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From: <jas...@us...> - 2003-09-22 15:03:50
|
Update of /cvsroot/genex/genex-www/content In directory sc8-pr-cvs1:/tmp/cvs-serv8923 Modified Files: genex-2-schema.ssi Log Message: new Index: genex-2-schema.ssi =================================================================== RCS file: /cvsroot/genex/genex-www/content/genex-2-schema.ssi,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** genex-2-schema.ssi 22 Sep 2003 15:01:00 -0000 1.6 --- genex-2-schema.ssi 22 Sep 2003 15:03:46 -0000 1.7 *************** *** 14,18 **** <li><a href="genex-2/Audit.html">Audit.html</a> <li><a href="genex-2/BlastHits.html">BlastHits.html</a> ! <li><a href="genex-2/ChangeLog.html">Contact.html</a> <li><a href="genex-2/Chromosome.html">Chromosome.html</a> <li><a href="genex-2/Citation.html">Citation.html</a> --- 14,18 ---- <li><a href="genex-2/Audit.html">Audit.html</a> <li><a href="genex-2/BlastHits.html">BlastHits.html</a> ! <li><a href="genex-2/ChangeLog.html">ChangeLog.html</a> <li><a href="genex-2/Chromosome.html">Chromosome.html</a> <li><a href="genex-2/Citation.html">Citation.html</a> |
|
From: <jas...@us...> - 2003-09-22 15:01:06
|
Update of /cvsroot/genex/genex-www/content In directory sc8-pr-cvs1:/tmp/cvs-serv8360 Modified Files: genex-2-schema.ssi Log Message: new Index: genex-2-schema.ssi =================================================================== RCS file: /cvsroot/genex/genex-www/content/genex-2-schema.ssi,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** genex-2-schema.ssi 11 Jun 2003 04:39:53 -0000 1.5 --- genex-2-schema.ssi 22 Sep 2003 15:01:00 -0000 1.6 *************** *** 14,21 **** <li><a href="genex-2/Audit.html">Audit.html</a> <li><a href="genex-2/BlastHits.html">BlastHits.html</a> <li><a href="genex-2/Chromosome.html">Chromosome.html</a> <li><a href="genex-2/Citation.html">Citation.html</a> <li><a href="genex-2/Contact.html">Contact.html</a> - <li><a href="genex-2/ContactType.html">ContactType.html</a> <li><a href="genex-2/ControlledVocab.html">ControlledVocab.html</a> <li><a href="genex-2/DerivedBioAssay.html">DerivedBioAssay.html</a> --- 14,21 ---- <li><a href="genex-2/Audit.html">Audit.html</a> <li><a href="genex-2/BlastHits.html">BlastHits.html</a> + <li><a href="genex-2/ChangeLog.html">Contact.html</a> <li><a href="genex-2/Chromosome.html">Chromosome.html</a> <li><a href="genex-2/Citation.html">Citation.html</a> <li><a href="genex-2/Contact.html">Contact.html</a> <li><a href="genex-2/ControlledVocab.html">ControlledVocab.html</a> <li><a href="genex-2/DerivedBioAssay.html">DerivedBioAssay.html</a> *************** *** 28,32 **** <li><a href="genex-2/FeatureExtractionSoftware.html">FeatureExtractionSoftware.html</a> <li><a href="genex-2/G2G.html">G2G.html</a> - <li><a href="genex-2/GenexAdmin.html">GenexAdmin.html</a> <li><a href="genex-2/GroupLink.html">GroupLink.html</a> <li><a href="genex-2/GroupSec.html">GroupSec.html</a> --- 28,31 ---- *************** *** 50,53 **** --- 49,53 ---- <li><a href="genex-2/QuantitationTypeDimension.html">QuantitationTypeDimension.html</a> <li><a href="genex-2/Reporter.html">Reporter.html</a> + <li><a href="genex-2/Role.html">Role.html</a> <li><a href="genex-2/SF_ExternalDBLink.html">SF_ExternalDBLink.html</a> <li><a href="genex-2/Sample.html">Sample.html</a> *************** *** 57,60 **** --- 57,61 ---- <li><a href="genex-2/Software.html">Software.html</a> <li><a href="genex-2/Species.html">Species.html</a> + <li><a href="genex-2/TableDef.html">TableDef.html</a> <li><a href="genex-2/UserSec.html">UserSec.html</a> |
|
From: <jas...@us...> - 2003-09-22 14:45:18
|
Update of /cvsroot/genex/genex-www/genex-2
In directory sc8-pr-cvs1:/tmp/cvs-serv5269
Added Files:
ChangeLog.html Role.html Scratch.html TableDef.html
Log Message:
new
--- NEW FILE: ChangeLog.html ---
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>
GeneX-2.0 DB: ChangeLog Table
</title>
</head>
<body bgcolor="#FFD78F">
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="3">
GeneX-2.0 DB: ChangeLog Table
</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Table Type</th><th>Inherits</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<th>DATA</th><td><a href="none.html">none</a></td><th></th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="5">Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>audit_fk</td><td>Audit</td><td>int</td><td>true</td><td>The audit entry when this data was last modified, it will be null if it is the creation event. We set the write_sql attribute to be false so that Postgres doesn't put a constraint on this column. It is automatically set by a trigger. </td>
</tr>
<tr bgcolor="#D8E4F7">
<td>cl_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td>
</tr>
<tr bgcolor="#D8E4F7">
<td>description</td><td>Description</td><td>text</td><td>false</td><td></td>
</tr>
<tr bgcolor="#D8E4F7">
<td>version_date</td><td>Date of Version Creation</td><td>datetime</td><td>false</td><td></td>
</tr>
<tr bgcolor="#D8E4F7">
<td>version_number</td><td>DB Version</td><td>char128</td><td>false</td><td></td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Primary Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>cl_pk</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="4">Foreign Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Unique Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Names</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="2">Index Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Name</th><th>Column Name</th>
</tr>
</table>
<br>
</body>
</html>
--- NEW FILE: Role.html ---
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>
GeneX-2.0 DB: Role Table
</title>
</head>
<body bgcolor="#FFD78F">
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="3">
GeneX-2.0 DB: Role Table
</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Table Type</th><th>Inherits</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<th>SUBSET</th><td><a href="none.html">none</a></td><th> Role is a generic association table that enables different DB entries to be assigned Roles. Roles enable applications to filter their actions. Roles can be assigned not only to users, but to DB tables, or data entries such as Contacts.</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="5">Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>other_fk</td><td>Other Foreign Key</td><td>int</td><td>true</td><td>This fkey points to the DB entry to which this role is assigned. It is not listed as a fkey constraint, because it can point to any table in the DB.</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>role_name</td><td>Role Name</td><td>char128</td><td>true</td><td>A controlled vocabulary</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>table_name</td><td>Table Name</td><td>char32</td><td>true</td><td>The table to which the entry specified by other_fk belongs.</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Primary Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="4">Foreign Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Unique Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Names</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>other_fk role_name</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="2">Index Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Name</th><th>Column Name</th>
</tr>
</table>
<br>
</body>
</html>
--- NEW FILE: Scratch.html ---
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>
GeneX-2.0 DB: Scratch Table
</title>
</head>
<body bgcolor="#FFD78F">
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="3">
GeneX-2.0 DB: Scratch Table
</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Table Type</th><th>Inherits</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<th>DATA</th><td><a href="none.html">none</a></td><th>The Scratch table defines the user scratch space used for storing intermediate analysis results before they are moved into the DerivedBioAssayData table</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="5">Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>bool1</td><td>Bool 1</td><td>bool</td><td>false</td><td>The first variable boolean column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>dba_fk</td><td>Derived BioAssay</td><td>int</td><td>true</td><td>The Derived BioAssay to which this data belongs</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>float1</td><td>Float 1</td><td>float</td><td>false</td><td>The first variable floating point column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>float2</td><td>Float 2</td><td>float</td><td>false</td><td>The second variable floating point column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>float3</td><td>Float 3</td><td>float</td><td>false</td><td>The third variable floating point column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>float4</td><td>Float 4</td><td>float</td><td>false</td><td>The fourth variable floating point column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>int1</td><td>Int 1</td><td>int</td><td>false</td><td>The first variable integer column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>int2</td><td>Int 2</td><td>int</td><td>false</td><td>The second variable integer column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>int3</td><td>Int 3</td><td>int</td><td>false</td><td>The third variable integer column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>int4</td><td>Int 4</td><td>int</td><td>false</td><td>The fourth variable integer column</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>spot_identifier</td><td>Spot Identifier</td><td>char128</td><td>true</td><td>The identifier used to identify a spot from an array</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Primary Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="4">Foreign Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>dba_fk</td><td><a href="DerivedBioAssay.html">DerivedBioAssay</a></td><td>dba_pk</td><td>ONE_TO_ONE</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Unique Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Names</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>spot_identifier dba_fk</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="2">Index Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Name</th><th>Column Name</th>
</tr>
</table>
<br>
</body>
</html>
--- NEW FILE: TableDef.html ---
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>
GeneX-2.0 DB: TableDef Table
</title>
</head>
<body bgcolor="#FFD78F">
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="3">
GeneX-2.0 DB: TableDef Table
