[med-svn] r2565 - in trunk/packages/agdbnet/trunk/debian: . patches template
tille at alioth.debian.org
tille at alioth.debian.org
Thu Oct 2 09:59:17 UTC 2008
Author: tille
Date: 2008-10-02 09:59:16 +0000 (Thu, 02 Oct 2008)
New Revision: 2565
Modified:
trunk/packages/agdbnet/trunk/debian/README.Debian
trunk/packages/agdbnet/trunk/debian/agdbnet_xml2sql
trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml
Log:
Adapted to new upstream tarball
Modified: trunk/packages/agdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/agdbnet/trunk/debian/README.Debian 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/README.Debian 2008-10-02 09:59:16 UTC (rev 2565)
@@ -19,7 +19,11 @@
to understand the meaning of the fields you have to configure. You
should also have a look at the examples directory which contains some
-example configuration files provided by the agdbnet authors.
+example configuration files provided by the agdbnet authors. It is
+a good idea to have a closer look at the example named nm_fhbp.xml
+because this reflects the latest version of an XML file example.
+The other examples contain some referenceX fields for PubMed references
+and a field for GenBank which is now handled differently.
To simplify the creation of the database you can find a script named
agdbnet_xml2sql in this directory. This script might serve as an
@@ -145,12 +149,11 @@
To enable apache to use this method you have to enable the
necessary modules via
- ln -s ../mods-available/auth_ldap.load /etc/apache2/mods-enabled
+ ln -s ../mods-available/ldap.load /etc/apache2/mods-enabled
ln -s ../mods-available/authnz_ldap.load /etc/apache2/mods-enabled
In principle this should be possible using apache-modconf
- apache-modconf apache enable auth_ldap
apache-modconf apache enable authnz_ldap
but in my tests this did not worked unfortunately so the method to
Modified: trunk/packages/agdbnet/trunk/debian/agdbnet_xml2sql
===================================================================
--- trunk/packages/agdbnet/trunk/debian/agdbnet_xml2sql 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/agdbnet_xml2sql 2008-10-02 09:59:16 UTC (rev 2565)
@@ -35,7 +35,7 @@
if [ -e "$SQLDIR"/"$XMLNAME".sql ] ; then
mv "$SQLDIR"/"$XMLNAME".sql "$SQLDIR"/"$XMLNAME".sql~
fi
-/usr/share/${pkg}/xml2sql.pl -u '"www-data"' "$XML" > "$SQLDIR"/"$XMLNAME".sql
+/usr/share/${pkg}/xml2sql.pl -u 'www-data' "$XML" > "$SQLDIR"/"$XMLNAME".sql
if psql -l | grep -wq "$XMLNAME" ; then
cat <<EOT
Modified: trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch 2008-10-02 09:59:16 UTC (rev 2565)
@@ -14,7 +14,7 @@
}
--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
+++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
-@@ -339,7 +339,7 @@
+@@ -343,7 +343,7 @@
}
if ($invalidXML) {
print $q->start_html( -title => "Invalid XML file" );
Modified: trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch 2008-10-02 09:59:16 UTC (rev 2565)
@@ -16,7 +16,7 @@
$system{'pass'} = 'remote';
--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
+++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
-@@ -146,7 +146,7 @@
+@@ -150,7 +150,7 @@
$system{'port'} = 5432;
}
if ( !$system{'user'} ) {
@@ -68,33 +68,6 @@
}
my $instance = $ARGV[0];
if ( !$instance ) {
-@@ -85,7 +85,7 @@
- PRIMARY KEY (id)
- );
-
--GRANT SELECT,UPDATE,INSERT,DELETE ON users TO $webuser;
-+GRANT SELECT,UPDATE,INSERT,DELETE ON users TO "$webuser";
-
- USERS
-
-@@ -128,7 +128,7 @@
- CREATE INDEX i_pmid ON refs (pmid);
- CREATE INDEX i_id ON refs (id);
-
--GRANT SELECT,UPDATE,INSERT,DELETE ON refs TO apache;
-+GRANT SELECT,UPDATE,INSERT,DELETE ON refs TO "www-data";
- REFS
-
- sub printtable {
-@@ -178,7 +178,7 @@
- }
- print $buffer;
- print "\n);\n";
-- print "\nGRANT SELECT,UPDATE,INSERT,DELETE ON $table TO $webuser;\n";
-+ print "\nGRANT SELECT,UPDATE,INSERT,DELETE ON $table TO \"$webuser\";\n";
- }
-
- sub locustype {
--- agdbnet_v1.0.4.orig/setup/refs.sql
+++ agdbnet_v1.0.4/setup/refs.sql
@@ -28,4 +28,4 @@
Modified: trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch 2008-10-02 09:59:16 UTC (rev 2565)
@@ -6,7 +6,7 @@
the connection string if $host == 'localhost'.
--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
+++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
-@@ -208,10 +208,19 @@
+@@ -212,10 +212,19 @@
}
sub dbconnect {
Modified: trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml
===================================================================
--- trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml 2008-10-01 07:44:19 UTC (rev 2564)
+++ trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml 2008-10-02 09:59:16 UTC (rev 2565)
@@ -14,6 +14,8 @@
longcode="##database##" webroot="/agdbnet" indexpage=""
description="##Description##"
downloadFASTAonly="yes"
+ reftable="yes"
+ genbanktable="yes"
>
</system>
@@ -23,12 +25,6 @@
<field type="int" length="##?##" userupdate="no" comments="primary key">id</field>
<field type="text" length="##?##" width="30" maindisplay="no">sequence</field>
<field type="int" length="##?##" comments="foreign key to peptide table">peptide_id</field>
-<field type="text" length="##?##" required="no" maindisplay="no">genbank</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference1</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference2</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference3</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference4</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference5</field>
<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date last modified">datestamp</field>
<field type="int" maindisplay="no" userupdate="no" length="4" comments="curator who entered data,link to users">curator</field>
@@ -37,12 +33,6 @@
<peptide>
<field type="int" length="##?##" userupdate="no" comments="primary key">id</field>
<field type="text" length="##?##" userupdate="no" width="30">sequence</field>
-<field type="text" length="##?##" required="no" maindisplay="no">genbank</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference1</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference2</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference3</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference4</field>
-<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference5</field>
<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date last modified">datestamp</field>
<field type="int" maindisplay="no" userupdate="no" length="4" comments="curator who entered data,link to users">curator</field>
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