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From: <jas...@us...> - 2002-11-07 14:55:55
|
Update of /cvsroot/genex/genex-server/Genex/Channel In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/Channel Modified Files: Channel.pm Log Message: new Index: Channel.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Channel/Channel.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 |
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From: <jas...@us...> - 2002-11-07 14:55:55
|
Update of /cvsroot/genex/genex-server/Genex/BlastHits In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/BlastHits Modified Files: BlastHits.pm Log Message: new Index: BlastHits.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/BlastHits/BlastHits.pm,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -d -r1.28 -r1.29 |
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From: <jas...@us...> - 2002-11-07 14:55:55
|
Update of /cvsroot/genex/genex-server/Genex/Audit In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/Audit Modified Files: Audit.pm Log Message: new Index: Audit.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Audit/Audit.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 |
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From: <jas...@us...> - 2002-11-07 14:55:55
|
Update of /cvsroot/genex/genex-server/Genex/ArrayDesign In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/ArrayDesign Modified Files: ArrayDesign.pm Log Message: new Index: ArrayDesign.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ArrayDesign/ArrayDesign.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 |
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From: <jas...@us...> - 2002-11-07 14:55:54
|
Update of /cvsroot/genex/genex-server/Genex/Array In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/Array Modified Files: Array.pm Log Message: new Index: Array.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Array/Array.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 |
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From: <jas...@us...> - 2002-11-07 14:55:54
|
Update of /cvsroot/genex/genex-server/Genex/AM_SuspectSpots In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/AM_SuspectSpots Modified Files: AM_SuspectSpots.pm Log Message: new Index: AM_SuspectSpots.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/AM_SuspectSpots/AM_SuspectSpots.pm,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 |
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From: <jas...@us...> - 2002-11-07 14:55:54
|
Update of /cvsroot/genex/genex-server/Genex/AM_Spots In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/AM_Spots Modified Files: AM_Spots.pm Log Message: new Index: AM_Spots.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/AM_Spots/AM_Spots.pm,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 |
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From: <jas...@us...> - 2002-11-07 14:55:54
|
Update of /cvsroot/genex/genex-server/Genex/AM_FactorValues In directory usw-pr-cvs1:/tmp/cvs-serv15488/Genex/AM_FactorValues Modified Files: AM_FactorValues.pm Log Message: new Index: AM_FactorValues.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/AM_FactorValues/AM_FactorValues.pm,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 |
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From: <jas...@us...> - 2002-11-07 14:53:51
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv15168
Modified Files:
Configure
Log Message:
* Configure (Repository):
GRAPHICS_DIR ==> GENEX_GRAPHICS_DIR
HTMLDIR ==> GENEX_HTMLDIR
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Configure 20 Oct 2002 21:17:08 -0000 1.8
--- Configure 7 Nov 2002 14:53:45 -0000 1.9
***************
*** 84,88 ****
$GENEX_CGI_URL $GENEX_DIR $GENEX_DIR_DEF $GENEX_EXTRALIBS $GENEX_HTML_URL
$GNUCUT $GNUMKDIR $GNUPLOT $GNUSORT $GNUTAIL $GNUTAR $GNUINSTALL
! $DOWNLOAD_DIR $CyberT_Demo_DIR $DTD_DIR $RCluster_Demo_DIR $GRAPHICS_DIR
$INCLUDE_DIR $TOP_LEVEL_DIR $XCLUSTER_DIR $GS $GXQUERY_DIR
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
--- 84,88 ----
$GENEX_CGI_URL $GENEX_DIR $GENEX_DIR_DEF $GENEX_EXTRALIBS $GENEX_HTML_URL
$GNUCUT $GNUMKDIR $GNUPLOT $GNUSORT $GNUTAIL $GNUTAR $GNUINSTALL
! $DOWNLOAD_DIR $CyberT_Demo_DIR $DTD_DIR $RCluster_Demo_DIR $GENEX_GRAPHICS_DIR
$INCLUDE_DIR $TOP_LEVEL_DIR $XCLUSTER_DIR $GS $GXQUERY_DIR
$ENV_HOME $HTMLDIR $HTMLDIR_DEF $HTML_ROOT_URL $HTMLTMPDIR
***************
*** 850,854 ****
}
$GENEX_HTMLDIR = $VARS{GENEX_HTMLDIR} = "$HTMLDIR/$GENEX_DIR";
! $GENEX_G2G_DIR = $VARS{GENEX_G2G_DIR} = "$HTMLDIR/$GENEX_DIR/g2g";
print STDERR "\nOK... HTMLDIR => $HTMLDIR\n";
print STDERR "\nOK... GENEX_HTMLDIR => $GENEX_HTMLDIR\n";
--- 850,854 ----
}
$GENEX_HTMLDIR = $VARS{GENEX_HTMLDIR} = "$HTMLDIR/$GENEX_DIR";
! $GENEX_G2G_DIR = $VARS{GENEX_G2G_DIR} = "$GENEX_HTMLDIR/g2g";
print STDERR "\nOK... HTMLDIR => $HTMLDIR\n";
print STDERR "\nOK... GENEX_HTMLDIR => $GENEX_HTMLDIR\n";
***************
*** 959,963 ****
if (!defined $CGITMPURL || !defined $HTMLTMPDIR) {
! $HTMLTMPDIR = "$HTMLDIR/genex/tmp";
$CGITMPURL = "$HTML_ROOT_URL/genex/tmp";
$VARS{HTMLTMPDIR} = $HTMLTMPDIR;
--- 959,963 ----
if (!defined $CGITMPURL || !defined $HTMLTMPDIR) {
! $HTMLTMPDIR = "$GENEX_HTMLDIR/tmp";
$CGITMPURL = "$HTML_ROOT_URL/genex/tmp";
$VARS{HTMLTMPDIR} = $HTMLTMPDIR;
***************
*** 1099,1105 ****
$VARS{DTD_HTML_URL} = $DTD_HTML_URL = "$GENEXML_URL/genexml-html";
$VARS{RCluster_Demo_DIR} = $RCluster_Demo_DIR = "$GENEX_DIR/RCluster-Demo";
! $VARS{GRAPHICS_DIR} = $GRAPHICS_DIR = "$GENEX_DIR/graphics";
$VARS{INCLUDE_DIR} = $INCLUDE_DIR = "$GENEX_DIR/include";
! $VARS{TOP_LEVEL_DIR} = $TOP_LEVEL_DIR = "$GENEX_DIR/top_level";
$VARS{XCLUSTER_DIR} = $XCLUSTER_DIR = "$GENEX_DIR/xcluster";
--- 1099,1105 ----
$VARS{DTD_HTML_URL} = $DTD_HTML_URL = "$GENEXML_URL/genexml-html";
$VARS{RCluster_Demo_DIR} = $RCluster_Demo_DIR = "$GENEX_DIR/RCluster-Demo";
! $VARS{GENEX_GRAPHICS_DIR}= $GENEX_GRAPHICS_DIR= "$GENEX_HTMLDIR/graphics";
$VARS{INCLUDE_DIR} = $INCLUDE_DIR = "$GENEX_DIR/include";
! $VARS{TOP_LEVEL_DIR} = $TOP_LEVEL_DIR = "$GENEX_DIR/top_level";
$VARS{XCLUSTER_DIR} = $XCLUSTER_DIR = "$GENEX_DIR/xcluster";
|
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From: <jas...@us...> - 2002-11-07 14:51:35
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv13299
Added Files:
MANIFEST.in
Log Message:
* MANIFEST.in (Repository):
new file documenting which local files get installed and where
--- NEW FILE: MANIFEST.in ---
$FILES = {
'apache/genex-2.conf' => '%%APACHE_CONF_DIR%%',
'G2G/mason/workspace.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/array-design.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/autohandler' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/bioassay.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/check-cookie.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/check-login.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/data-loader.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/data-sources.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/experiments.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/experimentset-create.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/generate_group.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/generate_user.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/group-maint.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/group-create.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/index.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/kill-cookie.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/logout.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/query.html' => '%%GENEX_WORKSPACE_DIR%%',
'G2G/mason/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/data-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/debug-args.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/g2g-request.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/hiddenlist.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/query-checkboxes.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/query-drop-down.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/comps/query-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',