</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Table Type</th><th>Inherits</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<th>DATA</th><td><a href="none.html">none</a></td><th>The TableDef table defines information about individual tables in the DB, such as their abbreviated names and their API names.</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="5">Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>api_name</td><td>API Name</td><td>char32</td><td>true</td><td>The name of the table in the programming language API, this usually contains mixed case, and will often remove underscores, etc.</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>audit_fk</td><td>Audit</td><td>int</td><td>true</td><td>The audit entry when this data was last modified, it will be null if it is the creation event. We set the write_sql attribute to be false so that Postgres doesn't put a constraint on this column. It is automatically set by a trigger. </td>
</tr>
<tr bgcolor="#D8E4F7">
<td>description</td><td>Description</td><td>text</td><td>false</td><td></td>
</tr>
<tr bgcolor="#D8E4F7">
<td>is_abstract</td><td>Is Abstract</td><td>bool</td><td>true</td><td>Whether this table is an abstract table that holds no real data, but instead provides an inheritance template.</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>lc_table_name</td><td>Lowercase Table Name</td><td>char32</td><td>true</td><td>The name of the table in all lowercase letters</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>table_name</td><td>Table Name</td><td>char32</td><td>true</td><td>The name of the table</td>
</tr>
<tr bgcolor="#D8E4F7">
<td>td_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Primary Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>td_pk</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="4">Foreign Key Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th>
</tr>
<tr bgcolor="#D8E4F7">
<td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="1">Unique Column Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Column Names</th>
</tr>
</table>
<br>
<table border="2">
<tr bgcolor="#BFD8D8">
<th colspan="2">Index Information</th>
</tr>
<tr bgcolor="#BFD8D8">
<th>Name</th><th>Column Name</th>
</tr>
</table>
<br>
</body>
</html>
|
|
From: <jas...@us...> - 2003-09-20 18:21:19
|
Update of /cvsroot/genex/genex-www/genex-2 In directory sc8-pr-cvs1:/tmp/cvs-serv21576 Removed Files: GenexAdmin.html ContactType.html Log Message: cruft --- GenexAdmin.html DELETED --- --- ContactType.html DELETED --- |
|
From: <jas...@us...> - 2003-06-11 04:39:57
|
Update of /cvsroot/genex/genex-www/content
In directory sc8-pr-cvs1:/tmp/cvs-serv14914/content
Modified Files:
genex-2-schema.ssi
Log Message:
new tables
Index: genex-2-schema.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/genex-2-schema.ssi,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** genex-2-schema.ssi 11 Jun 2003 04:29:12 -0000 1.4
--- genex-2-schema.ssi 11 Jun 2003 04:39:53 -0000 1.5
***************
*** 10,21 ****
<td>
<ul>
- <li><a href="genex-2/AM_FactorValues.html">AM_FactorValues.html</a>
- <li><a href="genex-2/AM_Spots.html">AM_Spots.html</a>
- <li><a href="genex-2/AM_SuspectSpots.html">AM_SuspectSpots.html</a>
<li><a href="genex-2/Array.html">Array.html</a>
<li><a href="genex-2/ArrayDesign.html">ArrayDesign.html</a>
<li><a href="genex-2/Audit.html">Audit.html</a>
<li><a href="genex-2/BlastHits.html">BlastHits.html</a>
- <li><a href="genex-2/Channel.html">Channel.html</a>
<li><a href="genex-2/Chromosome.html">Chromosome.html</a>
<li><a href="genex-2/Citation.html">Citation.html</a>
--- 10,17 ----
***************
*** 23,28 ****
--- 19,27 ----
<li><a href="genex-2/ContactType.html">ContactType.html</a>
<li><a href="genex-2/ControlledVocab.html">ControlledVocab.html</a>
+ <li><a href="genex-2/DerivedBioAssay.html">DerivedBioAssay.html</a>
+ <li><a href="genex-2/Describable.html">Describable.html</a>
<li><a href="genex-2/ExperimentFactors.html">ExperimentFactors.html</a>
<li><a href="genex-2/ExperimentSet.html">ExperimentSet.html</a>
+ <li><a href="genex-2/ExperimentSetLink.html">ExperimentSetLink.html</a>
<li><a href="genex-2/ExternalDatabase.html">ExternalDatabase.html</a>
<li><a href="genex-2/Feature.html">Feature.html</a>
***************
*** 36,39 ****
--- 35,39 ----
<li><a href="genex-2/Identifiable.html">Identifiable.html</a>
<li><a href="genex-2/MeasuredBioAssay.html">MeasuredBioAssay.html</a>
+ <li><a href="genex-2/PBA_FactorValues.html">PBA_FactorValues.html</a>
<li><a href="genex-2/Parameter.html">Parameter.html</a>
<li><a href="genex-2/ParameterValue.html">ParameterValue.html</a>
***************
*** 43,48 ****
<li><a href="genex-2/Protocol.html">Protocol.html</a>
<li><a href="genex-2/ProtocolApplication.html">ProtocolApplication.html</a>
<li><a href="genex-2/ProtocolStep.html">ProtocolStep.html</a>
! <li><a href="genex-2/QuantitationDimension.html">QuantitationDimension.html</a>
<li><a href="genex-2/QuantitationLink.html">QuantitationLink.html</a>
<li><a href="genex-2/QuantitationType.html">QuantitationType.html</a>
--- 43,49 ----
<li><a href="genex-2/Protocol.html">Protocol.html</a>
<li><a href="genex-2/ProtocolApplication.html">ProtocolApplication.html</a>
+ <li><a href="genex-2/ProtocolApplicationLink.html">ProtocolApplicationLink.html</a>
<li><a href="genex-2/ProtocolStep.html">ProtocolStep.html</a>
! <li><a href="genex-2/ProtocolStepApplication.html">ProtocolStepApplication.html</a>
<li><a href="genex-2/QuantitationLink.html">QuantitationLink.html</a>
<li><a href="genex-2/QuantitationType.html">QuantitationType.html</a>
***************
*** 52,62 ****
<li><a href="genex-2/Sample.html">Sample.html</a>
<li><a href="genex-2/SampleLink.html">SampleLink.html</a>
<li><a href="genex-2/Sessions.html">Sessions.html</a>
<li><a href="genex-2/Software.html">Software.html</a>
<li><a href="genex-2/Species.html">Species.html</a>
- <li><a href="genex-2/TL_FactorValues.html">TL_FactorValues.html</a>
- <li><a href="genex-2/TreatmentLevel.html">TreatmentLevel.html</a>
- <li><a href="genex-2/Treatment_AMs.html">Treatment_AMs.html</a>
<li><a href="genex-2/UserSec.html">UserSec.html</a>
</ul>
<hr>
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<li><a href="genex-2/Sample.html">Sample.html</a>
<li><a href="genex-2/SampleLink.html">SampleLink.html</a>
+ <li><a href="genex-2/Securable.html">Securable.html</a>
<li><a href="genex-2/Sessions.html">Sessions.html</a>
<li><a href="genex-2/Software.html">Software.html</a>
<li><a href="genex-2/Species.html">Species.html</a>
<li><a href="genex-2/UserSec.html">UserSec.html</a>
+
</ul>
<hr>
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*** 64,68 ****
<!-- Created: Mon Aug 20 13:38:19 MDT 2001 -->
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! Last modified: Wed Apr 16 15:14:00 MDT 2003
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--- 64,68 ----
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! Last modified: Tue Jun 10 22:38:16 MDT 2003
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From: <jas...@us...> - 2003-06-11 04:35:54
|
Update of /cvsroot/genex/genex-www/genex-2 In directory sc8-pr-cvs1:/tmp/cvs-serv13652/genex-2 Removed Files: AM_FactorValues.html AM_Spots.html AM_SuspectSpots.html Channel.html QuantitationDimension.html TL_FactorValues.html TreatmentLevel.html Treatment_AMs.html Log Message: cruft --- AM_FactorValues.html DELETED --- --- AM_Spots.html DELETED --- --- AM_SuspectSpots.html DELETED --- --- Channel.html DELETED --- --- QuantitationDimension.html DELETED --- --- TL_FactorValues.html DELETED --- --- TreatmentLevel.html DELETED --- --- Treatment_AMs.html DELETED --- |
Update of /cvsroot/genex/genex-www/genex-2
In directory sc8-pr-cvs1:/tmp/cvs-serv13332/genex-2
Added Files:
DerivedBioAssay.html Describable.html ExperimentSetLink.html
PBA_FactorValues.html ProtocolApplicationLink.html
ProtocolStepApplication.html Securable.html
Log Message:
new tables
--- NEW FILE: DerivedBioAssay.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: DerivedBioAssay Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: DerivedBioAssay Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The DerivedBioAssay table holds the meta-data associated with a data matrix stored in a dynamic data table</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>channel</td><td>Channel</td><td>char128</td><td>false</td><td>controlled vocab</td></tr><tr bgcolor="#D8E4F7"><td>data_table_name</td><td>DerivedBioAssay Data Table</td><td>char32</td><td>false</td><td>the name of the table that contains the numerical data for this DerivedBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>dba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>dba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: Describable.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: Describable Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: Describable Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Describable table is an abstract table that provides one column to its subclasses: description, as well as security information, and audit tracking information through Securable</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td>a verbose description of this object</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: ExperimentSetLink.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: ExperimentSetLink Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ExperimentSetLink Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExperimentSetLink table allows many BioAssay's (Physical, Measured or Derived) to belong to a given ExperimentSet, and it enables each BioAssay to belong to multiple ExperimentSet's.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>bioassay_fk</td><td>BioAssay</td><td>int</td><td>true</td><td>the foreign key to the BioAssay.</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Experiment Set</td><td>int</td><td>true</td><td>the experiment</td></tr><tr bgcolor="#D8E4F7"><td>table_name</td><td>BioAssay Table</td><td>char128</td><td>false</td><td>the name of the table to which the bioassay_fk points, either PhysicalBioAssay, MeasuredBioAssay, or DerivedBioAssay</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>bioassay_fk es_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>bioassay_fk</td><td>eslink_bioassay_fk</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>eslink_es_fk</td></tr></table><br></body></html>
--- NEW FILE: PBA_FactorValues.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: PBA_FactorValues Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: PBA_FactorValues Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>LINKING</th><th></th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ef_fk</td><td>Experiment Factor</td><td>int</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>Physical BioAssay</td><td>int</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>value</td><td>Value</td><td>char128</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>value_units</td><td>Value Units</td><td>char128</td><td>false</td><td>This is a controlled vocab</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>ef_fk</td><td><a href="ExperimentFactors.html">ExperimentFactors</a></td><td>ef_pk</td><td>LINKING_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td><a href="PhysicalBioAssay.html">PhysicalBioAssay</a></td><td>pba_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>pba_fk ef_fk value</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ef_fk</td><td>pba_factorvalues_ef_fk</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>pba_factorvalues_pba_fk</td></tr></table><br></body></html>
