so others can follow later.
https://lists.sourceforge.net/lists/listinfo/connotea-code-devel
Regards,
Martin Flack
|
|
From: Ganguly, A. <aga...@so...> - 2007-12-04 00:57:20
|
=20
=20
________________________________
From: Ganguly, Arindam=20
Sent: Monday, December 03, 2007 4:48 PM
To: 'Martin Flack'
Cc: 'ari...@gm...'
Subject: connotea install complete...but still some errors
=20
Hi martin,
I've been talking to you regarding the connotea install. I was able to
get the installation part complete and actually see and register on the
local implement of the site.
=20
I'm still seeing a couple of issues however. After logging in and
clicking on 'My Library'
I get the following error.
=20
Error exception report:
user aganguly (1) requests /user/aganguly bringing load to with db at
1196728958
http://localhost/bibliotech/bibliotech/user/aganguly
<http://localhost/bibliotech/bibliotech/user/aganguly>=20
undef error - DBD::mysql::st execute failed: Unknown column 'node' in
'where clause' [for Statement "SELECT metadata_type, metadata_value FROM
metadata WHERE node=3D'User:aganguly' AND version=3D'0'"] at
/usr/local/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52.
=20
Issue with the wiki-tookkit?
=20
Secondly doing a search returns=20
Error exception report:
user aganguly (1) requests /search?q=3Dtag bringing load to with db at
1196729034
http://localhost/bibliotech/bibliotech/search
<http://localhost/bibliotech/bibliotech/search>=20
undef error - DBD::mysql::st execute failed: Can't find FULLTEXT index
matching the column list [for Statement "SELECT ub.user_bookmark_id,
ub.user, ub.bookmark, ub.updated, ub.citation, ub.user_is_author
, ub.def_public, ub.private, ub.private_gang, ub.private_until,
ub.quarantined, ub.created, u.user_id, u.username, u.openurl_resolver,
u.openurl_name, u.updated, IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(g.gang_id),':/:',IFNULL(
g.name, '+NULL'),':/:',IFNULL(g.owner, '+NULL'),':/:',IFNULL(g.private,
'+NULL'),':/:',IFNULL(g.updated, '+NULL') ORDER BY ug.created SEPARATOR
'///'), '') AS _u_gangs_packed,=20
b.bookmark_id, b.url, b.hash, b.updated, b.citation,
ubd.user_bookmark_id, ubd.title, ubd.description, bd.bookmark_id,
bd.title, bd.created, ct.citation_id, ct.title, ct.journal, ct.volume,
ct.issue, ct.start_page, ct.end_page
, ct.pubmed, ct.doi, ct.asin, ct.ris_type, ct.raw_date, ct.date,
ct.last_modified_date, ct.user_supplied, ct.cs_module, ct.cs_type,
ct.cs_source, ct.created, j.journal_id, j.name, j.issn, j.coden
, j.country, j.medline_code, j.medline_ta, j.nlm_unique_id,
cta.citation_author_id, cta.citation, cta.author, cta.displayorder,
IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a.author_id),':/:',IFNULL(a.firstname, '+NULL'),':/:',IFNULL(
a.forename, '+NULL'),':/:',IFNULL(a.initials,
'+NULL'),':/:',IFNULL(a.middlename, '+NULL'),':/:',IFNULL(a.lastname,
'+NULL'),':/:',IFNULL(a.suffix, '+NULL'),':/:',IFNULL(
a.misc, '+NULL'),':/:',IFNULL(a.postal_address,
'+NULL'),':/:',IFNULL(a.affiliation, '+NULL'),':/:',IFNULL(a.email,
'+NULL'),':/:',IFNULL(a.user, '+NULL') ORDER BY=20
cta.displayorder SEPARATOR '///'), '') AS _ct_authors_packed,
ct2.citation_id, ct2.title, ct2.journal, ct2.volume, ct2.issue,
ct2.start_page, ct2.end_page, ct2.pubmed, ct2.doi, ct2.asin,
ct2.ris_type, ct2.raw_date
, ct2.date, ct2.last_modified_date, ct2.user_supplied, ct2.cs_module,
ct2.cs_type, ct2.cs_source, ct2.created, j2.journal_id, j2.name,
j2.issn, j2.coden, j2.country, j2.medline_code, j2.medline_ta
, j2.nlm_unique_id, cta2.citation_author_id, cta2.citation, cta2.author,
cta2.displayorder, IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a2.author_id),':/:',IFNULL(a2.firstname,
'+NULL'),':/:',IFNULL(a2.forename
, '+NULL'),':/:',IFNULL(a2.initials,
'+NULL'),':/:',IFNULL(a2.middlename, '+NULL'),':/:',IFNULL(a2.lastname,
'+NULL'),':/:',IFNULL(a2.suffix, '+NULL'),':/:',IFNULL(
a2.misc, '+NULL'),':/:',IFNULL(a2.postal_address,
'+NULL'),':/:',IFNULL(a2.affiliation, '+NULL'),':/:',IFNULL(a2.email,
'+NULL'),':/:',IFNULL(a2.user, '+NULL') ORDER BY=20
cta2.displayorder SEPARATOR '///'), '') AS _ct2_authors_packed,
IFNULL(GROUP_CONCAT(DISTINCT CONCAT(t2.tag_id),':/:',IFNULL(t2.name,
'+NULL') ORDER BY ubt2.created
SEPARATOR '///'), '') AS _ub_tags_packed, COUNT(DISTINCT
ub2.user_bookmark_id) as _ub_user_bookmarks_count, COUNT(DISTINCT
c2.comment_id) as _ub_comments_count, COUNT(DISTINCT
ub3.user_bookmark_id) as _ub_bookmark_is_linked_by_current_user,
COUNT(DISTINCT=20
t4.tag_id) as _ub_is_geotagged, MAX(UNIX_TIMESTAMP(ub.created))
FROM=20
(SELECT MAX(ub.user_bookmark_id) as max_user_bookmark_id, fm.sortvalue
as sortvalue
FROM user_bookmark ub
LEFT JOIN bookmark b ON (ub.bookmark=3Db.bookmark_id
)
INNER JOIN (SELECT fmat.user_bookmark_id,
MAX(score)*1000000000+UNIX_TIMESTAMP(ub.created) as sortvalue
FROM
(
SELECT user_bookmark_id, MAX(score) as score, 1 as positive FROM (SELECT
ubd_s.user_bookmark_id, 100 as score
FROM user_bookmark_details ubd_s
WHERE ubd_s.title =3D ?