'G2G/mason/workspace-comps/footer.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps',
'G2G/mason/workspace-comps/header.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps',
'G2G/mason/workspace-comps/main.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps',
'G2G/mason/workspace-comps/nav.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps',
'Genex/scripts/array-design-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/experimentset-create.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/cv-check.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/cv-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/externaldb-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/generate_group.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/generate_user.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/genex1-to-genex2.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/group-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/mbad-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/priveleges.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/protocol-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/qtdim-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/reporter-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/scanner-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/security-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/software-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/species-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/spotter-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/tab2xml.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/user-insert.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/xml2form.pl' => '%%GENEX_BIN_DIR%%',
'Genex/scripts/xml2sql.pl' => '%%GENEX_BIN_DIR%%',
'DB/controlled_vocab/ALS_SpotType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AL_Coating.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AL_DefaultSpotConcUnits.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AL_IdentifierCode.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AL_Medium.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AL_TechnologyType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AM_EquationType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AM_SpotMeasurementUnits.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/AM_Type.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/ContactType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/EF_MajorCategory.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/EF_MinorCategory.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/ES_QuantitySeriesType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/ES_TreatmentType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/Feature_SpotType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/HS_ThresholdType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/PRT_Type.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SCN_ModelDescription.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_AgeUnits.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_DevelopmentStageName.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_DevelopmentStageUnits.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_GeneticStatus.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_OrganType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_OrganismIntactness.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_PrimaryCellType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_SexMatingType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SMP_TissueType.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SPC_CellStructure.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SPC_GeneralClassification.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SPT_ModelDescription.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SW_Name.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/SW_Type.xml' => '%%GENEX_VOCAB_DIR%%',
'DB/controlled_vocab/USF_Type.xml' => '%%GENEX_VOCAB_DIR%%',
'graphics/genex-banner-new.gif' => '%%GENEX_GRAPHICS_DIR%%',
'DTD/table.dtd' => '%%GENEXML_DIR%%',
'DTD/tests.dtd' => '%%GENEXML_DIR%%',
}
|
|
From: <jas...@us...> - 2002-11-07 14:49:36
|
Update of /cvsroot/genex/genex-server/Genex/t
In directory usw-pr-cvs1:/tmp/cvs-serv11299/Genex/t
Modified Files:
AM_FactorValues.t AM_Spots.t AM_SuspectSpots.t Array.t
BlastHits.t ExperimentSet.t Feature.t
FeatureExtractionSoftware.t HotSpots.t PhysicalBioAssay.t
SF_ExternalDBLink.t Sample.t Species.t TreatmentLevel.t
Treatment_AMs.t
Log Message:
new
Index: AM_FactorValues.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/AM_FactorValues.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** AM_FactorValues.t 18 Sep 2002 20:45:48 -0000 1.6
--- AM_FactorValues.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 36,42 ****
result ($obj->ef_fk() == 555);
! # testing the am_fk attribute method
! $obj->am_fk(555);
! result ($obj->am_fk() == 555);
# testing the value attribute method
--- 36,42 ----
result ($obj->ef_fk() == 555);
! # testing the pba_fk attribute method
! $obj->pba_fk(555);
! result ($obj->pba_fk() == 555);
# testing the value attribute method
***************
*** 44,50 ****
result ($obj->value() == 555);
! # testing the am_obj attribute method
! $obj->am_obj(555);
! result ($obj->am_obj() == 555);
# testing the ef_obj attribute method
--- 44,50 ----
result ($obj->value() == 555);
! # testing the pba_obj attribute method
! $obj->pba_obj(555);
! result ($obj->pba_obj() == 555);
# testing the ef_obj attribute method
Index: AM_Spots.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/AM_Spots.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** AM_Spots.t 18 Sep 2002 20:45:48 -0000 1.6
--- AM_Spots.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 36,42 ****
result ($obj->ams_pk() == 555);
! # testing the am_fk attribute method
! $obj->am_fk(555);
! result ($obj->am_fk() == 555);
# testing the feature_fk attribute method
--- 36,42 ----
result ($obj->ams_pk() == 555);
! # testing the pba_fk attribute method
! $obj->pba_fk(555);
! result ($obj->pba_fk() == 555);
# testing the feature_fk attribute method
***************
*** 52,58 ****
result ($obj->feature_obj() == 555);
! # testing the am_obj attribute method
! $obj->am_obj(555);
! result ($obj->am_obj() == 555);
# testing the fetched attribute method
--- 52,58 ----
result ($obj->feature_obj() == 555);
! # testing the pba_obj attribute method
! $obj->pba_obj(555);
! result ($obj->pba_obj() == 555);
# testing the fetched attribute method
Index: AM_SuspectSpots.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/AM_SuspectSpots.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** AM_SuspectSpots.t 18 Sep 2002 20:45:48 -0000 1.6
--- AM_SuspectSpots.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 32,38 ****
my $obj = Bio::Genex::AM_SuspectSpots->new();
! # testing the am_fk attribute method
! $obj->am_fk(555);
! result ($obj->am_fk() == 555);
# testing the ams_fk attribute method
--- 32,38 ----
my $obj = Bio::Genex::AM_SuspectSpots->new();
! # testing the pba_fk attribute method
! $obj->pba_fk(555);
! result ($obj->pba_fk() == 555);
# testing the ams_fk attribute method
***************
*** 44,50 ****
result ($obj->ams_obj() == 555);
! # testing the am_obj attribute method
! $obj->am_obj(555);
! result ($obj->am_obj() == 555);
# testing the fetched attribute method
--- 44,50 ----
result ($obj->ams_obj() == 555);
! # testing the pba_obj attribute method
! $obj->pba_obj(555);
! result ($obj->pba_obj() == 555);
# testing the fetched attribute method
Index: Array.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Array.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Array.t 18 Sep 2002 20:45:12 -0000 1.1
--- Array.t 7 Nov 2002 14:49:32 -0000 1.2
***************
*** 7,11 ****
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..50\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