--- NEW FILE: ProtocolApplicationLink.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: ProtocolApplicationLink Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ProtocolApplicationLink Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ProtocolApplicationLink table allows many protocols used in an application to be specified. As many protocols as are appropriate to describe the application may be used, and the same protocol may be used in the different applications (a many-to-many relationship).</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>other_fk</td><td>other_fk</td><td>int</td><td>true</td><td>the foreign key to the table using the protocol. We do not make this a foreign key constraint in the DB because this can apply to many different tables.</td></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk</td><td>Protocol Application</td><td>int</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk</td><td><a href="ProtocolApplication.html">ProtocolApplication</a></td><td>proto_app_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>other_fk proto_app_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>other_fk</td><td>palink_other_fk</td></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk</td><td>palink_pa_fk</td></tr></table><br></body></html>
--- NEW FILE: ProtocolStepApplication.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: ProtocolStepApplication Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: ProtocolStepApplication Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ProtocolStepApplication table describes the concrete use in time by a person of a protocol step.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>activity_date</td><td>Activity Date</td><td>datetime</td><td>true</td><td> the date when the protocol step was performed</td></tr><tr bgcolor="#D8E4F7"><td>performer_con_fk</td><td>Protocol Step Performer</td><td>int</td><td>true</td><td> the person who performed the protocol step</td></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk</td><td>Protocol Application</td><td>int</td><td>true</td><td>The protocol application that this step is part of</td></tr><tr bgcolor="#D8E4F7"><td>proto_step_app_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>proto_step_fk</td><td>Protocol Step</td><td>int</td><td>true</td><td>The protocol step that was performed</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>proto_step_app_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>performer_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk</td><td><a href="ProtocolApplication.html">ProtocolApplication</a></td><td>proto_app_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>proto_step_fk</td><td><a href="ProtocolStep.html">ProtocolStep</a></td><td>proto_step_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>proto_app_fk proto_step_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: Securable.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: Securable Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: Securable Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The Securable table is an abstract table that provides security information, and audit tracking information</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int</td><td>true</td><td>The audit entry when this data was last modified, it will be null if it is the creation event. We set the write_sql attribute to be false so that Postgres doesn't put a constraint on this column. It is automatically set by a trigger. </td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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From: <jas...@us...> - 2003-06-11 04:29:14
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Update of /cvsroot/genex/genex-www/content In directory sc8-pr-cvs1:/tmp/cvs-serv12037/content Modified Files: genex-2-schema.ssi Log Message: new tables Index: genex-2-schema.ssi =================================================================== RCS file: /cvsroot/genex/genex-www/content/genex-2-schema.ssi,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** genex-2-schema.ssi 29 Aug 2002 19:47:26 -0000 1.3 --- genex-2-schema.ssi 11 Jun 2003 04:29:12 -0000 1.4 *************** *** 27,52 **** <li><a href="genex-2/ExternalDatabase.html">ExternalDatabase.html</a> <li><a href="genex-2/Feature.html">Feature.html</a> ! <li><a href="genex-2/FeatureExtraction.html">FeatureExtraction.html</a> <li><a href="genex-2/GenexAdmin.html">GenexAdmin.html</a> <li><a href="genex-2/GroupLink.html">GroupLink.html</a> <li><a href="genex-2/GroupSec.html">GroupSec.html</a> <li><a href="genex-2/HotSpots.html">HotSpots.html</a> <li><a href="genex-2/PhysicalBioAssay.html">PhysicalBioAssay.html</a> <li><a href="genex-2/Protocol.html">Protocol.html</a> ! <li><a href="genex-2/Provider.html">Provider.html</a> ! <li><a href="genex-2/QuantitationDimension.html">QuantitationTypeDimension.html</a> ! <li><a href="genex-2/QuantitationType.html">QuantitationType.html</a> <li><a href="genex-2/QuantitationLink.html">QuantitationLink.html</a> <li><a href="genex-2/SF_ExternalDBLink.html">SF_ExternalDBLink.html</a> <li><a href="genex-2/Sample.html">Sample.html</a> <li><a href="genex-2/SampleLink.html">SampleLink.html</a> ! <li><a href="genex-2/SampleProtocols.html">SampleProtocols.html</a> ! <li><a href="genex-2/Scanner.html">Scanner.html</a> ! <li><a href="genex-2/SequenceFeature.html">SequenceFeature.html</a> <li><a href="genex-2/Software.html">Software.html</a> <li><a href="genex-2/Species.html">Species.html</a> - <li><a href="genex-2/Spotter.html">Spotter.html</a> <li><a href="genex-2/TL_FactorValues.html">TL_FactorValues.html</a> - <li><a href="genex-2/TableAdmin.html">TableAdmin.html</a> <li><a href="genex-2/TreatmentLevel.html">TreatmentLevel.html</a> <li><a href="genex-2/Treatment_AMs.html">Treatment_AMs.html</a> --- 27,59 ---- <li><a href="genex-2/ExternalDatabase.html">ExternalDatabase.html</a> <li><a href="genex-2/Feature.html">Feature.html</a> ! <li><a href="genex-2/FeatureExtractionSoftware.html">FeatureExtractionSoftware.html</a> ! <li><a href="genex-2/G2G.html">G2G.html</a> <li><a href="genex-2/GenexAdmin.html">GenexAdmin.html</a> <li><a href="genex-2/GroupLink.html">GroupLink.html</a> <li><a href="genex-2/GroupSec.html">GroupSec.html</a> + <li><a href="genex-2/Hardware.html">Hardware.html</a> <li><a href="genex-2/HotSpots.html">HotSpots.html</a> + <li><a href="genex-2/Identifiable.html">Identifiable.html</a> + <li><a href="genex-2/MeasuredBioAssay.html">MeasuredBioAssay.html</a> + <li><a href="genex-2/Parameter.html">Parameter.html</a> + <li><a href="genex-2/ParameterValue.html">ParameterValue.html</a> + <li><a href="genex-2/Parameterizable.html">Parameterizable.html</a> <li><a href="genex-2/PhysicalBioAssay.html">PhysicalBioAssay.html</a> + <li><a href="genex-2/Procedure.html">Procedure.html</a> <li><a href="genex-2/Protocol.html">Protocol.html</a> ! <li><a href="genex-2/ProtocolApplication.html">ProtocolApplication.html</a> ! <li><a href="genex-2/ProtocolStep.html">ProtocolStep.html</a> ! <li><a href="genex-2/QuantitationDimension.html">QuantitationDimension.html</a> <li><a href="genex-2/QuantitationLink.html">QuantitationLink.html</a> + <li><a href="genex-2/QuantitationType.html">QuantitationType.html</a> + <li><a href="genex-2/QuantitationTypeDimension.html">QuantitationTypeDimension.html</a> + <li><a href="genex-2/Reporter.html">Reporter.html</a> <li><a href="genex-2/SF_ExternalDBLink.html">SF_ExternalDBLink.html</a> <li><a href="genex-2/Sample.html">Sample.html</a> <li><a href="genex-2/SampleLink.html">SampleLink.html</a> ! <li><a href="genex-2/Sessions.html">Sessions.html</a> <li><a href="genex-2/Software.html">Software.html</a> <li><a href="genex-2/Species.html">Species.html</a> <li><a href="genex-2/TL_FactorValues.html">TL_FactorValues.html</a> <li><a href="genex-2/TreatmentLevel.html">TreatmentLevel.html</a> <li><a href="genex-2/Treatment_AMs.html">Treatment_AMs.html</a> *************** *** 57,61 **** <!-- Created: Mon Aug 20 13:38:19 MDT 2001 --> <!-- hhmts start --> ! Last modified: Thu Aug 29 13:44:57 MDT 2002 <!-- hhmts end --> --- 64,68 ---- <!-- Created: Mon Aug 20 13:38:19 MDT 2001 --> <!-- hhmts start --> ! Last modified: Wed Apr 16 15:14:00 MDT 2003 <!-- hhmts end --> |
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From: <jas...@us...> - 2003-04-27 01:35:07
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv7875 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** MANIFEST.in 27 Apr 2003 01:27:23 -0000 1.15 --- MANIFEST.in 27 Apr 2003 01:35:03 -0000 1.16 *************** *** 30,34 **** 'apache/genex-2-handler.pl' => '%%LOCAL_ETC%%', ! 'Mason/status.html' => '%%GENEX_MASON_DIR%%', 'Mason/workspace/workspace.html' => '%%GENEX_WORKSPACE_DIR%%', --- 30,34 ---- 'apache/genex-2-handler.pl' => '%%LOCAL_ETC%%', ! 'Mason/status.html' => '%%GENEX_MASON_COMP_ROOT%%', 'Mason/workspace/workspace.html' => '%%GENEX_WORKSPACE_DIR%%', |
|
From: <jas...@us...> - 2003-04-27 01:27:26
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv3602 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** MANIFEST.in 26 Apr 2003 22:56:44 -0000 1.14 --- MANIFEST.in 27 Apr 2003 01:27:23 -0000 1.15 *************** *** 35,38 **** --- 35,39 ---- 'Mason/workspace/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/array-design.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/array-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/arrays.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%', *************** *** 62,65 **** --- 63,67 ---- 'Mason/workspace/protocol-application-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/procedure-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/physicalbioassay-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/parameter-value-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/sample-insert.html' => '%%GENEX_WORKSPACE_DIR%%', *************** *** 70,74 **** --- 72,78 ---- 'Mason/workspace/comps/ro_rw_group.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/fkey-menu.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/cv-menu.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/value-input.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/textarea-input.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/tableize.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/objs2table.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', |
|
From: <jas...@us...> - 2003-04-27 01:12:49
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv26914
Modified Files:
make_classes.pl
Log Message:
now creates all modules in Genex/Genex directory instead of
creating a seperate directory for each sub-module (thanks to
Allen Day <all...@uc...>) for this tip.