UNION
SELECT ub.user_bookmark_id, 100 as score
FROM bookmark_details bd_s
LEFT JOIN bookmark b_s ON (bd_s.bookmark_id=3Db_s.bookmark_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE bd_s.title =3D ? AND b_s.bookmark_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 99 as score
FROM citation c_s
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE c_s.title =3D ? AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 99 as score
FROM citation c_s
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE c_s.title =3D ? AND ub.user_bookmark_id
IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE j_s.name =3D ? AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id
, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE j_s.name =3D ? AND c_s.citation_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE j_s.medline_ta =3D ? AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT =20
ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE j_s.medline_ta =3D ? AND c_s.citation_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 97 as score
FROM author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE a_s.lastname =3D ? AND cta_s.citation_author_id IS NOT NULL AND
c_s.citation_id IS NOT NULL AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 97 as score
FROM author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE a_s.lastname =3D ? AND cta_s.citation_author_id IS NOT NULL AND
c_s.citation_id IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
=20
SELECT ubd_s.user_bookmark_id, 50 as score
FROM bibliotech_search.user_bookmark_details ubd_s
WHERE MATCH(ubd_s.title) AGAINST (?)
UNION
SELECT ub.user_bookmark_id, 50 as score
FROM bibliotech_search.bookmark_details bd_s
LEFT JOIN bookmark b_s ON (bd_s.bookmark_id=3Db_s.bookmark_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE MATCH(bd_s.title) AGAINST (?) AND b_s.bookmark_id IS NOT NULL
AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 49 as score
FROM bibliotech_search.citation c_s
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (
ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(c_s.title) AGAINST (?) AND b_s.bookmark_id IS NOT NULL
AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 49 as score
FROM bibliotech_search.citation c_s
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE MATCH(c_s.title) AGAINST (?) AND ub.user_bookmark_id IS NOT
NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(j_s.name) AGAINST (?) AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (
ub.citation=3Dc_s.citation_id)
WHERE MATCH(j_s.name) AGAINST (?) AND c_s.citation_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(j_s.medline_ta) AGAINST (?) AND c_s.citation_id IS NOT
NULL AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (
ub.citation=3Dc_s.citation_id)
WHERE MATCH(j_s.medline_ta) AGAINST (?) AND c_s.citation_id IS NOT
NULL AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 47 as score
FROM bibliotech_search.bookmark b_s
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE MATCH(b_s.url) AGAINST (?) AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ubd_s.user_bookmark_id, 45 as score
FROM bibliotech_search.user_bookmark_details ubd_s
WHERE MATCH(ubd_s.description) AGAINST (?)
UNION
SELECT ub.user_bookmark_id, 44 as score
FROM bibliotech_search.comment c_s
LEFT JOIN user_bookmark_comment ubc_s ON
(c_s.comment_id=3Dubc_s.comment)
LEFT JOIN user_bookmark ub ON
(ubc_s.user_bookmark=3Dub.user_bookmark_id)
WHERE MATCH(c_s.entry) AGAINST (?) AND ubc_s.user_bookmark_comment_id
IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
=20
SELECT ub.user_bookmark_id, 43 as score
FROM bibliotech_search.author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(a_s.lastname, a_s.forename, a_s.firstname) AGAINST (?)
AND cta_s.citation_author_id IS NOT NULL AND c_s.citation_id IS NOT NULL
AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 43 as score
FROM bibliotech_search.author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE MATCH(a_s.lastname, a_s.forename, a_s.firstname) AGAINST (?)
AND cta_s.citation_author_id IS NOT NULL AND c_s.citation_id IS NOT NULL
AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ubt_s.user_bookmark as user_bookmark_id, 20 as score
FROM tag t_s
LEFT JOIN user_bookmark_tag ubt_s ON (ubt_s.tag=3Dt_s.tag_id)
WHERE t_s.name =3D ? AND ubt_s.user_bookmark_tag_id IS NOT NULL
UNION
SELECT ubt_s.user_bookmark as user_bookmark_id, 20 as score
FROM bibliotech_search.tag t_s
LEFT JOIN user_bookmark_tag ubt_s ON (ubt_s.tag=3Dt_s.tag_id)
WHERE MATCH(t_s.name) AGAINST (?) AND ubt_s.user_bookmark_tag_id IS
NOT NULL
) as fmot1 GROUP BY user_bookmark_id
) as fmat
LEFT JOIN user_bookmark ub ON
(fmat.user_bookmark_id=3Dub.user_bookmark_id)
GROUP BY fmat.user_bookmark_id
HAVING SUM(fmat.positive) =3D ? AND MIN(fmat.positive) =3D ?
) as fm ON (ub.user_bookmark_id=3Dfm.user_bookmark_id)
WHERE ub.user_bookmark_id IS NOT NULL AND ((((ub.private =3D 0 AND
ub.private_gang IS NULL) OR (ub.private_until IS NOT NULL AND
ub.private_until <=3D NOW())) AND=20
ub.quarantined IS NULL) OR ub.user =3D ?)
GROUP BY b.bookmark_id
ORDER BY sortvalue DESC
LIMIT 0, 10) as ubp
LEFT JOIN user_bookmark ub ON
(ubp.max_user_bookmark_id=3Dub.user_bookmark_id)
LEFT JOIN user u ON (
ub.user=3Du.user_id)
LEFT JOIN user_bookmark_tag ubt2 ON
(ub.user_bookmark_id=3Dubt2.user_bookmark)
LEFT JOIN tag t2 ON (ubt2.tag=3Dt2.tag_id)
LEFT JOIN user_bookmark_details ubd ON
(ub.user_bookmark_id=3Dubd.user_bookmark_id
)
LEFT JOIN citation ct ON (ub.citation=3Dct.citation_id)
LEFT JOIN citation_author cta ON (ct.citation_id=3Dcta.citation)
LEFT JOIN author a ON (cta.author=3Da.author_id)
LEFT JOIN journal j ON (ct.journal=3Dj.journal_id
)
LEFT JOIN bookmark b ON (ub.bookmark=3Db.bookmark_id)
LEFT JOIN bookmark_details bd ON (b.bookmark_id=3Dbd.bookmark_id)
LEFT JOIN citation ct2 ON (b.citation=3Dct2.citation_id)
LEFT JOIN citation_author cta2 ON (ct2.citation_id=3Dcta2.citation
)
LEFT JOIN author a2 ON (cta2.author=3Da2.author_id)
LEFT JOIN journal j2 ON (ct2.journal=3Dj2.journal_id)
LEFT JOIN user_gang ug ON (u.user_id=3Dug.user)
LEFT JOIN gang g ON (ug.gang=3Dg.gang_id)
LEFT JOIN bookmark b2 ON (
ub.bookmark=3Db2.bookmark_id)
LEFT JOIN user_bookmark ub2 ON (b2.bookmark_id=3Dub2.bookmark AND
((((ub2.private =3D 0 AND ub2.private_gang IS NULL) OR =
(ub2.private_until
IS NOT NULL AND ub2.private_until <=3D NOW())) AND ub2.quarantined
IS NULL) OR ub2.user =3D ?))
LEFT JOIN user_bookmark_comment ubc2 ON
(ub2.user_bookmark_id=3Dubc2.user_bookmark)
LEFT JOIN comment c2 ON (ubc2.comment=3Dc2.comment_id)
LEFT JOIN user_bookmark ub3 ON =
(ubc2.user_bookmark=3Dub3.user_bookmark_id
AND ub3.user =3D ?)