--- 7,11 ----
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..53\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
***************
*** 52,55 ****
--- 52,59 ----
result ($obj->audit_fk() == 555);
+ # testing the ad_fk attribute method
+ $obj->ad_fk(555);
+ result ($obj->ad_fk() == 555);
+
# testing the sptr_fk attribute method
$obj->sptr_fk(555);
***************
*** 127,130 ****
--- 131,138 ----
$obj->audit_obj(555);
result ($obj->audit_obj() == 555);
+
+ # testing the ad_obj attribute method
+ $obj->ad_obj(555);
+ result ($obj->ad_obj() == 555);
# testing the sw_obj attribute method
Index: BlastHits.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/BlastHits.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** BlastHits.t 18 Sep 2002 20:45:48 -0000 1.6
--- BlastHits.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 36,42 ****
result ($obj->bh_pk() == 555);
! # testing the sf_fk attribute method
! $obj->sf_fk(555);
! result ($obj->sf_fk() == 555);
# testing the match_accession attribute method
--- 36,42 ----
result ($obj->bh_pk() == 555);
! # testing the rep_fk attribute method
! $obj->rep_fk(555);
! result ($obj->rep_fk() == 555);
# testing the match_accession attribute method
***************
*** 48,54 ****
result ($obj->expect_value() == 555);
! # testing the sf_obj attribute method
! $obj->sf_obj(555);
! result ($obj->sf_obj() == 555);
# testing the fetched attribute method
--- 48,54 ----
result ($obj->expect_value() == 555);
! # testing the rep_obj attribute method
! $obj->rep_obj(555);
! result ($obj->rep_obj() == 555);
# testing the fetched attribute method
Index: ExperimentSet.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/ExperimentSet.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ExperimentSet.t 18 Sep 2002 20:45:49 -0000 1.6
--- ExperimentSet.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 7,11 ****
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..58\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
--- 7,11 ----
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..61\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
***************
*** 80,87 ****
result ($obj->release_date() == 555);
- # testing the submission_date attribute method
- $obj->submission_date(555);
- result ($obj->submission_date() == 555);
-
# testing the local_accession attribute method
$obj->local_accession(555);
--- 80,83 ----
***************
*** 112,115 ****
--- 108,119 ----
result ($obj->audit_obj() == 555);
+ # testing the measuredbioassay_obj attribute method
+ $obj->measuredbioassay_obj(555);
+ result ($obj->measuredbioassay_obj() == 555);
+
+ # testing the measuredbioassay_fk attribute method
+ $obj->measuredbioassay_fk(555);
+ result ($obj->measuredbioassay_fk() == 555);
+
# testing the experimentfactors_obj attribute method
$obj->experimentfactors_obj(555);
***************
*** 120,130 ****
result ($obj->experimentfactors_fk() == 555);
! # testing the arraymeasurement_obj attribute method
! $obj->arraymeasurement_obj(555);
! result ($obj->arraymeasurement_obj() == 555);
! # testing the arraymeasurement_fk attribute method
! $obj->arraymeasurement_fk(555);
! result ($obj->arraymeasurement_fk() == 555);
# testing the treatmentlevel_obj attribute method
--- 124,134 ----
result ($obj->experimentfactors_fk() == 555);
! # testing the physicalbioassay_obj attribute method
! $obj->physicalbioassay_obj(555);
! result ($obj->physicalbioassay_obj() == 555);
! # testing the physicalbioassay_fk attribute method
! $obj->physicalbioassay_fk(555);
! result ($obj->physicalbioassay_fk() == 555);
# testing the treatmentlevel_obj attribute method
Index: Feature.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Feature.t,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Feature.t 18 Sep 2002 20:45:49 -0000 1.5
--- Feature.t 7 Nov 2002 14:49:32 -0000 1.6
***************
*** 7,11 ****
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..36\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
--- 7,11 ----
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..38\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
***************
*** 36,42 ****
result ($obj->feature_pk() == 555);
! # testing the al_fk attribute method
! $obj->al_fk(555);
! result ($obj->al_fk() == 555);
# testing the feature_type attribute method
--- 36,42 ----
result ($obj->feature_pk() == 555);
! # testing the ad_fk attribute method
! $obj->ad_fk(555);
! result ($obj->ad_fk() == 555);
# testing the feature_type attribute method
***************
*** 64,70 ****
result ($obj->pin_identifier() == 555);
! # testing the sf_fk attribute method
! $obj->sf_fk(555);
! result ($obj->sf_fk() == 555);
# testing the sub_sequence_start attribute method
--- 64,70 ----
result ($obj->pin_identifier() == 555);
! # testing the rep_fk attribute method
! $obj->rep_fk(555);
! result ($obj->rep_fk() == 555);
# testing the sub_sequence_start attribute method
***************
*** 92,102 ****
result ($obj->grid_image_location() == 555);
! # testing the sf_obj attribute method
! $obj->sf_obj(555);
! result ($obj->sf_obj() == 555);
! # testing the al_obj attribute method
! $obj->al_obj(555);
! result ($obj->al_obj() == 555);
# testing the fetched attribute method
--- 92,110 ----
result ($obj->grid_image_location() == 555);
! # testing the grid_row_image_location attribute method
! $obj->grid_row_image_location(555);
! result ($obj->grid_row_image_location() == 555);
! # testing the grid_col_image_location attribute method
! $obj->grid_col_image_location(555);
! result ($obj->grid_col_image_location() == 555);
!
! # testing the rep_obj attribute method
! $obj->rep_obj(555);
! result ($obj->rep_obj() == 555);
!
! # testing the ad_obj attribute method
! $obj->ad_obj(555);
! result ($obj->ad_obj() == 555);
# testing the fetched attribute method
Index: FeatureExtractionSoftware.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/FeatureExtractionSoftware.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** FeatureExtractionSoftware.t 15 Oct 2002 14:42:58 -0000 1.1
--- FeatureExtractionSoftware.t 7 Nov 2002 14:49:32 -0000 1.2
***************
*** 7,11 ****
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..21\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
--- 7,11 ----
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..26\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
***************
*** 32,35 ****
--- 32,55 ----
my $obj = Bio::Genex::FeatureExtractionSoftware->new();
+ # testing the fesw_pk attribute method
+ $obj->fesw_pk(555);
+ result ($obj->fesw_pk() == 555);
+
+ # testing the feature_identifier_string attribute method
+ $obj->feature_identifier_string(555);
+ result ($obj->feature_identifier_string() == 555);
+
+ # testing the data_start_regex1 attribute method
+ $obj->data_start_regex1(555);
+ result ($obj->data_start_regex1() == 555);
+
+ # testing the data_start_regex2 attribute method
+ $obj->data_start_regex2(555);
+ result ($obj->data_start_regex2() == 555);
+
+ # testing the data_end_regex attribute method
+ $obj->data_end_regex(555);
+ result ($obj->data_end_regex() == 555);
+
# testing the qd_fk attribute method
$obj->qd_fk(555);
***************
*** 61,65 ****
# testing the pkey_name method
! result($obj->pkey_name() eq 'sw_pk');
--- 81,85 ----
# testing the pkey_name method
! result($obj->pkey_name() eq 'fesw_pk');
Index: HotSpots.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/HotSpots.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** HotSpots.t 18 Sep 2002 20:45:49 -0000 1.6
--- HotSpots.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 36,42 ****
result ($obj->es_fk() == 555);
! # testing the sf_fk attribute method
! $obj->sf_fk(555);
! result ($obj->sf_fk() == 555);
# testing the threshold_type attribute method
--- 36,42 ----
result ($obj->es_fk() == 555);
! # testing the rep_fk attribute method
! $obj->rep_fk(555);
! result ($obj->rep_fk() == 555);
# testing the threshold_type attribute method
***************
*** 48,54 ****
result ($obj->es_obj() == 555);
! # testing the sf_obj attribute method
! $obj->sf_obj(555);