Index: make_classes.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/make_classes.pl,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** make_classes.pl 23 Apr 2003 21:24:23 -0000 1.31
--- make_classes.pl 27 Apr 2003 01:12:46 -0000 1.32
***************
*** 24,40 ****
my %OPTIONS;
$OPTIONS{root} = cwd();
! GetOptions(\%OPTIONS,
! 'make_pm',
! 'make_pod',
! 'help',
! 'force_test',
! 'force_makefile',
! 'control_only',
! 'linking_only',
! 'xml_directory=s',
! 'root=s',
! 'only=s',
! );
die $USAGE if exists $OPTIONS{help};
die "$USAGE\nMust define --xml_directory\n"
--- 24,41 ----
my %OPTIONS;
$OPTIONS{root} = cwd();
! my $rc = GetOptions(\%OPTIONS,
! 'make_pm',
! 'make_pod',
! 'help',
! 'force_test',
! 'force_makefile',
! 'control_only',
! 'linking_only',
! 'xml_directory=s',
! 'root=s',
! 'only=s',
! );
die $USAGE if exists $OPTIONS{help};
+ die $USAGE unless $rc;
die "$USAGE\nMust define --xml_directory\n"
***************
*** 186,190 ****
my $base = $args{target};
! my $dir = "$OPTIONS{root}/$base";
my $file = "$dir/$base.pm";
unless (-d $dir) {
--- 187,191 ----
my $base = $args{target};
! my $dir = "$OPTIONS{root}/Genex";
my $file = "$dir/$base.pm";
unless (-d $dir) {
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv18783
Modified Files:
array-design-insert.pl.in array-measurement-insert.pl.in
contact-insert-genex.pl.in contact-insert.pl.in
create-db-accounts.pl.in create_genex_class.pl.in
create_genex_db.pl.in cv-check.pl.in cv-insert.pl.in
db2xml.pl.in dbxml2tab.pl.in experimentset-create.pl.in
externaldb-insert.pl.in generate_group.pl.in
generate_user.pl.in group-insert.pl.in layout.pl.in
mbad-insert.pl.in parameter-insert.pl.in
parameter-value-insert.pl.in priveleges.pl.in
procedure-insert.pl.in protocol-application-insert.pl.in
protocol-insert.pl.in protocol-step-application-insert.pl.in
protocol-step-insert.pl.in qtdim-insert.pl.in
reporter-insert.pl.in sample-insert.pl.in scanner-insert.pl.in
security-insert.pl.in software-insert.pl.in
species-insert.pl.in spotter-insert.pl.in tab2xml.pl.in
user-insert.pl.in xml2form.pl.in
Log Message:
added GENEX_EXTRALIBS
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** array-design-insert.pl.in 21 Apr 2003 00:24:26 -0000 1.19
--- array-design-insert.pl.in 27 Apr 2003 01:05:17 -0000 1.20
***************
*** 15,19 ****
use File::Basename;
use Benchmark;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 15,19 ----
use File::Basename;
use Benchmark;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: array-measurement-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-measurement-insert.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** array-measurement-insert.pl.in 15 Oct 2002 14:44:16 -0000 1.4
--- array-measurement-insert.pl.in 27 Apr 2003 01:05:17 -0000 1.5
***************
*** 13,17 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use blib;
--- 13,17 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
Index: contact-insert-genex.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/contact-insert-genex.pl.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** contact-insert-genex.pl.in 22 Mar 2002 06:15:59 -0000 1.7
--- contact-insert-genex.pl.in 27 Apr 2003 01:05:17 -0000 1.8
***************
*** 16,20 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use XML::DOM;
--- 16,20 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use XML::DOM;
Index: contact-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/contact-insert.pl.in,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** contact-insert.pl.in 15 Apr 2003 17:46:37 -0000 1.10
--- contact-insert.pl.in 27 Apr 2003 01:05:17 -0000 1.11
***************
*** 16,20 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex;
--- 16,20 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
Index: create-db-accounts.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create-db-accounts.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** create-db-accounts.pl.in 9 Nov 2002 00:41:36 -0000 1.8
--- create-db-accounts.pl.in 27 Apr 2003 01:05:17 -0000 1.9
***************
*** 12,16 ****
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 12,16 ----
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: create_genex_class.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_class.pl.in,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** create_genex_class.pl.in 24 Apr 2003 21:26:15 -0000 1.24
--- create_genex_class.pl.in 27 Apr 2003 01:05:17 -0000 1.25
***************
*** 12,16 ****
use Getopt::Long;
! %%GENEX_EXTRALIBS%%
use blib;
--- 12,16 ----
use Getopt::Long;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
***************
*** 54,58 ****
my $XML_DIR;
my %OPTIONS;
! GetOptions(\%OPTIONS,
'target=s',
'support=s@',
--- 54,58 ----
my $XML_DIR;
my %OPTIONS;
! my $rc = GetOptions(\%OPTIONS,
'target=s',
'support=s@',
***************
*** 66,69 ****
--- 66,70 ----
);
die $USAGE if exists $OPTIONS{help};
+ die $USAGE unless $rc;
$target = $OPTIONS{target};
***************
*** 117,153 ****
#
! # first we make sure we have a directory
! my $dir = $MODULES . "/$module_name";
! unless (-e $dir) {
! mkdir($dir,0775) or die "couldn't create directory $dir";
! }
!
! #then a Makefile.PL
! my $file = $dir . '/Makefile.PL';
! if (!-f $file || exists $OPTIONS{force_makefile}) {
! open(OUT,">$file") or die "Couldn't open $file";
!
! # start a section with variable expansion *enabled*
! print OUT <<"EOT";
! sub MY::top_targets {
! package MY; # so that "SUPER" works right
! my \$inherited = shift->SUPER::top_targets(\@_);
! \$inherited =~ s/(man|html)ifypods//g;
! \$inherited;
! }
!
! WriteMakefile(
! 'NAME' => '$full_module_name',
! 'SKIP' => [qw( test makeaperl manifypods htmlifypods xs_o static)],
! 'VERSION_FROM' => '../Genex.pm', # finds \$VERSION
! );
! EOT
! close(OUT);
! }
# then we need a module file
! $file = $dir . '/' . $module_name . '.pm';
! open(OUT,">$file") or die "Couldn't open $file";
my $VERSION = get_file_version($file);
########################################
--- 118,129 ----
#
! my $dir = "$MODULES/Genex";
# then we need a module file
! my $file = "$dir/$module_name.pm";
! die "Couldn't open $file"
! unless -f $file;
my $VERSION = get_file_version($file);
+ open(OUT,">$file");
########################################
Index: create_genex_db.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_db.pl.in,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** create_genex_db.pl.in 12 Jan 2003 22:07:20 -0000 1.10
--- create_genex_db.pl.in 27 Apr 2003 01:05:17 -0000 1.11
***************
*** 7,11 ****
use constant UPDATE_INSERT => 'UPDATE OR INSERT';
! %%GENEX_EXTRALIBS%%
# use blib;
--- 7,11 ----
use constant UPDATE_INSERT => 'UPDATE OR INSERT';
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: cv-check.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/cv-check.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cv-check.pl.in 22 Mar 2002 06:15:59 -0000 1.5
--- cv-check.pl.in 27 Apr 2003 01:05:17 -0000 1.6
***************
*** 11,15 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use XML::DOM;
--- 11,15 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use XML::DOM;
Index: cv-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/cv-insert.pl.in,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** cv-insert.pl.in 23 Nov 2002 05:11:24 -0000 1.17
--- cv-insert.pl.in 27 Apr 2003 01:05:17 -0000 1.18
***************
*** 11,15 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 11,15 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: db2xml.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/db2xml.pl.in,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** db2xml.pl.in 26 Jul 2001 13:34:32 -0000 1.38
--- db2xml.pl.in 27 Apr 2003 01:05:17 -0000 1.39
***************
*** 141,145 ****
###
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 141,145 ----
###
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: dbxml2tab.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/dbxml2tab.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** dbxml2tab.pl.in 21 Nov 2001 01:06:09 -0000 1.1
--- dbxml2tab.pl.in 27 Apr 2003 01:05:17 -0000 1.2
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
Index: experimentset-create.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/experimentset-create.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** experimentset-create.pl.in 7 Nov 2002 14:43:33 -0000 1.1
--- experimentset-create.pl.in 27 Apr 2003 01:05:17 -0000 1.2
***************
*** 16,20 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex;
--- 16,20 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
Index: externaldb-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/externaldb-insert.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** externaldb-insert.pl.in 22 Mar 2002 06:15:59 -0000 1.8
--- externaldb-insert.pl.in 27 Apr 2003 01:05:17 -0000 1.9
***************
*** 11,15 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use blib;
--- 11,15 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
Index: generate_group.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/generate_group.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_group.pl.in 12 Oct 2002 21:49:41 -0000 1.1
--- generate_group.pl.in 27 Apr 2003 01:05:17 -0000 1.2
***************
*** 6,10 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex qw(timestamp $SU_USERNAME $SU_PASSWORD);
--- 6,10 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex qw(timestamp $SU_USERNAME $SU_PASSWORD);
Index: generate_user.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/generate_user.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_user.pl.in 12 Oct 2002 21:49:41 -0000 1.1
--- generate_user.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 6,10 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex qw(timestamp $SU_USERNAME $SU_PASSWORD);
--- 6,10 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex qw(timestamp $SU_USERNAME $SU_PASSWORD);
Index: group-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/group-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** group-insert.pl.in 7 Nov 2002 14:45:47 -0000 1.2
--- group-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.3
***************
*** 17,21 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex;
--- 17,21 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
Index: layout.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/layout.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** layout.pl.in 18 Sep 2002 21:17:33 -0000 1.5