LEFT JOIN user_bookmark_tag ubt4 ON
(ub.user_bookmark_id=3Dubt4.user_bookmark)
LEFT JOIN tag t4 ON (ubt4.tag=3Dt4.tag_id AND t4.name =3D ?)
WHERE ub.user_bookmark_id IS NOT NULL
GROUP BY ubp.max_user_bookmark_id
ORDER BY sortvalue DESC" with ParamValues: 11=3D"tag", 21=3D"tag", =
7=3D"tag",
26=3D1, 17=3D"tag", 2=3D"tag", 22=3D"tag", 1=3D"tag", 18=3D"tag", =
0=3D"tag",
30=3D'geotagged', 23=3D"tag", 16=3D"tag", 13=3D"tag", 29=3D'1', =
27=3D'1', 25=3D1,
6=3D"tag", 28=3D'1', 3=3D"tag", 9=3D"tag", 12=3D"tag", 20=3D"tag", =
14=3D"tag",
15=3D"tag", 8=3D"tag", 4=3D"tag", 24=3D"tag", 19=3D"tag", 10=3D"tag", =
5=3D"tag"] at
/usr/local/lib/perl5/site_perl/5.8.8/DBIx/ContextualFetch.pm line 52.
SQL is:
----------
SELECT ub.user_bookmark_id, ub.user, ub.bookmark, ub.updated,
ub.citation, ub.user_is_author, ub.def_public, ub.private,
ub.private_gang, ub.private_until, ub.quarantined, ub.created, u.user_id
, u.username, u.openurl_resolver, u.openurl_name, u.updated,
IFNULL(GROUP_CONCAT(DISTINCT CONCAT(g.gang_id),':/:',IFNULL(g.name,
'+NULL'),':/:',IFNULL(g.owner, '+NULL'),':/:',IFNULL(
g.private, '+NULL'),':/:',IFNULL(g.updated, '+NULL') ORDER BY ug.created
SEPARATOR '///'), '') AS _u_gangs_packed, b.bookmark_id, b.url, b.hash,
b.updated, b.citation, ubd.user_bookmark_id
, ubd.title, ubd.description, bd.bookmark_id, bd.title, bd.created,
ct.citation_id, ct.title, ct.journal, ct.volume, ct.issue,
ct.start_page, ct.end_page, ct.pubmed, ct.doi, ct.asin, ct.ris_type,
ct.raw_date, ct.date, ct.last_modified_date
, ct.user_supplied, ct.cs_module, ct.cs_type, ct.cs_source, ct.created,
j.journal_id, j.name, j.issn, j.coden, j.country, j.medline_code,
j.medline_ta, j.nlm_unique_id, cta.citation_author_id,=20
cta.citation, cta.author, cta.displayorder, IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a.author_id),':/:',IFNULL(a.firstname,
'+NULL'),':/:',IFNULL(a.forename, '+NULL'),':/:',IFNULL(a.initials
, '+NULL'),':/:',IFNULL(a.middlename, '+NULL'),':/:',IFNULL(a.lastname,
'+NULL'),':/:',IFNULL(a.suffix, '+NULL'),':/:',IFNULL(a.misc,
'+NULL'),':/:',IFNULL(
a.postal_address, '+NULL'),':/:',IFNULL(a.affiliation,
'+NULL'),':/:',IFNULL(a.email, '+NULL'),':/:',IFNULL(a.user, '+NULL')
ORDER BY cta.displayorder SEPARATOR '///'), '') AS _ct_authors_packed,=20
ct2.citation_id, ct2.title, ct2.journal, ct2.volume, ct2.issue,
ct2.start_page, ct2.end_page, ct2.pubmed, ct2.doi, ct2.asin,
ct2.ris_type, ct2.raw_date, ct2.date, ct2.last_modified_date,
ct2.user_supplied, ct2.cs_module,=20
ct2.cs_type, ct2.cs_source, ct2.created, j2.journal_id, j2.name,
j2.issn, j2.coden, j2.country, j2.medline_code, j2.medline_ta,
j2.nlm_unique_id, cta2.citation_author_id, cta2.citation, cta2.author
, cta2.displayorder, IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a2.author_id),':/:',IFNULL(a2.firstname,
'+NULL'),':/:',IFNULL(a2.forename, '+NULL'),':/:',IFNULL(a2.initials,
'+NULL'),':/:',IFNULL(
a2.middlename, '+NULL'),':/:',IFNULL(a2.lastname,
'+NULL'),':/:',IFNULL(a2.suffix, '+NULL'),':/:',IFNULL(a2.misc,
'+NULL'),':/:',IFNULL(a2.postal_address, '+NULL'),':/:',IFNULL(
a2.affiliation, '+NULL'),':/:',IFNULL(a2.email,
'+NULL'),':/:',IFNULL(a2.user, '+NULL') ORDER BY cta2.displayorder
SEPARATOR '///'), '') AS _ct2_authors_packed,
IFNULL(GROUP_CONCAT(DISTINCT CONCAT(
t2.tag_id),':/:',IFNULL(t2.name, '+NULL') ORDER BY ubt2.created
SEPARATOR '///'), '') AS _ub_tags_packed, COUNT(DISTINCT
ub2.user_bookmark_id) as _ub_user_bookmarks_count, COUNT(DISTINCT=20
c2.comment_id) as _ub_comments_count, COUNT(DISTINCT
ub3.user_bookmark_id) as _ub_bookmark_is_linked_by_current_user,
COUNT(DISTINCT t4.tag_id) as _ub_is_geotagged,
MAX(UNIX_TIMESTAMP(ub.created))
FROM=20
(SELECT MAX(
ub.user_bookmark_id) as max_user_bookmark_id, fm.sortvalue as sortvalue
FROM user_bookmark ub
LEFT JOIN bookmark b ON (ub.bookmark=3Db.bookmark_id)
INNER JOIN (SELECT fmat.user_bookmark_id,
MAX(score)*1000000000+UNIX_TIMESTAMP(
ub.created) as sortvalue
FROM
(
SELECT user_bookmark_id, MAX(score) as score, 1 as positive FROM (SELECT
ubd_s.user_bookmark_id, 100 as score
FROM user_bookmark_details ubd_s
WHERE ubd_s.title =3D ?
=20
UNION
SELECT ub.user_bookmark_id, 100 as score
FROM bookmark_details bd_s
LEFT JOIN bookmark b_s ON (bd_s.bookmark_id=3Db_s.bookmark_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark
)
WHERE bd_s.title =3D ? AND b_s.bookmark_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 99 as score
FROM citation c_s
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE c_s.title =3D ? AND b_s.bookmark_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 99 as score
=20
FROM citation c_s
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE c_s.title =3D ? AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE j_s.name =3D ? AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id
)
WHERE j_s.name =3D ? AND c_s.citation_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE j_s.medline_ta =3D ? AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 98 as score
FROM journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id
)
WHERE j_s.medline_ta =3D ? AND c_s.citation_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 97 as score
FROM author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE a_s.lastname =3D ? AND cta_s.citation_author_id IS NOT NULL AND
c_s.citation_id IS NOT NULL AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 97 as score
FROM author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE a_s.lastname =3D ? AND cta_s.citation_author_id IS NOT NULL AND
c_s.citation_id IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
=20
SELECT ubd_s.user_bookmark_id, 50 as score
FROM bibliotech_search.user_bookmark_details ubd_s
WHERE MATCH(ubd_s.title) AGAINST (?)