! result ($obj->sf_obj() == 555);
# testing the fetched attribute method
--- 48,54 ----
result ($obj->es_obj() == 555);
! # testing the rep_obj attribute method
! $obj->rep_obj(555);
! result ($obj->rep_obj() == 555);
# testing the fetched attribute method
Index: PhysicalBioAssay.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/PhysicalBioAssay.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** PhysicalBioAssay.t 18 Sep 2002 20:45:12 -0000 1.1
--- PhysicalBioAssay.t 7 Nov 2002 14:49:32 -0000 1.2
***************
*** 88,91 ****
--- 88,99 ----
result ($obj->audit_obj() == 555);
+ # testing the samplelink_obj attribute method
+ $obj->samplelink_obj(555);
+ result ($obj->samplelink_obj() == 555);
+
+ # testing the samplelink_fk attribute method
+ $obj->samplelink_fk(555);
+ result ($obj->samplelink_fk() == 555);
+
# testing the am_factorvalues_obj attribute method
$obj->am_factorvalues_obj(555);
***************
*** 103,114 ****
$obj->treatment_ams_fk(555);
result ($obj->treatment_ams_fk() == 555);
-
- # testing the am_spots_obj attribute method
- $obj->am_spots_obj(555);
- result ($obj->am_spots_obj() == 555);
-
- # testing the am_spots_fk attribute method
- $obj->am_spots_fk(555);
- result ($obj->am_spots_fk() == 555);
# testing the es_obj attribute method
--- 111,114 ----
Index: SF_ExternalDBLink.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/SF_ExternalDBLink.t,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** SF_ExternalDBLink.t 18 Sep 2002 20:45:49 -0000 1.5
--- SF_ExternalDBLink.t 7 Nov 2002 14:49:32 -0000 1.6
***************
*** 32,38 ****
my $obj = Bio::Genex::SF_ExternalDBLink->new();
! # testing the sf_fk attribute method
! $obj->sf_fk(555);
! result ($obj->sf_fk() == 555);
# testing the ed_fk attribute method
--- 32,38 ----
my $obj = Bio::Genex::SF_ExternalDBLink->new();
! # testing the rep_fk attribute method
! $obj->rep_fk(555);
! result ($obj->rep_fk() == 555);
# testing the ed_fk attribute method
***************
*** 44,50 ****
result ($obj->external_identifier() == 555);
! # testing the sf_obj attribute method
! $obj->sf_obj(555);
! result ($obj->sf_obj() == 555);
# testing the ed_obj attribute method
--- 44,50 ----
result ($obj->external_identifier() == 555);
! # testing the rep_obj attribute method
! $obj->rep_obj(555);
! result ($obj->rep_obj() == 555);
# testing the ed_obj attribute method
Index: Sample.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Sample.t,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Sample.t 18 Sep 2002 20:45:49 -0000 1.8
--- Sample.t 7 Nov 2002 14:49:32 -0000 1.9
***************
*** 7,11 ****
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..64\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
--- 7,11 ----
# (It may become useful if the test is moved to ./t subdirectory.)
! BEGIN { $| = 1; print "1..68\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
***************
*** 183,186 ****
--- 183,194 ----
$obj->audit_obj(555);
result ($obj->audit_obj() == 555);
+
+ # testing the samplelink_obj attribute method
+ $obj->samplelink_obj(555);
+ result ($obj->samplelink_obj() == 555);
+
+ # testing the samplelink_fk attribute method
+ $obj->samplelink_fk(555);
+ result ($obj->samplelink_fk() == 555);
# testing the sampleprotocols_obj attribute method
Index: Species.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Species.t,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Species.t 18 Sep 2002 20:45:49 -0000 1.18
--- Species.t 7 Nov 2002 14:49:32 -0000 1.19
***************
*** 182,185 ****
--- 182,193 ----
result ($obj->audit_obj() == 555);
+ # testing the reporter_obj attribute method
+ $obj->reporter_obj(555);
+ result ($obj->reporter_obj() == 555);
+
+ # testing the reporter_fk attribute method
+ $obj->reporter_fk(555);
+ result ($obj->reporter_fk() == 555);
+
# testing the chromosome_obj attribute method
$obj->chromosome_obj(555);
***************
*** 189,200 ****
$obj->chromosome_fk(555);
result ($obj->chromosome_fk() == 555);
-
- # testing the sequencefeature_obj attribute method
- $obj->sequencefeature_obj(555);
- result ($obj->sequencefeature_obj() == 555);
-
- # testing the sequencefeature_fk attribute method
- $obj->sequencefeature_fk(555);
- result ($obj->sequencefeature_fk() == 555);
# testing the fetched attribute method
--- 197,200 ----
Index: TreatmentLevel.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/TreatmentLevel.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** TreatmentLevel.t 18 Sep 2002 20:45:49 -0000 1.6
--- TreatmentLevel.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 40,46 ****
result ($obj->es_fk() == 555);
! # testing the ratio_am_fk attribute method
! $obj->ratio_am_fk(555);
! result ($obj->ratio_am_fk() == 555);
# testing the name attribute method
--- 40,46 ----
result ($obj->es_fk() == 555);
! # testing the ratio_pba_fk attribute method
! $obj->ratio_pba_fk(555);
! result ($obj->ratio_pba_fk() == 555);
# testing the name attribute method
***************
*** 48,54 ****
result ($obj->name() == 555);
! # testing the ratio_am_obj attribute method
! $obj->ratio_am_obj(555);
! result ($obj->ratio_am_obj() == 555);
# testing the tl_factorvalues_obj attribute method
--- 48,54 ----
result ($obj->name() == 555);
! # testing the ratio_pba_obj attribute method
! $obj->ratio_pba_obj(555);
! result ($obj->ratio_pba_obj() == 555);
# testing the tl_factorvalues_obj attribute method
Index: Treatment_AMs.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Treatment_AMs.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Treatment_AMs.t 18 Sep 2002 20:45:49 -0000 1.6
--- Treatment_AMs.t 7 Nov 2002 14:49:32 -0000 1.7
***************
*** 32,38 ****
my $obj = Bio::Genex::Treatment_AMs->new();
! # testing the am_fk attribute method
! $obj->am_fk(555);
! result ($obj->am_fk() == 555);
# testing the tl_fk attribute method
--- 32,38 ----
my $obj = Bio::Genex::Treatment_AMs->new();
! # testing the pba_fk attribute method
! $obj->pba_fk(555);
! result ($obj->pba_fk() == 555);
# testing the tl_fk attribute method
***************
*** 40,46 ****
result ($obj->tl_fk() == 555);
! # testing the am_obj attribute method
! $obj->am_obj(555);
! result ($obj->am_obj() == 555);
# testing the tl_obj attribute method
--- 40,46 ----
result ($obj->tl_fk() == 555);
! # testing the pba_obj attribute method
! $obj->pba_obj(555);
! result ($obj->pba_obj() == 555);
# testing the tl_obj attribute method
|
|
From: <jas...@us...> - 2002-11-07 14:49:13
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv11051/Genex/scripts
Modified Files:
xml2sql.pl.in
Log Message:
* scripts/xml2sql.pl.in (Repository):
fixed call to xml2sql() to add DB handle
Index: xml2sql.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/xml2sql.pl.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** xml2sql.pl.in 18 Sep 2002 21:07:08 -0000 1.3
--- xml2sql.pl.in 7 Nov 2002 14:49:10 -0000 1.4
***************
*** 10,13 ****
--- 10,14 ----
use blib;
use XML::Xerces;
+ use Bio::Genex::Connect;
use Bio::Genex::XMLUtils;
use Getopt::Long;
***************
*** 31,36 ****
}
my ($sql,$all_tables,$audit_tables,$all_views)
! = Bio::Genex::XMLUtils::xml2sql(@ARGV);
printf STDERR "Created tables: %s\n", join(', ', @{$all_tables});
--- 32,38 ----
}
+ my $dbh = Bio::Genex::Connect->new();
my ($sql,$all_tables,$audit_tables,$all_views)
! = Bio::Genex::XMLUtils::xml2sql($dbh,@ARGV);
printf STDERR "Created tables: %s\n", join(', ', @{$all_tables});
|
|
From: <jas...@us...> - 2002-11-07 14:48:51
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv10724/Genex/scripts
Modified Files:
mbad-insert.pl.in
Log Message:
* scripts/mbad-insert.pl.in (Repository):
added die if not all features were found
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** mbad-insert.pl.in 20 Oct 2002 14:52:25 -0000 1.2
--- mbad-insert.pl.in 7 Nov 2002 14:48:48 -0000 1.3
***************
*** 219,224 ****
#### Verify that the input file exists
! my $file = $ARGV[0] or die "No input files\n$USAGE";
! foreach $file (@ARGV) {
open(IN,$file)
or $dbh->error(@error_args,
--- 219,226 ----
#### Verify that the input file exists
! die "No input files\n$USAGE"
! unless scalar @ARGV;
!