--- layout.pl.in 27 Apr 2003 01:05:18 -0000 1.6
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use blib;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** mbad-insert.pl.in 10 Apr 2003 08:02:18 -0000 1.12
--- mbad-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.13
***************
*** 125,129 ****
@qts = map {$_->[1]->qt_obj}
sort {$a->[0] <=> $b->[0]}
! map {[$_->order,$_]} @qts;
my @col_nums = map {$_->column_number} @qts;
--- 125,129 ----
@qts = map {$_->[1]->qt_obj}
sort {$a->[0] <=> $b->[0]}
! map {[$_->dimension_order,$_]} @qts;
my @col_nums = map {$_->column_number} @qts;
Index: parameter-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/parameter-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** parameter-insert.pl.in 22 Apr 2003 01:22:26 -0000 1.2
--- parameter-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.3
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: parameter-value-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/parameter-value-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** parameter-value-insert.pl.in 22 Apr 2003 00:58:50 -0000 1.1
--- parameter-value-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: priveleges.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/priveleges.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** priveleges.pl.in 22 Mar 2002 06:15:59 -0000 1.5
--- priveleges.pl.in 27 Apr 2003 01:05:18 -0000 1.6
***************
*** 9,13 ****
use Carp;
use Getopt::Long;
! %%GENEX_EXTRALIBS%%
use Bio::Genex qw($SU_USERNAME $SU_PASSWORD);
use Bio::Genex::DBUtils;
--- 9,13 ----
use Carp;
use Getopt::Long;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex qw($SU_USERNAME $SU_PASSWORD);
use Bio::Genex::DBUtils;
Index: procedure-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/procedure-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** procedure-insert.pl.in 17 Apr 2003 17:56:02 -0000 1.2
--- procedure-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.3
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: protocol-application-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-application-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-application-insert.pl.in 23 Apr 2003 21:22:23 -0000 1.1
--- protocol-application-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: protocol-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-insert.pl.in,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** protocol-insert.pl.in 17 Apr 2003 05:06:26 -0000 1.10
--- protocol-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.11
***************
*** 16,20 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 16,20 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: protocol-step-application-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-step-application-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-step-application-insert.pl.in 23 Apr 2003 21:22:24 -0000 1.1
--- protocol-step-application-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
***************
*** 126,130 ****
message=>"Couldn't locate ProtocolStep entry for value: $OPTIONS{proto_step_fk}")
unless defined $proto_step_db;
! $psa_db->protocol_step_obj($proto_step_db);
my ($proto_app_db) = Bio::Genex::ProtocolApplication->get_all_objects($dbh,
--- 126,130 ----
message=>"Couldn't locate ProtocolStep entry for value: $OPTIONS{proto_step_fk}")
unless defined $proto_step_db;
! $psa_db->proto_step_obj($proto_step_db);
my ($proto_app_db) = Bio::Genex::ProtocolApplication->get_all_objects($dbh,
Index: protocol-step-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-step-insert.pl.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** protocol-step-insert.pl.in 22 Apr 2003 01:22:26 -0000 1.2
--- protocol-step-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.3
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
***************
*** 34,38 ****
my $rc = GetOptions(\%OPTIONS,
'dbname=s',
! 'order=i',
'proto_fk=i',
'proc_fk=i',
--- 34,38 ----
my $rc = GetOptions(\%OPTIONS,
'dbname=s',
! 'protocol_order=i',
'proto_fk=i',
'proc_fk=i',
***************
*** 51,55 ****
--proto_fk=num : the protocol foreign key
--proto_fk=num : the procedure foreign key
! --order=num : the order of this step in the protocol
--username=name : the DB username to login as
--password=word : the DB password to login with
--- 51,55 ----
--proto_fk=num : the protocol foreign key
--proto_fk=num : the procedure foreign key
! --protocol_order=num : the order of this step in the protocol
--username=name : the DB username to login as
--password=word : the DB password to login with
***************
*** 80,85 ****
my @error_args = (caller=>$0);
! die "Must specify --order\n$USAGE"
! unless exists $OPTIONS{order};
die "Must specify --proto_fk\n$USAGE"
unless exists $OPTIONS{proto_fk};
--- 80,85 ----
my @error_args = (caller=>$0);
! die "Must specify --protocol_order\n$USAGE"
! unless exists $OPTIONS{protocol_order};
die "Must specify --proto_fk\n$USAGE"
unless exists $OPTIONS{proto_fk};
***************
*** 107,111 ****
my $ps_db = Bio::Genex::ProtocolStep->new(ro_groupname_obj=>$ro_group_db,
rw_groupname_obj=>$rw_group_db,
! order=>$OPTIONS{order},
);
--- 107,111 ----
my $ps_db = Bio::Genex::ProtocolStep->new(ro_groupname_obj=>$ro_group_db,
rw_groupname_obj=>$rw_group_db,
! protocol_order=>$OPTIONS{protocol_order},
);
Index: qtdim-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/qtdim-insert.pl.in,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** qtdim-insert.pl.in 11 Jan 2003 19:29:15 -0000 1.5
--- qtdim-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.6
***************
*** 15,18 ****
--- 15,21 ----
use Bio::MAGE::XMLUtils;
use Getopt::Long;
+
+ use lib qw(%%GENEX_EXTRALIBS%%);
+
use Bio::Genex qw(error);
use Bio::Genex::Connect;
***************
*** 206,210 ****
my $i;
foreach my $mage_qt (@mage_qts) {
! $i++; # track the order attribute
# ensure we have the necessary pieces
--- 209,213 ----
my $i;
foreach my $mage_qt (@mage_qts) {
! $i++; # track the dimension_order attribute
# ensure we have the necessary pieces
***************
*** 266,270 ****
}
my $qtl_db = Bio::Genex::QuantitationLink->new(qd_obj=>$qtdim_db,
! order=>$i,
qt_obj=>$qt_db,
);
--- 269,273 ----
}
my $qtl_db = Bio::Genex::QuantitationLink->new(qd_obj=>$qtdim_db,
! dimension_order=>$i,
qt_obj=>$qt_db,
);
Index: reporter-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/reporter-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** reporter-insert.pl.in 11 Oct 2002 02:18:47 -0000 1.1
--- reporter-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 11,15 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use blib;
--- 11,15 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use blib;
Index: sample-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/sample-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** sample-insert.pl.in 21 Apr 2003 00:21:35 -0000 1.1
--- sample-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.2
***************
*** 14,18 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 14,18 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: scanner-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/scanner-insert.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** scanner-insert.pl.in 11 Oct 2002 02:18:23 -0000 1.9
--- scanner-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.10
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: security-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/security-insert.pl.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** security-insert.pl.in 22 Mar 2002 06:15:59 -0000 1.6
--- security-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.7
***************
*** 11,15 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use XML::DOM;
--- 11,15 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use XML::DOM;
Index: software-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/software-insert.pl.in,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** software-insert.pl.in 11 Oct 2002 02:18:23 -0000 1.12
--- software-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.13
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: species-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/species-insert.pl.in,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** species-insert.pl.in 11 Oct 2002 02:18:23 -0000 1.12
--- species-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.13
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: spotter-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/spotter-insert.pl.in,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** spotter-insert.pl.in 11 Oct 2002 02:18:23 -0000 1.11
--- spotter-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.12
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
# use blib;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
Index: tab2xml.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/tab2xml.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** tab2xml.pl.in 12 Apr 2001 01:16:11 -0000 1.4
--- tab2xml.pl.in 27 Apr 2003 01:05:18 -0000 1.5
***************
*** 15,19 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use XML::DOM;
--- 15,19 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use XML::DOM;
Index: user-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/user-insert.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** user-insert.pl.in 9 Apr 2003 21:41:18 -0000 1.8
--- user-insert.pl.in 27 Apr 2003 01:05:18 -0000 1.9
***************
*** 17,21 ****
use Getopt::Long;
use File::Basename;
! %%GENEX_EXTRALIBS%%
use Bio::Genex;
--- 17,21 ----
use Getopt::Long;
use File::Basename;
! use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
Index: xml2form.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/xml2form.pl.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** xml2form.pl.in 10 May 2001 23:14:57 -0000 1.3
--- xml2form.pl.in 27 Apr 2003 01:05:18 -0000 1.4
***************
*** 4,8 ****
use Getopt::Long;
! %%GENEX_EXTRALIBS%%
# use blib;
use Bio::Genex qw(error);
--- 4,8 ----
use Getopt::Long;
! use lib qw(%%GENEX_EXTRALIBS%%);
# use blib;
use Bio::Genex qw(error);
|
|
From: <jas...@us...> - 2003-04-27 01:01:57