UNION
SELECT ub.user_bookmark_id, 50 as score
FROM bibliotech_search.bookmark_details bd_s
LEFT JOIN bookmark b_s ON (bd_s.bookmark_id=3Db_s.bookmark_id)
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE MATCH(bd_s.title) AGAINST (?) AND b_s.bookmark_id IS NOT NULL
AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 49 as score
FROM bibliotech_search.citation c_s
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (
ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(c_s.title) AGAINST (?) AND b_s.bookmark_id IS NOT NULL
AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 49 as score
FROM bibliotech_search.citation c_s
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE MATCH(c_s.title) AGAINST (?) AND ub.user_bookmark_id IS NOT
NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(j_s.name) AGAINST (?) AND c_s.citation_id IS NOT NULL AND
b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (
ub.citation=3Dc_s.citation_id)
WHERE MATCH(j_s.name) AGAINST (?) AND c_s.citation_id IS NOT NULL AND
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(j_s.medline_ta) AGAINST (?) AND c_s.citation_id IS NOT
NULL AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 48 as score
FROM bibliotech_search.journal j_s
LEFT JOIN citation c_s ON (c_s.journal=3Dj_s.journal_id)
LEFT JOIN user_bookmark ub ON (
ub.citation=3Dc_s.citation_id)
WHERE MATCH(j_s.medline_ta) AGAINST (?) AND c_s.citation_id IS NOT
NULL AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 47 as score
FROM bibliotech_search.bookmark b_s
LEFT JOIN user_bookmark ub ON (b_s.bookmark_id=3Dub.bookmark)
WHERE MATCH(b_s.url) AGAINST (?) AND ub.user_bookmark_id IS NOT NULL
UNION
SELECT ubd_s.user_bookmark_id, 45 as score
FROM bibliotech_search.user_bookmark_details ubd_s
WHERE MATCH(ubd_s.description) AGAINST (?)
UNION
SELECT ub.user_bookmark_id, 44 as score
FROM bibliotech_search.comment c_s
LEFT JOIN user_bookmark_comment ubc_s ON
(c_s.comment_id=3Dubc_s.comment)
LEFT JOIN user_bookmark ub ON
(ubc_s.user_bookmark=3Dub.user_bookmark_id)
WHERE MATCH(c_s.entry) AGAINST (?) AND ubc_s.user_bookmark_comment_id
IS NOT NULL AND ub.user_bookmark_id IS NOT NULL
UNION
=20
SELECT ub.user_bookmark_id, 43 as score
FROM bibliotech_search.author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.bookmark=3Db_s.bookmark_id)
WHERE MATCH(a_s.lastname, a_s.forename, a_s.firstname) AGAINST (?)
AND cta_s.citation_author_id IS NOT NULL AND c_s.citation_id IS NOT NULL
AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ub.user_bookmark_id, 43 as score
FROM bibliotech_search.author a_s
LEFT JOIN citation_author cta_s ON =
(a_s.author_id=3Dcta_s.author)
LEFT JOIN citation c_s ON (c_s.citation_id=3Dcta_s.citation)
LEFT JOIN bookmark b_s ON (b_s.citation=3Dc_s.citation_id)
LEFT JOIN user_bookmark ub ON (ub.citation=3Dc_s.citation_id)
WHERE MATCH(a_s.lastname, a_s.forename, a_s.firstname) AGAINST (?)
AND cta_s.citation_author_id IS NOT NULL AND c_s.citation_id IS NOT NULL
AND b_s.bookmark_id IS NOT NULL AND=20
ub.user_bookmark_id IS NOT NULL
UNION
SELECT ubt_s.user_bookmark as user_bookmark_id, 20 as score
FROM tag t_s
LEFT JOIN user_bookmark_tag ubt_s ON (ubt_s.tag=3Dt_s.tag_id)
WHERE t_s.name =3D ? AND ubt_s.user_bookmark_tag_id IS NOT NULL
UNION
SELECT ubt_s.user_bookmark as user_bookmark_id, 20 as score
FROM bibliotech_search.tag t_s
LEFT JOIN user_bookmark_tag ubt_s ON (ubt_s.tag=3Dt_s.tag_id)
WHERE MATCH(t_s.name) AGAINST (?) AND ubt_s.user_bookmark_tag_id IS
NOT NULL
) as fmot1 GROUP BY user_bookmark_id
) as fmat
LEFT JOIN user_bookmark ub ON
(fmat.user_bookmark_id=3Dub.user_bookmark_id)
GROUP BY fmat.user_bookmark_id
HAVING SUM(fmat.positive) =3D ? AND MIN(fmat.positive) =3D ?
) as fm ON (ub.user_bookmark_id=3Dfm.user_bookmark_id)
WHERE ub.user_bookmark_id IS NOT NULL AND ((((ub.private =3D 0 AND
ub.private_gang IS NULL) OR (ub.private_until IS NOT NULL AND
ub.private_until <=3D NOW())) AND=20
ub.quarantined IS NULL) OR ub.user =3D ?)
GROUP BY b.bookmark_id
ORDER BY sortvalue DESC
LIMIT 0, 10) as ubp
LEFT JOIN user_bookmark ub ON
(ubp.max_user_bookmark_id=3Dub.user_bookmark_id)
LEFT JOIN user u ON (
ub.user=3Du.user_id)
LEFT JOIN user_bookmark_tag ubt2 ON
(ub.user_bookmark_id=3Dubt2.user_bookmark)
LEFT JOIN tag t2 ON (ubt2.tag=3Dt2.tag_id)
LEFT JOIN user_bookmark_details ubd ON
(ub.user_bookmark_id=3Dubd.user_bookmark_id
)
LEFT JOIN citation ct ON (ub.citation=3Dct.citation_id)
LEFT JOIN citation_author cta ON (ct.citation_id=3Dcta.citation)
LEFT JOIN author a ON (cta.author=3Da.author_id)
LEFT JOIN journal j ON (ct.journal=3Dj.journal_id
)
LEFT JOIN bookmark b ON (ub.bookmark=3Db.bookmark_id)
LEFT JOIN bookmark_details bd ON (b.bookmark_id=3Dbd.bookmark_id)
LEFT JOIN citation ct2 ON (b.citation=3Dct2.citation_id)
LEFT JOIN citation_author cta2 ON (ct2.citation_id=3Dcta2.citation
)
LEFT JOIN author a2 ON (cta2.author=3Da2.author_id)
LEFT JOIN journal j2 ON (ct2.journal=3Dj2.journal_id)
LEFT JOIN user_gang ug ON (u.user_id=3Dug.user)
LEFT JOIN gang g ON (ug.gang=3Dg.gang_id)
LEFT JOIN bookmark b2 ON (
ub.bookmark=3Db2.bookmark_id)
LEFT JOIN user_bookmark ub2 ON (b2.bookmark_id=3Dub2.bookmark AND
((((ub2.private =3D 0 AND ub2.private_gang IS NULL) OR =
(ub2.private_until
IS NOT NULL AND ub2.private_until <=3D NOW())) AND ub2.quarantined
IS NULL) OR ub2.user =3D ?))