! foreach my $file (@ARGV) {
open(IN,$file)
or $dbh->error(@error_args,
***************
*** 231,234 ****
--- 233,238 ----
my $name = $file;
$name =~ s|.*/||;
+
+ # we need a better way to set the name FIXME
my @args = (name=>$name,
ro_groupname_obj=>$ro_group,
***************
*** 282,289 ****
}
}
$insert_sth->finish();
- print STDERR "Found $count data lines\n" if $OPTIONS{debug};
print STDERR "Finished\n";
--- 286,297 ----
}
+ $dbh->error(@error_args,
+ no_errstr=>1,
+ message=>"Didn't find the proper number of features. Was expecting " . scalar keys %features . ", but found $count")
+ unless scalar keys %features == $count;
+ print STDERR "Found $count data lines\n" if $OPTIONS{debug};
}
$insert_sth->finish();
print STDERR "Finished\n";
|
|
From: <jas...@us...> - 2002-11-07 14:45:50
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv8181/Genex/scripts
Modified Files:
group-insert.pl.in
Log Message:
* scripts/group-insert.pl.in (Repository):
implemented all documented options
Index: group-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/group-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** group-insert.pl.in 13 Oct 2002 07:22:45 -0000 1.1
--- group-insert.pl.in 7 Nov 2002 14:45:47 -0000 1.2
***************
*** 13,17 ****
use strict;
! use blib;
use Carp;
use Getopt::Long;
--- 13,17 ----
use strict;
! # use blib;
use Carp;
use Getopt::Long;
***************
*** 29,34 ****
--- 29,37 ----
my $rc = GetOptions(\%OPTIONS,
'group=s',
+ 'ro_groupname=s',
+ 'rw_groupname=s',
'username=s',
'password=s',
+ 'description=s',
'dbname=s',
'debug',
***************
*** 92,97 ****
if exists $OPTIONS{description};
! $g->insert_db($dbh);
! print "Finished\n";
if ($OPTIONS{debug}) {
--- 95,101 ----
if exists $OPTIONS{description};
! my $pk = $g->insert_db($dbh);
! print STDOUT "$pk\n";
! print STDERR "Finished\n";
if ($OPTIONS{debug}) {
|
|
From: <jas...@us...> - 2002-11-07 14:45:00
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv7650/Genex/scripts
Modified Files:
create_genex_db.pl.in
Log Message:
* scripts/create_genex_db.pl.in (Repository):
fixed call to xml2sql() to add DB handle
all grants now done here and not in xml2sql()
better USAGE
Index: create_genex_db.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_db.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** create_genex_db.pl.in 20 Oct 2002 21:15:35 -0000 1.5
--- create_genex_db.pl.in 7 Nov 2002 14:44:57 -0000 1.6
***************
*** 28,37 ****
my $USAGE = <<"EOU";
! usage: $0 [required flags] file1 ...
! required flags:
--dbname=name : the name of the DB to create
--functions=file : the path to the SQL functions XML file
--username=name : the DB username to login as
--password=word : the DB password to login with
--help : print this message
EOU
--- 28,39 ----
my $USAGE = <<"EOU";
! usage: $0 [required args] [optional args] file1 ...
! required args:
--dbname=name : the name of the DB to create
--functions=file : the path to the SQL functions XML file
--username=name : the DB username to login as
--password=word : the DB password to login with
+ optional args:
+ --admin_db=name : the DB to connect to in order to create the new DB
--help : print this message
EOU
***************
*** 125,129 ****
PASSWORD=>$OPTIONS{password});
! my ($script,$all_tables,$trigger_tables) = xml2sql(@ARGV);
print STDERR "\n\n\tCreating Tables ...\n\n";
--- 127,131 ----
PASSWORD=>$OPTIONS{password});
! my ($script,$all_tables,$trigger_tables,$views) = xml2sql($dbh,@ARGV);
print STDERR "\n\n\tCreating Tables ...\n\n";
***************
*** 134,148 ****
if $dbh->err;
! # create the SQL for the permissions on the Sessions table
! my $sessions = 'Sessions';
! my $sql = $dbh->create_grant_sql(TABLE=>$sessions,
USERS=>['PUBLIC'],
! PERMS=>['ALL'],
);
$dbh->do($sql);
$dbh->error(@error_args,
sql=>$sql,
! message=>'Adding Permissions to the $sessions table')
if $dbh->err;
--- 136,176 ----
if $dbh->err;
! my $sql;
! print STDERR "\n\n\nSetting Permissions on Tables ...\n\n";
! foreach my $table (@{$all_tables}) {
! my @perms = qw(ALL);
! $sql .= $dbh->create_grant_sql(TABLE=>$table,
! USERS=>['genex'],
! PERMS=>\@perms,
! );
! if ($table eq 'Sessions') {
! @perms = qw(INSERT SELECT UPDATE DELETE);
! $sql .= $dbh->create_grant_sql(TABLE=>$table,
! USERS=>['PUBLIC'],
! PERMS=>\@perms,
! );
! }
! }
!
! $dbh->do($sql);
! $dbh->error(@error_args,
! sql=>$sql,
! message=>'Adding Permissions to tables')
! if $dbh->err;
!