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv22489 Modified Files: GenexUtils.pm Log Message: added $CACHE_FILE_FILE_NAME Index: GenexUtils.pm =================================================================== RCS file: /cvsroot/genex/genex-server/GenexUtils.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** GenexUtils.pm 20 Dec 2002 05:35:04 -0000 1.3 --- GenexUtils.pm 27 Apr 2003 01:01:53 -0000 1.4 *************** *** 2,6 **** require Exporter; ! use vars qw(@ISA @EXPORT_OK $CACHE_FILE_PATH $CACHE_FILE_NAME $ERR_FH $ERRORS $ERR_FILE); use strict; use Term::ReadKey; --- 2,6 ---- require Exporter; ! use vars qw(@ISA @EXPORT_OK $CACHE_FILE_PATH $CACHE_FILE_FILE_NAME $CACHE_FILE_NAME $ERR_FH $ERRORS $ERR_FILE); use strict; use Term::ReadKey; *************** *** 9,13 **** $ERR_FILE = 'genex-errors.txt'; $CACHE_FILE_PATH = 'Bio/Genex'; ! $CACHE_FILE_NAME = "$CACHE_FILE_PATH/Config.pm"; @ISA = qw(Exporter); --- 9,14 ---- $ERR_FILE = 'genex-errors.txt'; $CACHE_FILE_PATH = 'Bio/Genex'; ! $CACHE_FILE_FILE_NAME = 'Config.pm'; ! $CACHE_FILE_NAME = "$CACHE_FILE_PATH/$CACHE_FILE_FILE_NAME"; @ISA = qw(Exporter); *************** *** 24,27 **** --- 25,29 ---- $ERR_FILE $CACHE_FILE_PATH + $CACHE_FILE_FILE_NAME $CACHE_FILE_NAME ); |
|
From: <jas...@us...> - 2003-04-27 00:56:09
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv17177 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.129 retrieving revision 1.130 diff -C2 -d -r1.129 -r1.130 *** ChangeLog 26 Apr 2003 23:28:20 -0000 1.129 --- ChangeLog 27 Apr 2003 00:56:06 -0000 1.130 *************** *** 16,19 **** --- 16,26 ---- that must be wrapped like: 'use lib qw(%%GENEX_EXTRALIBS%%') + * Mason/workspace/comps/tableize.mason (Repository): + * Mason/workspace/comps/objs2table.mason (Repository): + now returns a list in array context and prints out HTML in scalar context + + * Mason/workspace/protocol-insert.html.in (Repository): + now uses components for all parts + * Mason/workspace/protocol-step-insert.html.in (Repository): fixed 'order' => 'protocol_order' |
|
From: <jas...@us...> - 2003-04-27 00:53:57
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv16813 Added Files: index.html Log Message: new files |
|
From: <jas...@us...> - 2003-04-27 00:52:40
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv15732
Modified Files:
objs2table.mason tableize.mason
Log Message:
now returns a list in array context and prints out HTML in scalar context
Index: objs2table.mason
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/comps/objs2table.mason,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** objs2table.mason 22 Apr 2003 01:19:40 -0000 1.1
--- objs2table.mason 27 Apr 2003 00:52:36 -0000 1.2
***************
*** 1,7 ****
- % foreach my $row (@rows) {
- <tr><% $row %></tr>
- % }
<%args>
$objects
</%args>
<%once>
--- 1,7 ----
<%args>
$objects
+ $check=>0
+ $check_header=>''
+ $check_name=>''
</%args>
<%once>
***************
*** 9,12 ****
--- 9,16 ----
</%once>
<%init>;
+ # make sure we get all the info we need for checkboxes
+ die "Must include check_header and check_name"
+ if $check and not ($check_header and $check_name);
+
my @rows;
my $cgi = CGI->new('');
***************
*** 21,24 ****
--- 25,33 ----
push(@rows,$cgi->th(\@column_copy));
+ # include the header if we've been asked to have a checkbox column
+ if ($check) {
+ $rows[0] = "<th>$check_header</th>" . $rows[0];
+ }
+
foreach my $object (@{$objects}) {
my %tmp_values;
***************
*** 33,37 ****
--- 42,57 ----
push(@values, $tmp_values{$name2column{$_}});
}
+
+ # add the checkbox if we've been asked to
+ unshift(@values,
+ qq[<input type="checkbox" name="$check_name" value="$tmp_values{$name2column{'Accession Number'}}"></input>])
+ if $check;
+
push(@rows,$cgi->td([map {!defined $_ ? ' ' : $_} @values]));
+ }
+ if (wantarray) {
+ return @rows;
+ } else {
+ $m->print('<tr>' . join("</tr>\n<tr>",@rows) . '</tr>');
}
</%init>
Index: tableize.mason
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/comps/tableize.mason,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** tableize.mason 22 Apr 2003 01:19:40 -0000 1.1
--- tableize.mason 27 Apr 2003 00:52:36 -0000 1.2
***************
*** 1,5 ****
- <table>
- <% $result %>
- </table>
<%args>
$rows => 1
--- 1,2 ----
***************
*** 26,37 ****
# rearrange into a pretty table
! my($row,$column);
unshift(@$colheaders,'') if @$colheaders && @$rowheaders;
- $result .= "<tr>" if @{$colheaders};
foreach (@{$colheaders}) {
$result .= "<th>$_</th>";
}
for ($row=0;$row<$rows;$row++) {
! $result .= "<tr>";
$result .= "<th>$rowheaders->[$row]</th>" if @$rowheaders;
for ($column=0;$column<$columns;$column++) {
--- 23,35 ----
# rearrange into a pretty table
! my(@rows,$row,$column);
unshift(@$colheaders,'') if @$colheaders && @$rowheaders;
foreach (@{$colheaders}) {
$result .= "<th>$_</th>";
}
+ push(@rows,$result) if @{$colheaders};
+
for ($row=0;$row<$rows;$row++) {
! $result = '';
$result .= "<th>$rowheaders->[$row]</th>" if @$rowheaders;
for ($column=0;$column<$columns;$column++) {
***************
*** 39,44 ****
if defined($elements[$column*$rows + $row]);
}
! $result .= "</tr>";
}
</%init>
--- 37,48 ----
if defined($elements[$column*$rows + $row]);
}
! push(@rows,$result);
}
+
+ if (wantarray) {
+ return @rows;
+ } else {
+ $m->print('<table><tr>' . join("</tr>\n<tr>",@rows) . '</tr></table>');
+ }
</%init>
|
|
From: <jas...@us...> - 2003-04-27 00:50:57
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv14605
Added Files:
cv-menu.mason textarea-input.mason
Log Message:
new
--- NEW FILE: cv-menu.mason ---
<h2><% $type %></h2>
<p>Choose the <b><% $type %></b> that describes the type of
<% $entry_name %>.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th><% $type %></th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& query-drop-down.mason, name=>$cgi_param_name, array_ref=>$array_ref &>
</td>
</tr>
</tbody>
</table>
<%args>
$cgi_param_name
$entry_name
$type
$array_ref
</%args>
<%once>
</%once>
<%init>
</%init>
--- NEW FILE: textarea-input.mason ---
<h2><% $value_name %></h2>
<p>Choose the <b><% $value_name %></b> that will be given to the
<% $entry_name %> entry you create.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th><% $value_name %></th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="<% $cgi_param_name %>"
rows="<% $rows %>"
cols="<% $cols %>"></textarea>
</td>
</tr>
</tbody>
</table>
<%args>
$entry_name
$cgi_param_name
$value_name
$default_value => ''
$rows => 5
$cols => 65
</%args>
<%once>
</%once>
<%init>
</%init>
|
|
From: <jas...@us...> - 2003-04-27 00:50:00
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv13746
Modified Files:
protocol-insert.html.in
Log Message:
now uses components for all parts
Index: protocol-insert.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/protocol-insert.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-insert.html.in 26 Apr 2003 21:12:41 -0000 1.1
--- protocol-insert.html.in 27 Apr 2003 00:49:57 -0000 1.2
***************
*** 13,157 ****
% } else {
! <h2>Read Group</h2>
! <p>Choose the <b>read group</b> that will be given to the
! protocol you are creating.</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 the
! protocol you are creating.</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 protocol. 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="proto_name" size="65" maxlength="128">
! </td>
! </tr>
! </tbody>
! </table>
<hr noshade size=5>
! <h2>Protocol Type</h2>
! <p>Choose the <b>Protocol Type</b> that describes the type of
! protocol.</p>
! <table bgcolor="#D8E4F7" border="1" cols="1">
! <thead bgcolor="#FFD78F">
! <tr>
! <th>Protocol Type</th>
! </tr>
! </thead>
! <tbody>
! <tr>
! <td>
! <& comps/query-drop-down.mason, name=>"protocol_type",
! array_ref=>\@protocol_types &>
! </td>
! </tr>
! </tbody>
! </table>
<hr noshade size=5>
! <h2>Protocol Description</h2> <p>Describe the protocol. 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>Protocol Description</th>
! </tr>
! </thead>
! <tbody>
! <tr>
! <td>
! <textarea name="proto_desc" rows="5" cols="65"></textarea>
! </td>
! </tr>
! </tbody>
! </table>
! <hr noshade size=5>
- <h2>URI</h2>
- <p> Provide an informational URI for the protocol (if any). 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>URI</th>
- </tr>
- </thead>
- <tbody>
- <tr>
- <td>
- <input type="text" name="uri" size="65" maxlength="128"/>
- </td>
- </tr>
- </tbody>
- </table>
<hr noshade size=5>
! <h2>Provider Contact</h2>
! <p>Choose the <b>Contact</b> entry who provided the protocol
! (if any).</p>
! <p>The entry must exist in the DB first, click <a
! href="contact-insert.html">here</a> if you need to enter the Contact info, then
! return to this page and hit your browsers <b>Reload</b> button.</p>
! <table bgcolor="#D8E4F7" border="1" cols="1">
! <thead bgcolor="#FFD78F">
! <tr>
! <th>Provider Contact</th>
! </tr>
! </thead>
! <tbody>
! <tr>
! <td>
! <& comps/query-drop-down.mason, name=>"provider",
! array_ref=>\@contacts &>
! </td>
! </tr>
! </tbody>
! </table>
<hr noshade size=5>
--- 13,51 ----
% } else {
!
! <& comps/ro_rw_group.mason, type=>$cur_class &>
<hr noshade size=5>
! <& comps/value-input.mason,
! value_name=>'Name',
! cgi_param_name=>'proto_name',
! entry_name=>$cur_class &>
<hr noshade size=5>
! <& comps/cv-menu.mason,
! cgi_param_name=>'protocol_type',
! entry_name=>$cur_class, type=>'Protocol Type',
! array_ref=>\@protocol_types &>
<hr noshade size=5>
! <& comps/textarea-input.mason,
! cgi_param_name=>'protocol_desc',
! entry_name=>$cur_class,
! value_name=>'Protocol Description',
! &>
<hr noshade size=5>
! <& comps/value-input.mason,
! value_name=>'URI',
! cgi_param_name=>'uri',
! entry_name=>$cur_class &>
<hr noshade size=5>
! <& comps/contacts.mason, type=>"$cur_class" &>
<hr noshade size=5>
***************
*** 187,192 ****
use Bio::Genex::Connect;
use Bio::Genex::Config;
- use Bio::Genex::Contact;
- use Bio::Genex::GroupSec;
use Bio::Genex::Protocol;
use Bio::Genex::ControlledVocab;
--- 81,84 ----
***************
*** 203,214 ****
# Apache::DB->handler;
- $dbh->assert_table_defined('GroupSec');
- $dbh->assert_table_defined('Protocol');
-
- my @groups;
- my $no_type = 'NONE';
- my @protocol_types = ([$no_type,$no_type]);
- my @contacts = ([$no_type,$no_type]);
my $data = '';
if ($submit) {
unless ($proto_desc) {
--- 95,102 ----
# Apache::DB->handler;
my $data = '';
+ my $no_type = 'NONE';
+ my @protocol_types;
+ my $cur_class = 'Protocol';
if ($submit) {
unless ($proto_desc) {
***************
*** 258,272 ****
}
} else {
- my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
- foreach my $gs_db (@gs_dbs) {
- push(@groups,[$gs_db->name,$gs_db->name]);
- }
-
- my @con_dbs = Bio::Genex::Contact->get_all_objects($dbh);
- foreach my $con_db (@con_dbs) {
- push(@contacts,[$con_db->con_pk,'[' . $con_db->contact_person .