LEFT JOIN user_bookmark_comment ubc2 ON
(ub2.user_bookmark_id=3Dubc2.user_bookmark)
LEFT JOIN comment c2 ON (ubc2.comment=3Dc2.comment_id)
LEFT JOIN user_bookmark ub3 ON =
(ubc2.user_bookmark=3Dub3.user_bookmark_id
AND ub3.user =3D ?)
LEFT JOIN user_bookmark_tag ubt4 ON
(ub.user_bookmark_id=3Dubt4.user_bookmark)
LEFT JOIN tag t4 ON (ubt4.tag=3Dt4.tag_id AND t4.name =3D ?)
WHERE ub.user_bookmark_id IS NOT NULL
GROUP BY ubp.max_user_bookmark_id
ORDER BY sortvalue DESC
----------
$VAR1 =3D {
'freematch' =3D> [
'tag'
],
'join_ub' =3D> '((((
ub.private =3D 0 AND ub.private_gang IS NULL) OR (ub.private_until IS =
NOT
NULL AND ub.private_until <=3D NOW())) AND ub.quarantined IS NULL) OR
ub.user =3D ?)',
'order_by' =3D> 'ORDER BY sortvalue DESC',
'having' =3D> '',
'wbind' =3D> [],
'bind_ub' =3D> [
'1'
],
'bind_ub3' =3D> [
'1'
],
'group_by' =3D> 'GROUP BY b.bookmark_id',
'limit' =3D> 'LIMIT 0, 10',
'bind_t4' =3D> [
'geotagged'
],
'select' =3D> [
'MAX(ub.user_bookmark_id)',
'ub.user',
'ub.bookmark',
'ub.updated',
'ub.citation',
'ub.user_is_author',
'
ub.def_public',
'ub.private',
'ub.private_gang',
'ub.private_until',
'ub.quarantined
',
'ub.created',
'u.user_id',
'u.username',
'u.openurl_resolver',
'
u.openurl_name',
'u.updated',
'IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(g.gang_id),\':/:\',IFNULL(g.name, \'+NULL\'),\':/:\',IFNULL(
g.owner, \'+NULL\'),\':/:\',IFNULL(g.private,
\'+NULL\'),\':/:\',IFNULL(g.updated, \'+NULL\') ORDER BY ug.created
SEPARATOR \'///\'), \'\') AS _u_gangs_packed',
=20
'b.bookmark_id',
'b.url',
'b.hash',
'b.updated',
'b.citation
',
'ubd.user_bookmark_id',
'ubd.title',
'ubd.description',
'bd.bookmark_id',
=20
'bd.title',
'bd.created',
'ct.citation_id',
'ct.title',
'
ct.journal',
'ct.volume',
'ct.issue',
'ct.start_page',
'ct.end_page',
'
ct.pubmed',
'ct.doi',
'ct.asin',
'ct.ris_type',
'ct.raw_date',
'
ct.date',
'ct.last_modified_date',
'ct.user_supplied',
'ct.cs_module',
'ct.cs_type
',
'ct.cs_source',
'ct.created',
'j.journal_id',
'j.name
',
'j.issn',
'j.coden',
'j.country',
'j.medline_code',
'
j.medline_ta',
'j.nlm_unique_id',
'cta.citation_author_id',
'cta.citation',
'cta.author
',
'cta.displayorder',
'IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a.author_id),\':/:\',IFNULL(a.firstname,
\'+NULL\'),\':/:\',IFNULL(
a.forename, \'+NULL\'),\':/:\',IFNULL(a.initials,
\'+NULL\'),\':/:\',IFNULL(a.middlename,
\'+NULL\'),\':/:\',IFNULL(a.lastname, \'+NULL\'),\':/:\',IFNULL(a.suffix
, \'+NULL\'),\':/:\',IFNULL(a.misc,
\'+NULL\'),\':/:\',IFNULL(a.postal_address,
\'+NULL\'),\':/:\',IFNULL(a.affiliation,
\'+NULL\'),\':/:\',IFNULL(a.email, \'+NULL\'),\':/:\',IFNULL(
a.user, \'+NULL\') ORDER BY cta.displayorder SEPARATOR \'///\'), \'\')
AS _ct_authors_packed',
'ct2.citation_id',
'ct2.title',
'ct2.journal',
'ct2.volume',
'ct2.issue',
'ct2.start_page',
'
ct2.end_page',
'ct2.pubmed',
'ct2.doi',
'ct2.asin',
'ct2.ris_type',
'
ct2.raw_date',
'ct2.date',
'ct2.last_modified_date',
'ct2.user_supplied',
'ct2.cs_module
',
'ct2.cs_type',
'ct2.cs_source',
'ct2.created',
'j2.journal_id',
'
j2.name',
'j2.issn',
'j2.coden',
'j2.country',
'j2.medline_code
',
'j2.medline_ta',
'j2.nlm_unique_id',
'cta2.citation_author_id',
'cta2.citation
',
'cta2.author',
'cta2.displayorder',
'IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(a2.author_id),\':/:\',IFNULL(a2.firstname
, \'+NULL\'),\':/:\',IFNULL(a2.forename,
\'+NULL\'),\':/:\',IFNULL(a2.initials,
\'+NULL\'),\':/:\',IFNULL(a2.middlename,
\'+NULL\'),\':/:\',IFNULL(a2.lastname
, \'+NULL\'),\':/:\',IFNULL(a2.suffix,
\'+NULL\'),\':/:\',IFNULL(a2.misc,
\'+NULL\'),\':/:\',IFNULL(a2.postal_address,
\'+NULL\'),\':/:\',IFNULL(a2.affiliation
, \'+NULL\'),\':/:\',IFNULL(a2.email, \'+NULL\'),\':/:\',IFNULL(a2.user,
\'+NULL\') ORDER BY cta2.displayorder SEPARATOR \'///\'), \'\') AS
_ct2_authors_packed',
'IFNULL(GROUP_CONCAT(DISTINCT
CONCAT(t2.tag_id),\':/:\',IFNULL(t2.name, \'+NULL\') ORDER BY
ubt2.created SEPARATOR \'///\'), \'\') AS _ub_tags_packed',
'COUNT(DISTINCT ub2.user_bookmark_id) as
_ub_user_bookmarks_count',
'COUNT(DISTINCT c2.comment_id) as
_ub_comments_count',
'COUNT(DISTINCT=20
ub3.user_bookmark_id) as _ub_bookmark_is_linked_by_current_user',
'COUNT(DISTINCT t4.tag_id) as _ub_is_geotagged',
'MAX(UNIX_TIMESTAMP(ub.created)) AS sortvalue'
],
'join_ub2' =3D> '((((ub2.private =3D 0 AND ub2.private_gang IS
NULL) OR (ub2.private_until IS NOT NULL AND ub2.private_until <=3D =
NOW()))
AND ub2.quarantined IS NULL) OR=20
ub2.user =3D ?)',
'where' =3D> 'ub.user_bookmark_id IS NOT NULL',
'join_ub3' =3D> 'ub3.user =3D ?',
'join_t4' =3D> ' <http://t4.name>=20
t4.name =3D ?',
'class' =3D> 'Bibliotech::User_Bookmark',
'hbind' =3D> [],
'bind_ub2' =3D> $VAR1->{'bind_ub'}
};
$VAR2 =3D [
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
'tag',
1,
1,
'1',
'1',
'1',
'geotagged'
];
=20
=20
Do you have any suggestions?