! print STDERR "\n\n\nSetting Permissions on Views ...\n\n";
! $sql = '';
! foreach my $view (@{$views}) {
! $sql .= $dbh->create_grant_sql(TABLE=>$view,
USERS=>['PUBLIC'],
! PERMS=>[qw(SELECT INSERT UPDATE DELETE)],
);
+
+ }
$dbh->do($sql);
$dbh->error(@error_args,
sql=>$sql,
! message=>'Adding Permissions to the views')
if $dbh->err;
|
|
From: <jas...@us...> - 2002-11-07 14:43:37
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv7048/Genex/scripts
Added Files:
experimentset-create.pl.in fix-als.pl
Log Message:
new apps
--- NEW FILE: experimentset-create.pl.in ---
%%START_PERL%%
#
# experimentset-create.pl:
# script for creating a new experiment set in GeneX
#
# author: Jason E. Stewart (ja...@op...)
#
# Copyright 2002 Open Informatics
#
my $VERSION = '$Id: experimentset-create.pl.in,v 1.1 2002/11/07 14:43:33 jason_e_stewart Exp $ ';
use strict;
# use blib;
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::ExperimentSet;
my %OPTIONS;
$OPTIONS{dbname} = '%%DB_NAME%%';
$OPTIONS{ro_groupname} = '%%GENEX_PUBLIC_GROUP%%';
$OPTIONS{rw_groupname} = '%%GENEX_SUPERUSER_GROUP%%';
my $rc = GetOptions(\%OPTIONS,
'name=s',
'ro_groupname=s',
'rw_groupname=s',
'biology_description=s',
'analysis_description=s',
'treatment_type=s',
'quantity_series_type=s',
'archive_bundle_ref=s',
'username=s',
'password=s',
'dbname=s',
'debug',
);
my $USAGE = <<"EOU";
usage: $0 [required params] [options]
require params:
--name=string : name of the experiment
--username=name : name of user to login to DB as
--password=word : password to use for DB login
options:
--dbname=name : name of DB to use (defaults to '%%DB_NAME%%')
--ro_groupname=name : name of RO group (defaults to '%%GENEX_PUBLIC_GROUP%%')
--rw_groupname=name : name of RW group (defaults to '%%GENEX_SUPERUSER_GROUP%%')
--biology_description=text : the biological question being addressed
--analysis_description=text : the analysis performed
--treatment_type=type : taken from CV
--quantity_series_type=type : taken from CV
--archive_bundle_ref=path : the file path to the archival data
--debug : rollback instead of commit
--help : this message
EOU
die "Bad option: $rc\n$USAGE" unless $rc;
die "$USAGE" if exists $OPTIONS{help};
die "Must specify --username\n$USAGE"
unless exists $OPTIONS{username};
die "Must specify --password\n$USAGE"
unless exists $OPTIONS{password};
die "Must specify --name\n$USAGE"
unless exists $OPTIONS{name};
my $dbh = Bio::Genex::Connect->new(USER=>$OPTIONS{username},
PASSWORD=>$OPTIONS{password},
DBNAME=>$OPTIONS{dbname},
TRANSACTION=>1,
);
die "Bad username or password"
unless defined $dbh;
my @error_args = (caller=>$0);
# prefetch the objects we need
my ($ro_group) = Bio::Genex::GroupSec->get_objects($dbh,
$OPTIONS{ro_groupname});
$dbh->error(@error_args,
msg=>"Group $OPTIONS{ro_groupname} doesn't exist in DB",
) unless defined $ro_group;
my ($rw_group) = Bio::Genex::GroupSec->get_objects($dbh,
$OPTIONS{rw_groupname});
$dbh->error(@error_args,
msg=>"Group $OPTIONS{rw_groupname} doesn't exist in DB",
) unless defined $rw_group;
# get rid of the non-object options
delete @OPTIONS{qw(ro_groupname
rw_groupname
username
password
dbname
debug)
};
my $es_db = Bio::Genex::ExperimentSet->new(ro_groupname_obj=>$ro_group,
rw_groupname_obj=>$rw_group,
%OPTIONS,
);
$es_db->insert_db($dbh);
print "Finished\n";
if ($OPTIONS{debug}) {
$dbh->rollback();
} else {
$dbh->commit();
}
$dbh->disconnect();
exit(0);
--- NEW FILE: fix-als.pl ---
#!/usr/local/bin/perl5.7.2 -w
use strict;
use XML::Xerces;
use Getopt::Long;
use blib;
use Bio::Genex qw($SU_USERNAME $SU_PASSWORD $DBNAME dbi_error error);
use Bio::Genex::DBUtils qw(:CREATE);
use vars qw(%ALS %USF);
my %OPTIONS;
my $rc = GetOptions(\%OPTIONS,
'usf=s',
'als=s',
);
my $USAGE = <<"EOU";
usage: $0 --als=file_name
EOU
die "Bad option: $rc\n$USAGE" unless $rc;
die "Must specify --als\n$USAGE" unless exists $OPTIONS{als};
package ALS_DocumentHandler;
use strict;
use vars qw(@ISA);
@ISA = qw(XML::Xerces::PerlDocumentHandler);
sub start_element {
my ($self,$element,$attr_list) = @_;
return unless $element eq 'array_layout_spot';
my %hash = $attr_list->to_hash();
$::ALS{$hash{spot_identifier}} = $::USF{$hash{sequence_feature_id}};
}
package main;
# open up a writeable connection
my $dbh = Bio::Genex::current_connection(DBNAME=>$OPTIONS{dbname},
USER => $SU_USERNAME,
PASSWORD => $SU_PASSWORD,
TRANSACTION => 1,
);
my @error_args = (caller=>$0,dbh=>$dbh);
my $sql = <<SQL;
SELECT sf_name,sf_pk
FROM sequencefeature
SQL
my $ref = $dbh->selectall_arrayref($sql)
or dbi_error(@error_args,
message=>"Couldn't select sequence features",
sql=>$sql);
foreach (@{$ref}) {
$USF{$_->[0]} = $_->[1];
}
my $doc_handler = ALS_DocumentHandler->new();
my $SAX = XML::Xerces::SAXParser->new();
$SAX->setDocumentHandler($doc_handler);
# add an error handler so we don't get Abort's with no message
my $err_handler = XML::Xerces::PerlErrorHandler->new();
$SAX->setErrorHandler($err_handler);
my $input_source;
eval {
$input_source = XML::Xerces::LocalFileInputSource->new($OPTIONS{als});
};
error(caller=> __PACKAGE__ . '::xml2db',
message=>"Couldn't create input source: " . $@->getMessage())
if $@;
# turn on the parser and let the handler do the work
eval {
$SAX->parse($input_source);
};
error(caller=> __PACKAGE__ . '::xml2db',
message=>"Couldn't parse input source: " . $@->getMessage())
if $@;
$sql = create_update_sql($dbh,
TABLE=>'Feature',
SET=>{'sf_fk'=>'?'},
WHERE=>'spot_identifier=?',
);
my $sth = $dbh->prepare($sql) ||
dbi_error(@error_args,
sql=>$sql,
message=>"Couldn't prepare update sql"
);
print STDERR "Found ", scalar keys %ALS, " Features\n";
print STDERR "SQL: $sql\n";
foreach (keys %ALS) {