- ":" . $con_db->organization . ']']);
- }
-
my @pt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
column=>'vocab_name',
--- 146,149 ----
|
|
From: <jas...@us...> - 2003-04-27 00:49:16
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv13368 Modified Files: arrays.html.in Log Message: added GENEX_EXTRALIBS Index: arrays.html.in =================================================================== RCS file: /cvsroot/genex/genex-server/Mason/workspace/arrays.html.in,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** arrays.html.in 21 Apr 2003 00:29:37 -0000 1.2 --- arrays.html.in 27 Apr 2003 00:49:13 -0000 1.3 *************** *** 9,12 **** --- 9,14 ---- </%attr> <%once>; + use lib qw(%%GENEX_EXTRALIBS%%); + use Bio::Genex; use Bio::Genex::Config; |
|
From: <jas...@us...> - 2003-04-27 00:47:41
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv11997
Added Files:
array-insert.html.in
Log Message:
new
--- NEW FILE: array-insert.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($error) {
<% $data %>
% } elsif ($submit) {
<h2><% $data %></h2>
% } else {
<& comps/ro_rw_group.mason, type=>$cur_class &>
<hr noshade size=5>
<& comps/value-input.mason,
value_name=>"Name",
cgi_param_name=>"array_name",
entry_name=>$cur_class &>
<hr noshade size=5>
<& comps/fkey-menu.mason,
class=>"ArrayDesign",
script=>"array-design.html",
cgi_param_name=>"ad_fk",
array_ref=>\@array_designs,
entry_name=>$cur_class &>
<hr noshade size=5>
<& comps/cv-menu.mason,
cgi_param_name=>'technology_type',
entry_name=>$cur_class, type=>'Technology Type',
array_ref=>\@technology_types &>
<hr noshade size=5>
<& comps/textarea-input.mason,
cgi_param_name=>"array_desc",
entry_name=>$cur_class,
value_name=>"Physical BioAssay Description",
&>
<hr noshade size=5>
<& comps/contacts.mason, type=>"$cur_class" &>
<hr noshade size=5>
<input type="submit" name="submit" value="Create Physical BioAssay" size="33">
<& comps/hiddenlist.mason, name=>"debug", value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$provider => ''
$read_group => ''
$write_group => ''
$array_desc => ''
$ad_fk => ''
$array_name => ''
$technology_type => ''
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/array-insert.html"
name=>'GeneX DB Array Creation Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/array-insert.html"
</%attr>
<%once>
use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::Array;
use Bio::Genex::ArrayDesign;
use Bio::Genex::ControlledVocab;
# use Apache::DB ();
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $error;
# Apache::DB->init;
# Apache::DB->handler;
my $data = '';
my $cur_class = 'Array';
$dbh->assert_table_defined($cur_class);
my @array_designs;
my @technology_types;
if ($submit) {
# handle required arguments
unless ($ad_fk) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>ad_fk</b> not provided</p>
EOE
goto ERROR;
}
unless ($array_name) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>array_name</b> not provided</p>
EOE
goto ERROR;
}
unless ($technology_type) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>technology_type</b> not provided</p>
EOE
goto ERROR;
}
my @pks;
my $array_db = Bio::Genex::Array->new();
$array_db->name($array_name);
$array_db->technology_type($technology_type);
$array_db->ro_groupname($read_group);
$array_db->rw_groupname($write_group);
$array_db->ad_fk($ad_fk);
if ($provider) {
$array_db->provider_con_fk($provider);
}
if ($array_desc) {
$array_desc =~ s/\'//;
$array_db->description($array_desc);
}
my $pk = $array_db->insert_db($dbh);
unless (defined $pk) {
$error = 1;
$data = <<EOE;
<p>DBI Error while Inserting $cur_class</p>
<p>Error output = <$DBI::errstr></p>
EOE
goto ERROR;
} else {
$data = "$cur_class, $array_name, Successfully Created with pkey: $pk";
}
} else {
my @ad_dbs = Bio::Genex::ArrayDesign->get_all_objects($dbh);
foreach my $ad_db (@ad_dbs) {
push(@array_designs,[$ad_db->ad_pk,
$ad_db->name,
]);
}
my @tt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
column=>'vocab_name',
value=>'AL_TechnologyType',
);
foreach my $tt_db (@tt_dbs) {
push(@technology_types,[$tt_db->term_string,$tt_db->term_string]);
}
}
ERROR : {
$data = qq[<font color="red"><h2>ERROR</h2><b>$data</b></font>]
if $error;
}
</%init>
|
|
From: <jas...@us...> - 2003-04-27 00:46:55
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv11447
Modified Files:
autohandler.in
Log Message:
removed debuggin cruft
Index: autohandler.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/autohandler.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** autohandler.in 26 Apr 2003 21:23:40 -0000 1.6
--- autohandler.in 27 Apr 2003 00:46:52 -0000 1.7
***************
*** 37,43 ****
my $index = "$Bio::Genex::Config->{GENEX_MASON_URL}/index.html";
- print STDERR "Found index=<$index>,src=<$src>\n";
- print STDERR "Using Bio::Genex::Config=<$INC{'Bio/Genex/Config.pm'}>\n";
-
# we localize $dbh and $session so that they last only the duration of the request
local $dbh;
--- 37,40 ----
|
|
From: <jas...@us...> - 2003-04-27 00:46:43
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv10973
Added Files:
sample-protocols.html.in physicalbioassay-insert.html.in
Log Message:
new
--- NEW FILE: sample-protocols.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($error) {
<h2><% $data %></h2>
% } elsif ($submit) {
<h2><% $data %></h2>
% } elsif ($sample_fk) {
<h2>Associating Protocol Application Events with Sample <% $sample_name %></h2>
<table bgcolor="#D8E4F7" width="444" border="1">
<theader>
<th colspan="100"><b>Protocol Application Entries</b></th>
</theader>
<& comps/objs2table.mason, objects=>\@protocol_app_dbs,
check=>1, check_header=>'Include', check_name=>'include_protocol'
&>
</table>
<input type="submit" name="submit"
value="Add Protocols to Sample" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<& comps/hiddenlist.mason, name=>'sample_fk', value=>$sample_fk &>
<hr noshade size=5>
% } else {
<h2>Choose a Sample</h2>
<p>In order to associate <b>Protocol Applications</b> with
a <b>Sample</b>, your must first choose the <b>Sample</b>
entry which is being applied</p>
<p>Then you will have the opportunity to associate the
<b>Protocol Applications</b> events events for this
<b>Sample</b></p>
<& comps/fkey-menu.mason,
class=>'Sample',
script=>'sample-insert.html',
cgi_param_name=>'sample_fk',
array_ref=>\@samples,
entry_name=>$cur_class &>
<hr noshade size=5>
<input type="submit" name="sample"
value="Choose Sample" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$sample => ''
$sample_fk => ''
$include_protocol => ''
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-protocols.html"
name=>'GeneX DB Sample Protocols Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-protocols.html"
</%attr>
<%once>
use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
use Bio::Genex::Config;
use Bio::Genex::Sample;
use Bio::Genex::ProtocolApplication;
use Bio::Genex::ProtocolApplicationLink;
use Bio::Genex::Protocol;
# use Apache::DB ();
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $cur_class = 'Sample';
my $other_class = 'ProtocolStepApplication';
# Apache::DB->init;
# Apache::DB->handler;
my $no_type = 'NONE';
my $data = '';
my $error;
my @samples;
my @protocol_app_dbs;
my $sample_name;
my $sample_db;
if ($sample) {
$sample_db = Bio::Genex::Sample->new(dbh=>$dbh,id=>$sample_fk);
$sample_name = $sample_db->name;
@protocol_app_dbs = Bio::Genex::ProtocolApplication->get_all_objects($dbh);
} elsif ($submit) {
my @pks;
my @protocol_pks = ref($include_protocol) eq 'ARRAY' ? @{$include_protocol}
: $include_protocol;
foreach my $proto_pk (@protocol_pks) {
my $proto_db =
Bio::Genex::ProtocolApplicationLink->new(proto_app_fk=>$proto_pk,
other_fk=>$sample_fk,
);
my $pk = $proto_db->insert_db($dbh);
unless (defined $pk) {
$error = 1;
$data = <<EOE;
<p>Inserting Protocol Application: $proto_pk, Sample: $sample_fk</p>
<p>Error output = <$DBI::errstr></p>
EOE
goto ERROR;
}
push(@pks,$pk);
}
$data = "Protocols Successfully Added with primary keys: " . join(' ', @pks);
} else {
my @samp_dbs = Bio::Genex::Sample->get_all_objects($dbh);
foreach my $samp_db (@samp_dbs) {
push(@samples,[$samp_db->smp_pk,
$samp_db->name,
]);
}
}
ERROR : {
$data = qq[<font color="red"><h2>ERROR</h2><b>$data</b></font>]
if $error;
}
</%init>
--- NEW FILE: physicalbioassay-insert.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($error) {
<% $data %>
% } elsif ($submit) {
<h2><% $data %></h2>
% } else {
<& comps/ro_rw_group.mason, type=>$cur_class &>
<hr noshade size=5>
<& comps/value-input.mason,
value_name=>"Name",
cgi_param_name=>"pba_name",
entry_name=>$cur_class &>
<hr noshade size=5>
<& comps/fkey-menu.mason,
class=>"ExperimentSet",
script=>"experimentset-create.html",
cgi_param_name=>"es_fk",
array_ref=>\@experiments,
entry_name=>$cur_class &>
<hr noshade size=5>
<& comps/fkey-menu.mason,
class=>"Array",
script=>"array-insert.html",