=20
Thanks
arindam
|
|
From: Martin F. <ma...@ne...> - 2007-11-29 01:19:27
|
Hi Arindam, It should just be a few details. I will take a look at this. html is now site/default. Martin Ganguly, Arindam wrote: > Hi, > So I just realized that the documentation for the code install doesn't > quite synch with the version 1.8. Folders being referred to appear to be > from 1.7 and below. The default config files also refer to the lower > version. > > Any chance I can get a hold of a Bibliotech.conf file that reflects the > directory struc of ver 1.8. also do I need to edit the dir structure > from the download file. For instance the sub directory 'html' doesn't > appear anymore in 1.8.. its site. > > Anyweays I'm getting error with the configuration file and it cant seem > to locate the Bibliotech::Apache. > > If I had something go off of..would be helpful > > Thank you > arindam |
|
From: Ganguly, A. <aga...@so...> - 2007-11-29 01:15:51
|
Hi, So I just realized that the documentation for the code install doesn't quite synch with the version 1.8. Folders being referred to appear to be from 1.7 and below. The default config files also refer to the lower version. Any chance I can get a hold of a Bibliotech.conf file that reflects the directory struc of ver 1.8. also do I need to edit the dir structure from the download file. For instance the sub directory 'html' doesn't appear anymore in 1.8.. its site.=20 Anyweays I'm getting error with the configuration file and it cant seem to locate the Bibliotech::Apache. If I had something go off of..would be helpful Thank you arindam -----Original Message----- From: Martin Flack [mailto:ma...@ne...]=20 Sent: Wednesday, November 28, 2007 8:37 AM To: Ganguly, Arindam Cc: con...@li... Subject: Re: [Connotea-code-devel] connotea instal Ganguly, Arindam wrote: > Setting to the apache config..restarting the server comes back with a > PerlOption 'Parent' requires an ithreads enabled Perl. >=20 > =20 >=20 > Is that an issue with my perl installation? If so does anybody know what > options are required to enable ithreads on a new perl installation? Yes, probably. It may work without it; I think it was more of a safety=20 precaution against conflicts with other instances. Martin |
|
From: Martin F. <ma...@ne...> - 2007-11-28 16:37:32
|
Ganguly, Arindam wrote: > Setting to the apache config..restarting the server comes back with a > PerlOption 'Parent' requires an ithreads enabled Perl. > > > > Is that an issue with my perl installation? If so does anybody know what > options are required to enable ithreads on a new perl installation? Yes, probably. It may work without it; I think it was more of a safety precaution against conflicts with other instances. Martin |
|
From: Ganguly, A. <aga...@so...> - 2007-11-27 22:43:52
|
Hi ,
I'm trying to install a local copy of connotea.
=20
Adding
PerlOptions +Parent
PerlSwitches -I/var/www/perl/...
PerlModule Bibliotech::Apache
PerlModule Bibliotech::AuthCookie
<Location /bibliotech>
SetHandler perl-script
PerlHandler Bibliotech::Apache
PerlAuthenHandler Bibliotech::AuthCookie::authen_handler
AuthName Bibliotech
AuthType basic
require valid-user
#ErrorDocument 503 /paused.html
ErrorDocument 503 /unavailable.html
</Location>
=20
=20
Setting to the apache config..restarting the server comes back with a
PerlOption 'Parent' requires an ithreads enabled Perl.
=20
Is that an issue with my perl installation? If so does anybody know what
options are required to enable ithreads on a new perl installation?
=20
Thanks
arindam
=20
|
|
From: Mulvany, I. <i.m...@na...> - 2007-11-23 13:36:21
|
Hi, In order to roll out a major upgrade to Connotea we are going to be taking the service down for a few hours tonight. We are scheduled to be down from 11pm EST tonight and should be back up a few hours after that. - Ian ******************************************************************************** DISCLAIMER: This e-mail is confidential and should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage mechanism. Neither Macmillan Publishers Limited nor any of its agents accept liability for any statements made which are clearly the sender's own and not expressly made on behalf of Macmillan Publishers Limited or one of its agents. Please note that neither Macmillan Publishers Limited nor any of its agents accept any responsibility for viruses that may be contained in this e-mail or its attachments and it is your responsibility to scan the e-mail and attachments (if any). No contracts may be concluded on behalf of Macmillan Publishers Limited or its agents by means of e-mail communication. Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** |
|
From: Martin F. <ma...@ne...> - 2007-11-20 17:12:58
|
Hi Noel, We don't support ScienceDirect. If memory serves, it requires some collaboration with the publisher that we were working on and it didn't quite come through, but I expect we'll revisit the issue at some point. Sorry about that. Martin Flack Noel O'Boyle wrote: > Dear Martin, > > It seems to be working fine for Nature, but I am not having any > success with ScienceDirect. For example, the excellent paper at > http://dx.doi.org/10.1016/j.jmb.2007.02.065 has very poor metadata via > Webcite, and if you paste in the URL it resolves to (on my machine): > http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4N68NPG-3&_user=1495569&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=72b3560144a49d56f9f6383b6c6d3747 > you get absolutely no metadata. > > Also, this paper has a PMID (17400244) but this is not detected by Webcite. > > Noel > > On 19/11/2007, Martin Flack <ma...@ne...> wrote: >> Hi Noel, >> >> It's running here although we intended to move it to a subdomain so this >> URL may change: >> >> http://www.connotea.org/webcite >> >> Martin Flack >> >> Noel O'Boyle wrote: >>> In relation to: >>> ===================== >>> From: Adie, Euan <e.adie@na...> - 2007-09-03 12:52 >>>> o Alpha-version stand-alone citation server capability. >>> If I can big up this bullet point a bit: the idea behind this is that you >>> can use the Connotea code as a web service - POST an URI and get back the >>> citation for whatever resource it points to in JSON, XML or RIS formats. >>> >>> Should hopefully make literature based mashups much, much easier: no more >>> regexp'ing out DOIs in Greasemonkey scripts... >>> >>> Euan >>> ===================== >>> >>> Does Connotea have this webservice up and running? Certainly, the API >>> docs don't mention it. (I know, I know, I could set it up myself...) >>> It would also be useful to know how it works. >>> >>> Noel >> |
|
From: Noel O'B. <bao...@gm...> - 2007-11-20 13:26:16
|
Dear Martin, It seems to be working fine for Nature, but I am not having any success with ScienceDirect. For example, the excellent paper at http://dx.doi.org/10.1016/j.jmb.2007.02.065 has very poor metadata via Webcite, and if you paste in the URL it resolves to (on my machine): http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4N68NPG-3&_user=1495569&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000053194&_version=1&_urlVersion=0&_userid=1495569&md5=72b3560144a49d56f9f6383b6c6d3747 you get absolutely no metadata. Also, this paper has a PMID (17400244) but this is not detected by Webcite. Noel On 19/11/2007, Martin Flack <ma...@ne...> wrote: > Hi Noel, > > It's running here although we intended to move it to a subdomain so this > URL may change: > > http://www.connotea.org/webcite > > Martin Flack > > Noel O'Boyle wrote: > > In relation to: > > ===================== > > From: Adie, Euan <e.adie@na...> - 2007-09-03 12:52 > >> o Alpha-version stand-alone citation server capability. > > > > If I can big up this bullet point a bit: the idea behind this is that you > > can use the Connotea code as a web service - POST an URI and get back the > > citation for whatever resource it points to in JSON, XML or RIS formats. > > > > Should hopefully make literature based mashups much, much easier: no more > > regexp'ing out DOIs in Greasemonkey scripts... > > > > Euan > > ===================== > > > > Does Connotea have this webservice up and running? Certainly, the API > > docs don't mention it. (I know, I know, I could set it up myself...) > > It would also be useful to know how it works. > > > > Noel > > |