$sth->execute($ALS{$_},$_) ||
dbi_error(@error_args,
sql=>$sql,
sth=>$sth,
message=>"Couldn't execute update sql for spot: $_"
);
}
print STDERR "Finished\n";
$dbh->commit();
# $dbh->rollback();
$dbh->disconnect();
exit(0);
|
|
From: <jas...@us...> - 2002-11-07 14:42:37
|
Update of /cvsroot/genex/genex-server/Genex/XMLUtils
In directory usw-pr-cvs1:/tmp/cvs-serv6513a/Genex/XMLUtils
Modified Files:
XMLUtils.pm.in
Log Message:
* XMLUtils/XMLUtils.pm.in (Repository):
started using create_view_sql()
removed all GRANT's
Index: XMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/XMLUtils/XMLUtils.pm.in,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** XMLUtils.pm.in 15 Oct 2002 14:52:55 -0000 1.25
--- XMLUtils.pm.in 7 Nov 2002 14:42:34 -0000 1.26
***************
*** 305,309 ****
}
! =item ($sql,\@all_tables,\@audit_tables,\@all_views = xml2sql(@file_name_list);
Description: A method for converting an XML description of a relation
--- 305,309 ----
}
! =item ($sql,\@all_tables,\@audit_tables,\@all_views = xml2sql($dbh,@file_name_list);
Description: A method for converting an XML description of a relation
***************
*** 321,326 ****
sub xml2sql {
! my (@files,$MASTER_SEQ) = @_;
! $MASTER_SEQ = 'GENEX_ID_SEQ' unless defined $MASTER_SEQ;
my @defer_fkeys;
--- 321,327 ----
sub xml2sql {
! my ($dbh,@files) = @_;
! assert_dbh($dbh);
! my $MASTER_SEQ = 'GENEX_ID_SEQ';
my @defer_fkeys;
***************
*** 531,556 ****
# if this table or view has security the selectable view we create
# will enforce it in the where clause, otherwise it's public
- my $WHERE = '';
- my $from = qq[$table_name];
- if ($has_ro_groupname) {
- $WHERE = 'WHERE ro_groupname=GroupLink.groupname AND GroupLink.username=user()';
- $from .= ', GroupLink'
- unless $table_name eq 'GroupLink';
- }
my @inherited_columns;
if ($inherits_from ne 'none') {
@inherited_columns = $docs{$inherits_from}->getElementsByTagName('column');
}
- my $columns = join(",\n", map {$table_name . '."' . $_->getAttribute('name'). '"'}
- @columns, @inherited_columns);
my $view = "$ {table_name}_view";
! my $sql = <<SQL;
! CREATE VIEW $view AS
! SELECT $columns
! FROM $from
! $WHERE;
- GRANT SELECT ON $view TO PUBLIC;
- SQL
# we defer creation of the view until after all tables are created
# this way we don't need to know when GroupLink is created
--- 532,554 ----
# if this table or view has security the selectable view we create
# will enforce it in the where clause, otherwise it's public
my @inherited_columns;
if ($inherits_from ne 'none') {
@inherited_columns = $docs{$inherits_from}->getElementsByTagName('column');
}
my $view = "$ {table_name}_view";
! my @from = ($table_name);
! my @args = (VIEW=>$view,
! COLUMNS=>[map {[$table_name,$_->getAttribute('name')]}
! @columns, @inherited_columns],
! );
! if ($has_ro_groupname) {
! push(@args,WHERE=>'ro_groupname=GroupLink.groupname AND GroupLink.username=user()');
! push(@from,'GroupLink')
! unless $table_name eq 'GroupLink';
! }
! push(@args,FROM=>\@from);
!
! my $sql = $dbh->create_view_sql(@args);
# we defer creation of the view until after all tables are created
# this way we don't need to know when GroupLink is created
***************
*** 572,579 ****
push(@column_sql,qq[CREATE INDEX $attrs{name} on $table_name ( "$attrs{column_id}" );]);
}
-
- # now we only grant priveleges to genex
- push(@column_sql,qq[GRANT ALL on $table_name to genex;])
- unless $table->getAttribute('type') eq 'VIEW';
$output .= join("\n", @column_sql) . "\n";
--- 570,573 ----
|
|
From: <jas...@us...> - 2002-11-07 14:41:25
|
Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv5498/Genex
Modified Files:
Genex.pm.in
Log Message:
* Genex.pm.in (Repository):
modified version format to be recognized
new version (2.7.20021106)
Index: Genex.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Genex.pm.in,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** Genex.pm.in 13 Oct 2002 05:58:26 -0000 1.47
--- Genex.pm.in 7 Nov 2002 14:41:20 -0000 1.48
***************
*** 58,62 ****
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.0-2002-10-12';
# Preloaded methods go here.
--- 58,62 ----
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20021106';
# Preloaded methods go here.
|
|
From: <jas...@us...> - 2002-11-07 14:40:13
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv4751/G2G/mason
Modified Files:
group-maint.html.in
Log Message:
* G2G/mason/group-maint.html.in (Repository):
fixed error output
Index: group-maint.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/group-maint.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** group-maint.html.in 20 Oct 2002 13:45:12 -0000 1.1
--- group-maint.html.in 7 Nov 2002 14:40:10 -0000 1.2
***************
*** 1,5 ****
% if (($response_page eq "NEW")) {
<center>
! <h1>Group Member Assicoation Modification</h1>
<form action="<% $action %>"><br></br>
<br></br>
--- 1,5 ----
% if (($response_page eq "NEW")) {
<center>
! <h1>Group Member Maintenance</h1>
<form action="<% $action %>"><br></br>
<br></br>
***************
*** 10,14 ****
<tbody>
<tr>
! <td valign="top">Which Group would you like to add or
remove members?<br></br>
</td>
--- 10,14 ----
<tbody>
<tr>
! <td valign="top">To which Group would you like to add or
remove members?<br></br>
</td>
***************
*** 41,49 ****
<br></br>
! % if ($response_page eq "BadGroup"){
! <h3><font color="red">You chose an invalid group to
! associate this user with</font>
</h3>
! % }
<b>Check/Uncheck the Users you wish to be associated with/dissociated from this group.</b>
--- 41,49 ----
<br></br>
! % if ($response_page eq "BadGroup") {
! <h3><font color="red"><em><% $groupname %></em> is an invalid groupname</font>
</h3>
!