|
From: Martin F. <ma...@ne...> - 2007-11-19 18:36:23
|
Hi Noel, It's running here although we intended to move it to a subdomain so this URL may change: http://www.connotea.org/webcite Martin Flack Noel O'Boyle wrote: > In relation to: > ===================== > From: Adie, Euan <e.adie@na...> - 2007-09-03 12:52 >> o Alpha-version stand-alone citation server capability. > > If I can big up this bullet point a bit: the idea behind this is that you > can use the Connotea code as a web service - POST an URI and get back the > citation for whatever resource it points to in JSON, XML or RIS formats. > > Should hopefully make literature based mashups much, much easier: no more > regexp'ing out DOIs in Greasemonkey scripts... > > Euan > ===================== > > Does Connotea have this webservice up and running? Certainly, the API > docs don't mention it. (I know, I know, I could set it up myself...) > It would also be useful to know how it works. > > Noel |
|
From: Noel O'B. <bao...@gm...> - 2007-11-19 11:29:54
|
In relation to: ===================== From: Adie, Euan <e.adie@na...> - 2007-09-03 12:52 > o Alpha-version stand-alone citation server capability. If I can big up this bullet point a bit: the idea behind this is that you can use the Connotea code as a web service - POST an URI and get back the citation for whatever resource it points to in JSON, XML or RIS formats. Should hopefully make literature based mashups much, much easier: no more regexp'ing out DOIs in Greasemonkey scripts... Euan ===================== Does Connotea have this webservice up and running? Certainly, the API docs don't mention it. (I know, I know, I could set it up myself...) It would also be useful to know how it works. Noel |
|
From: Martin F. <ma...@ne...> - 2007-10-31 06:41:08
|
Alex, As I mentioned in the other email to -devel, it's a result of the grouping applied to the results. The first way is grouping on URL and the second way is grouping on posting. These were intended to be intuitive ways to group things for the HTML interface. If your interest is more for API access, take a look at the output from /data/bookmarks?q=xxx or /data/bookmarks/tag/xxx as I have just enabled the bookmarks entity output and this might be a more useful way to see the data. Martin Alexander DeLuca wrote: > Excellent questions. > > Me too; I am also interested in responses to this. > > Thanks in advance, > > ..alex... > > On Oct 27, 2007 3:47 AM, Mohsen Safavi (Gmail) <moh...@gm...> > wrote: > >> Hi, >> >> Could someone please help me understand how the free text searching in >> Connotea works? I am bewildered as why, for example, bookmarks returned >> by the following two URIs are so different: >> >> http://www.connotea.org/search?q=17237074 >> >> and >> >> http://www.connotea.org/uri/51b96f63f9a113c5c0df8a3a9b4f6f18 >> >> The first URI is a free text search for PMID of 17237074, and the second >> retrieves bookmarks pointing to Pubmed abstract whose PMID is, again, >> 17237074. >> Generally, the first URI should be more sensitive (returning all >> bookmarks returned by the second URI+ some bookmarks that point to the >> same abstract with different URI), but it only returns 2 bookmarks, >> while the second URI returns 3! To make it more confusing: the bookmark >> created by ekawas is retrieved by the first URI but not by the second >> one, while the bookmark created by mwilkinson is in the results of the >> second URI but not the first one (all bookmarks are Pubmed abstracts). >> Why does this happen? >> >> Thanks in advance for any help, >> Mohsen >> >> con...@li... wrote: >>> Send Connotea-code-devel mailing list submissions to >>> con...@li... >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >>> or, via email, send a message with subject or body 'help' to >>> con...@li... >>> >>> You can reach the person managing the list at >>> con...@li... >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Connotea-code-devel digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Connotea API noop problem (Noel O'Boyle) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 23 Oct 2007 15:22:27 +0100 >>> From: "Noel O'Boyle" <bao...@gm...> >>> Subject: [Connotea-code-devel] Connotea API noop problem >>> To: con...@li... >>> Message-ID: >>> <a88...@ma...> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> Dear all, >>> >>> Is there a problem with the Connotea API at the moment? When I try to >> access >>> http://www.connotea.org/data/noop, I get >>> "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 >>> OK. >>> >>> Regards, >>> Noel >>> >>> >>> >>> ------------------------------ >>> >>> >> ------------------------------------------------------------------------- >>> This SF.net email is sponsored by: Splunk Inc. >>> Still grepping through log files to find problems? Stop. >>> Now Search log events and configuration files using AJAX and a browser. >>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Connotea-code-devel mailing list >>> Con...@li... >>> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >>> >>> >>> End of Connotea-code-devel Digest, Vol 18, Issue 6 >>> ************************************************** >>> >>> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Connotea-code-devel mailing list >> Con...@li... >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> > > > |
|
From: Alexander D. <doc...@gm...> - 2007-10-30 02:00:33
|
Excellent questions. Me too; I am also interested in responses to this. Thanks in advance, ..alex... On Oct 27, 2007 3:47 AM, Mohsen Safavi (Gmail) <moh...@gm...> wrote: > Hi, > > Could someone please help me understand how the free text searching in > Connotea works? I am bewildered as why, for example, bookmarks returned > by the following two URIs are so different: > > http://www.connotea.org/search?q=17237074 > > and > > http://www.connotea.org/uri/51b96f63f9a113c5c0df8a3a9b4f6f18 > > The first URI is a free text search for PMID of 17237074, and the second > retrieves bookmarks pointing to Pubmed abstract whose PMID is, again, > 17237074. > Generally, the first URI should be more sensitive (returning all > bookmarks returned by the second URI+ some bookmarks that point to the > same abstract with different URI), but it only returns 2 bookmarks, > while the second URI returns 3! To make it more confusing: the bookmark > created by ekawas is retrieved by the first URI but not by the second > one, while the bookmark created by mwilkinson is in the results of the > second URI but not the first one (all bookmarks are Pubmed abstracts). > Why does this happen? > > Thanks in advance for any help, > Mohsen > > con...@li... wrote: > > Send Connotea-code-devel mailing list submissions to > > con...@li... > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > or, via email, send a message with subject or body 'help' to > > con...@li... > > > > You can reach the person managing the list at > > con...@li... > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Connotea-code-devel digest..." > > > > > > Today's Topics: > > > > 1. Connotea API noop problem (Noel O'Boyle) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 23 Oct 2007 15:22:27 +0100 > > From: "Noel O'Boyle" <bao...@gm...> > > Subject: [Connotea-code-devel] Connotea API noop problem > > To: con...@li... > > Message-ID: > > <a88...@ma...> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Dear all, > > > > Is there a problem with the Connotea API at the moment? When I try to > access > > http://www.connotea.org/data/noop, I get > > "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 > > OK. > > > > Regards, > > Noel > > > > > > > > ------------------------------ > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > > ------------------------------ > > > > _______________________________________________ > > Connotea-code-devel mailing list > > Con...@li... > > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > > > > End of Connotea-code-devel Digest, Vol 18, Issue 6 > > ************************************************** > > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > -- ..alex... doc...@gm... Alexander DeLuca, M.D., MPH Senior Consultant, Pain Relief Network http://www.painreliefnetwork.org/ http://www.doctordeluca.com/wordpress/ http://www.doctordeluca.com/ - There is no medical treatment for non-problematic substance use... there is only punishment. |
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From: Martin F. <ma...@ne...> - 2007-10-29 21:13:55
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Hi Mohsen, As you may have deduced by now from reading further emails from you, the first link is grouping by URL and the other links are rolled up and represented by the "and x others", whereas the second link is an unrolling of the posts for the first URL. Martin Mohsen Safavi (Gmail) wrote: > Hi, > > Could someone please help me understand how the free text searching in > Connotea works? I am bewildered as why, for example, bookmarks returned > by the following two URIs are so different: > > http://www.connotea.org/search?q=17237074 > > and > > http://www.connotea.org/uri/51b96f63f9a113c5c0df8a3a9b4f6f18 > > The first URI is a free text search for PMID of 17237074, and the second > retrieves bookmarks pointing to Pubmed abstract whose PMID is, again, > 17237074. > Generally, the first URI should be more sensitive (returning all > bookmarks returned by the second URI+ some bookmarks that point to the > same abstract with different URI), but it only returns 2 bookmarks, > while the second URI returns 3! To make it more confusing: the bookmark > created by ekawas is retrieved by the first URI but not by the second > one, while the bookmark created by mwilkinson is in the results of the > second URI but not the first one (all bookmarks are Pubmed abstracts). > Why does this happen? > > Thanks in advance for any help, > Mohsen > > con...@li... wrote: >> Send Connotea-code-devel mailing list submissions to >> con...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> or, via email, send a message with subject or body 'help' to >> con...@li... >> >> You can reach the person managing the list at >> con...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Connotea-code-devel digest..." >> >> >> Today's Topics: >> >> 1. Connotea API noop problem (Noel O'Boyle) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 23 Oct 2007 15:22:27 +0100 >> From: "Noel O'Boyle" <bao...@gm...> >> Subject: [Connotea-code-devel] Connotea API noop problem >> To: con...@li... >> Message-ID: >> <a88...@ma...> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear all, >> >> Is there a problem with the Connotea API at the moment? When I try to access >> http://www.connotea.org/data/noop, I get >> "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 >> OK. >> >> Regards, >> Noel >> >> >> >> ------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> >> ------------------------------ >> >> _______________________________________________ >> Connotea-code-devel mailing list >> Con...@li... >> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel >> >> >> End of Connotea-code-devel Digest, Vol 18, Issue 6 >> ************************************************** >> >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel |
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From: Mohsen S. (Gmail) <moh...@gm...> - 2007-10-27 07:47:18
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Hi, Could someone please help me understand how the free text searching in Connotea works? I am bewildered as why, for example, bookmarks returned by the following two URIs are so different: http://www.connotea.org/search?q=17237074 and http://www.connotea.org/uri/51b96f63f9a113c5c0df8a3a9b4f6f18 The first URI is a free text search for PMID of 17237074, and the second retrieves bookmarks pointing to Pubmed abstract whose PMID is, again, 17237074. Generally, the first URI should be more sensitive (returning all bookmarks returned by the second URI+ some bookmarks that point to the same abstract with different URI), but it only returns 2 bookmarks, while the second URI returns 3! To make it more confusing: the bookmark created by ekawas is retrieved by the first URI but not by the second one, while the bookmark created by mwilkinson is in the results of the second URI but not the first one (all bookmarks are Pubmed abstracts). Why does this happen? Thanks in advance for any help, Mohsen con...@li... wrote: > Send Connotea-code-devel mailing list submissions to > con...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > or, via email, send a message with subject or body 'help' to > con...@li... > > You can reach the person managing the list at > con...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Connotea-code-devel digest..." > > > Today's Topics: > > 1. Connotea API noop problem (Noel O'Boyle) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Oct 2007 15:22:27 +0100 > From: "Noel O'Boyle" <bao...@gm...> > Subject: [Connotea-code-devel] Connotea API noop problem > To: con...@li... > Message-ID: > <a88...@ma...> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all, > > Is there a problem with the Connotea API at the moment? When I try to access > http://www.connotea.org/data/noop, I get > "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 > OK. > > Regards, > Noel > > > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > ------------------------------ > > _______________________________________________ > Connotea-code-devel mailing list > Con...@li... > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel > > > End of Connotea-code-devel Digest, Vol 18, Issue 6 > ************************************************** > > |
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From: Martin F. <ma...@ne...> - 2007-10-23 17:01:29
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Sorry - fixed! Martin Noel O'Boyle wrote: > Dear all, > > Is there a problem with the Connotea API at the moment? When I try to access > http://www.connotea.org/data/noop, I get > "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 > OK. > > Regards, > Noel |
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From: Noel O'B. <bao...@gm...> - 2007-10-23 14:22:33
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Dear all, Is there a problem with the Connotea API at the moment? When I try to access http://www.connotea.org/data/noop, I get "Bibliotech::WebAPI::Answer=HASH(0xd8bc190)" instead of a simple 200 OK. Regards, Noel |
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