! % } else {
<b>Check/Uncheck the Users you wish to be associated with/dissociated from this group.</b>
***************
*** 74,77 ****
--- 74,79 ----
</form>
</center>
+ % }
+
% }
|
|
From: <jas...@us...> - 2002-11-07 14:39:28
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv4282/G2G/mason
Modified Files:
index.html
Log Message:
new files
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/index.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** index.html 20 Oct 2002 13:58:32 -0000 1.3
--- index.html 7 Nov 2002 14:39:24 -0000 1.4
***************
*** 15,18 ****
--- 15,21 ----
<li><a href="array-design.html">array-design.html</a></li>
<li><a href="bioassay.html">bioassay.html</a></li>
+ <li><a
+ href="experimentset-create.html">experimentset-create.html</a></li>
+ <li><a href="group-create.html">group-create.html</a></li>
</ul>
<%attr>
|
|
From: <jas...@us...> - 2002-11-07 14:39:08
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv4125/G2G/mason
Modified Files:
kill-cookie.html
Log Message:
removed NCGR logo
Index: kill-cookie.html
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/kill-cookie.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** kill-cookie.html 11 Oct 2002 01:15:24 -0000 1.2
--- kill-cookie.html 7 Nov 2002 14:39:05 -0000 1.3
***************
*** 2,17 ****
<head><title><% $name %></title></head>
<body bgcolor=white>
- <table border=0 cellpadding=0 cellspacing=0>
- <tr>
- <td align=right valign=top>
- <img src="http://amadeus/genex2/genex/graphics/genexlogo.jpg">
- </td>
- <!-- this <td> is a kludge to align the two images w/o the NCGR
- logo -->
- <td align=left valign=middle><p> </p><br>
- <img src="http://amadeus/genex2/genex/graphics/databaseserver.jpg">
- </td>
- </tr>
- </table>
<h2>You GeneX cookie has been eradicated</h2>
</body>
--- 2,5 ----
|
|
From: <jas...@us...> - 2002-11-07 14:38:51
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv3918/G2G/mason
Added Files:
experimentset-create.html.in group-create.html.in
Log Message:
new
--- NEW FILE: experimentset-create.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($submit) {
<h2><% $data %></h2>
% } else {
<h2>Read Group</h2>
<p>Choose the <b>read group</b> that will be given to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Write Group</h2>
<p>Choose the <b>write group</b> that will be given to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Name</h2>
<p>Choose a <b>Name</b> for your experiment. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Name</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<input type="text" name="exp_name" size="65" maxlength="128">
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Treatment Type</h2>
<p>Choose the <b>Treatment Type</b> that describes the type of
experiment you are conducting.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Treatment Type</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"treatment_type",
array_ref=>\@treatment_types &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Quantity Series Type</h2>
<p>If the <b>Treatment Type</b> you chose was <b>Quantity
Series</b> then specify what type of series it is. This is not
applicable for other treatment types</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Quantity Series Type</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"quantity_series_type",
array_ref=>\@quantity_series_types &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Biology Description</h2>
<p>Describe the biological basis for the experiment. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Biology Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="bio_desc" rows="5" cols="65"></textarea>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Analysis Description</h2>
<p>Describe the analysis performed in the experiment. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Analysis Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="anal_desc" rows="5" cols="65"></textarea>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Create ExperimentSet" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$read_group => ''
$write_group => ''
$anal_desc => ''
$bio_desc => ''
$treatment_type => ''
$quantity_series_type => ''
$exp_name => ''
</%args>
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/experimentset-create.html'
name=>'GeneX DB ExperimentSet Creation Page'
path=>'%%GENEX_WORKSPACE_URL%%/experimentset-create.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::ExperimentSet;
use Bio::Genex::ControlledVocab;
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('ExperimentSet');
my @groups;
my $no_type = 'NONE';
my @treatment_types = ([$no_type,$no_type]);
my @quantity_series_types = ([$no_type,$no_type]);
my $data = '';
if ($submit) {
$exp_name =~ s/\'//;
my $cmd = '%%GENEX_BIN_DIR%%/experimentset-create.pl';
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
"--name='$exp_name'",
);
if ($bio_desc) {
$bio_desc =~ s/\'//;
push(@args,"--biology_description='$bio_desc'");
}
if ($anal_desc) {
$anal_desc =~ s/\'//;
push(@args,"--analysis_description='$anal_desc'");
}
if ($treatment_type ne $no_type) {
push(@args,"--treatment_type=$treatment_type");
}
if ($quantity_series_type ne $no_type) {
push(@args,"--quantity_series_type=$quantity_series_type");
}
my @pks;
my $command = join(' ', $cmd, @args);
my $pk = `$command`;
if ($?) {
$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = <$!></p>
EOE
} else {
push(@pks,$pk);
$data = "@pks";
}
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
my @tt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
column=>'vocab_name',
value=>'ES_TreatmentType',
);
foreach my $tt_db (@tt_dbs) {
push(@treatment_types,[$tt_db->term_string,$tt_db->term_string]);
}
my @qst_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
column=>'vocab_name',
value=>'ES_QuantitySeriesType',
);
foreach my $qst_db (@qst_dbs) {
push(@quantity_series_types,[$qst_db->term_string,$qst_db->term_string]);
}
}
</%init>
--- NEW FILE: group-create.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($submit) {
<h2><% $data %></h2>
% } else {
<h2>Read Group</h2>
<p>Choose the <b>read group</b> that controls who can see the
information of this group.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Write Group</h2>
<p>Choose the <b>write group</b> that controls who can modify
the information of this group.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Name</h2>
<p>Choose a <b>Name</b> for your group. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Name</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<input type="text" name="group_name" size="65" maxlength="128">
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Description</h2>
<p>Describe the group. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="description" rows="5" cols="65"></textarea>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Create Group" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$read_group => ''
$write_group => ''
$description => ''
$group_name => ''
</%args>
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/group-create.html'
name=>'GeneX DB Group Creation Page'
path=>'%%GENEX_WORKSPACE_URL%%/group-create.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('GroupSec');
my @groups;
my $data = '';
if ($submit) {
$group_name =~ s/\'//;
my $cmd = '%%GENEX_BIN_DIR%%/group-insert.pl';
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
"--group='$group_name'",
);
if ($description) {
$description =~ s/\'//;
push(@args,"--description='$description'");
}
my @pks;
my $command = join(' ', $cmd, @args);
my $pk = `$command`;
if ($?) {
$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = <$!></p>
EOE
} else {
$data = <<EOT;
<p>You can now populate the group <a
href="%%GENEX_WORKSPACE_URL%%/group-maint.html?submitted=true&groupname=$pk">here</a></p>
EOT
}
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
}
</%init>
|
|
From: <jas...@us...> - 2002-11-07 14:38:03
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv3422/G2G/mason
Modified Files:
data-loader.html.in
Log Message:
* G2G/mason/data-loader.html.in (Repository):
removed debugging cruft
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/data-loader.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** data-loader.html.in 20 Oct 2002 13:45:12 -0000 1.1
--- data-loader.html.in 7 Nov 2002 14:37:58 -0000 1.2
***************
*** 205,210 ****
"--es_pk=$es_pk",
"--ad_pk=$ad_pk",
! # "--fe_sw_pk=$fe_sw_pk",
! "--fe_sw_pk=3",
);
my @pks;
--- 205,209 ----
"--es_pk=$es_pk",
"--ad_pk=$ad_pk",
! "--fe_sw_pk=$fe_sw_pk",
);
my @pks;
|
|
From: <jas...@us...> - 2002-11-07 14:37:16
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory usw-pr-cvs1:/tmp/cvs-serv2997/DB/xml
Modified Files:
ExperimentSet.xml
Log Message:
* DB/xml/ExperimentSet.xml (Repository):
removed creation_data - it is redundant with audit info
Index: ExperimentSet.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ExperimentSet.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ExperimentSet.xml 20 Oct 2002 14:03:05 -0000 1.6
--- ExperimentSet.xml 7 Nov 2002 14:37:13 -0000 1.7
***************
*** 90,98 ****
type="datetime"
comment=""/>
- <column name="creation_date"
- full_name="Creation Date"
- not_null="true"
- type="datetime"
- comment=" indicates when the experiment was created"/>
<column name="local_accession"
full_name="Local Accession Number"
--- 90,93 ----
|
|
From: <jas...@us...> - 2002-11-07 14:36:15
|
Update of /cvsroot/genex/genex-server/DB/curated_data In directory usw-pr-cvs1:/tmp/cvs-serv2103/DB/curated_data Modified Files: 1200-mangle.txt Log Message: missing END tag Index: 1200-mangle.txt =================================================================== RCS file: /cvsroot/genex/genex-server/DB/curated_data/1200-mangle.txt,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** 1200-mangle.txt 15 Oct 2002 19:21:41 -0000 1.1 --- 1200-mangle.txt 7 Nov 2002 14:36:10 -0000 1.2 *************** *** 5412,5413 **** --- 5412,5414 ---- 5375 14 4 8 11 reporter05295 403.451752 117.776596 271.68515 166.662659 2.420769 2283.482666 344.287231 1049.236328 335.958527 6.796918 5376 14 4 8 12 reporter05296 780.031128 130.627655 482.258331 190.472534 4.095242 1952.742432 278.664886 996.180115 264.244812 7.389899 + End Data |