cgi_param_name=>"array_fk",
array_ref=>\@arrays,
entry_name=>$cur_class &>
<hr noshade size=5>
<& comps/textarea-input.mason,
cgi_param_name=>"pba_desc",
entry_name=>$cur_class,
value_name=>"Physical BioAssay Description",
&>
<hr noshade size=5>
<& comps/contacts.mason, type=>"$cur_class" &>
<hr noshade size=5>
<input type="submit" name="submit" value="Create Physical BioAssay" size="33">
<& comps/hiddenlist.mason, name=>"debug", value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$provider => ''
$read_group => ''
$write_group => ''
$pba_desc => ''
$es_fk => ''
$array_fk => ''
$pba_name => ''
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/physicalbioassay-insert.html"
name=>'GeneX DB Physical BioAssay Creation Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/physicalbioassay-insert.html"
</%attr>
<%once>
use lib qw(%%GENEX_EXTRALIBS%%);
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::Contact;
use Bio::Genex::GroupSec;
use Bio::Genex::PhysicalBioAssay;
use Bio::Genex::ControlledVocab;
# use Apache::DB ();
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $error;
# Apache::DB->init;
# Apache::DB->handler;
my $data = '';
my $cur_class = 'PhysicalBioAssay';
$dbh->assert_table_defined($cur_class);
my @experiments;
my @arrays;
if ($submit) {
# handle required arguments
unless ($es_fk) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>es_fk</b> not provided</p>
EOE
goto ERROR;
}
unless ($array_fk) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>array_fk</b> not provided</p>
EOE
goto ERROR;
}
unless ($pba_name) {
$error = 1;
$data = <<EOE;
<p>Required argument <b>pba_name</b> not provided</p>
EOE
goto ERROR;
}
my @pks;
my $pba_db = Bio::Genex::PhysicalBioAssay->new();
$pba_db->name($pba_name);
$pba_db->ro_groupname($read_group);
$pba_db->rw_groupname($write_group);
$pba_db->es_fk($es_fk);
$pba_db->array_fk($array_fk);
if ($provider) {
$pba_db->provider_con_fk($provider);
}
if ($pba_desc) {
$pba_desc =~ s/\'//;
$pba_db->description($pba_desc);
}
my $pk = $pba_db->insert_db($dbh);
unless (defined $pk) {
$error = 1;
$data = <<EOE;
<p>DBI Error while Inserting $cur_class</p>
<p>Error output = <$DBI::errstr></p>
EOE
goto ERROR;
} else {
$data = "$cur_class, $pba_name, Successfully Created with pkey: $pk";
}
} else {
my @exp_dbs = Bio::Genex::ExperimentSet->get_all_objects($dbh);
foreach my $exp_db (@exp_dbs) {
push(@experiments,[$exp_db->es_pk,
$exp_db->name,
]);
}
my @array_dbs = Bio::Genex::Array->get_all_objects($dbh);
foreach my $array_db (@array_dbs) {
push(@arrays,[$array_db->array_pk,
$array_db->name,
]);
}
}
ERROR : {
$data = qq[<font color="red"><h2>ERROR</h2><b>$data</b></font>]
if $error;
}
</%init>
|
|
From: <jas...@us...> - 2003-04-26 23:29:12
|
Update of /cvsroot/genex/genex-server/DB/xml In directory sc8-pr-cvs1:/tmp/cvs-serv30849/DB/xml Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/DB/xml/ChangeLog,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ChangeLog 23 Apr 2003 21:12:41 -0000 1.2 --- ChangeLog 26 Apr 2003 23:29:08 -0000 1.3 *************** *** 1,2 **** --- 1,16 ---- + 2003-04-26 Jason E. Stewart <ja...@op...> + + * ProtocolStepApplication.xml (Repository): + What: changed protocol_step_fk => proto_step_fk + Why: to match the name of the primary key in the ProtocolStep + table, which is proto_step_pk + + * QuantitationLink.xml (Repository): + * ProtocolStep.xml (Repository): + What: changed order => protocol_order + Why: 'order' is an SQL reserverd word and causes Postgres to barf + if it is not properly handled, and it is too hard to figure out + all the cases of how to properly handle it + 2003-04-23 Jason E. Stewart <ja...@op...> |
|
From: <jas...@us...> - 2003-04-26 23:28:24
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv29854
Modified Files:
TODO ChangeLog
Log Message:
usual
Index: TODO
===================================================================
RCS file: /cvsroot/genex/genex-server/TODO,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** TODO 16 Apr 2003 23:30:23 -0000 1.22
--- TODO 26 Apr 2003 23:28:20 -0000 1.23
***************
*** 1,14 ****
TODO
=======
Wed Apr 16 14:57:39 MDT 2003
* Make a synonym table for DB table names and column names
* start removing all the unnecessary '%%FOO%%' flags and .in files now
that we can use $Bio::Genex::Config->{FOO} directly
Mon Apr 7 10:20:59 MDT 2003
! * why is quantitationdimension and quantitationdimension_view in the
DB?
! * add return to index to all mason apps
! * need to quote groupname in 'create-experiment.html'
Thu Oct 17 13:41:31 MDT 2002
--- 1,64 ----
TODO
=======
+ Sat Apr 26 15:30:10 MDT 2003
+ * fix protocol-insert.html to indicate required fields
+ * fix Mason apps to use ro_rw_group.mason and other components
+ * fix Mason apps to show error properly
+ * fix Mason apps to show primary key after insert
+ * start entering todo items into SF bug tracker
+ * document how to rename the default perl installation:
+ /usr/bin/perl Configure --GENEX_DIR
+ * added GENEX_NAME and use it instead of GENEX_DIR for the default
+ names of the DB, etc.
+ * document how to install the Perl API in a private location
+ /usr/bin/perl Configure --PRIVATE_PERL_API
+
+
+ Thu Apr 24 09:40:30 MDT 2003
+ * handle GENEX_EXTRALIBS by using a BEGIN block:
+ begin {
+ use Bio::Genex::Config;
+ use lib $Bio::Genex::Config->{GENEX_EXTRALIBS};
+ }
+ this will eliminate all pl.in substitutions except START_PERL
+ * fix the subroutine in Install that checks the perl version to use GENEX_EXTRALIBS
+
+ Mon Apr 21 10:22:59 MDT 2003
+ * add emission energy to channel table
+ * add PhysicalBioAssay insertion program and GUI
+ * fix schema html pages
+ * add archive_data_uri column to PhysicalBioAssay to be the directory
+ that holds all on-disk but not in DB data for the PBA, like the .DAT,
+ .CEL, .RPT files
+ * add per-user upload directories
+ - add Unix user when creating new Genex user (for samba)
+ * for scripts like group-create.html that have a link to a
+ followup program, check that the user has the privelege to modify
+ the newly created data, otherwise, they get a wierd error
+ * start identifying permission groups for various tables, e.g. admin,
+ curator, user
+ * investigate the --controlled flag for create_genex_class.pl, and see
+ if things are happening as they should
+ * fix ProtocolStep table so that there is a unique index on
+ protocol_fk, order
+
+ Sun Apr 20 13:50:13 MDT 2003
+ * data-sources.html broken
+ * query.html broken because Provider is gone
+ fixed => * add ParameterValue insertion program and GUI
+ fixed => * add Sample insertion program and GUI
+
Wed Apr 16 14:57:39 MDT 2003
* Make a synonym table for DB table names and column names
* start removing all the unnecessary '%%FOO%%' flags and .in files now
that we can use $Bio::Genex::Config->{FOO} directly
+ * fix install so that Perl API files can be installed into a private
+ directory
Mon Apr 7 10:20:59 MDT 2003
! fixed => * why is quantitationdimension and quantitationdimension_view in the
DB?
! fixed => * add return to index to all mason apps
! fixed => * need to quote groupname in 'create-experiment.html'
Thu Oct 17 13:41:31 MDT 2002
***************
*** 24,141 ****
- QC: test data sets (Affy - MAS4/5, QuantArray, GenePix)
- talk to Brandon about Caltech MAGE work
-
- Sat May 26 23:38:47 MDT 2001
- * update INSTALL to explain Xerces installation
-
- Mon Feb 5 21:04:50 MST 2001
- * fix db-update script to use Genex.pm classes instead of raw SQL
-
- Tue Jan 23 09:17:48 MST 2001
- fixed ==> * remove CSF
- fixed ==> * fix broken DTD's
- fixed ==> * remove default passwords for readonly/genex
- * get rid of jpywork dir from CVS
- fixed ==> * add Term::ReadKey to required mods for install-all
- * fix MANIFEST
-
- Tue Jan 16 11:21:14 MST 2001
- fixed ==> * Move over to Class::ObjectTemplate::DB
-
- Fri Jan 12 14:57:30 MST 2001
- fixed ==> * db2xml shouldn't check passwords
- fixed ==> * make sure no CVS files get copied
- * why don't GNU apps get reset accepting cache defaults?
-
- Sat Jan 6 14:33:43 MST 2001
- fixed ==> * DTD shouldn't copy CVS
- fixed ==> * use $^X if it's a full path (check with -x), use startperl otherwise.
- fixed ==> * add checks for DB actually existing
- fixed ==> * add Genex.pm html into html installation tree
- fixed ==> * add dtd2html
- fixed ==> * must crap out if required perl modules not installed
-
- Fri Jan 5 16:42:54 MST 2001
- fixed ==> * GENEX_CGIDIR/samples must be created by install-all.pl
- fixed ==> * runa.so isn't created by the time install-all tries to install it
- fixed ==> * SUBMISSION_HOME should be set automatically after local root
- fixed ==> * questions should go to STDOUT, diagnostics should go to STDERR
-
- Thu Dec 28 13:45:54 MST 2000
- * Get rid of global variables and just use %Vars
-
- = change --SLOW to --FAST and invert the tests so that it it will by defulat go
- slow unless youwant it to go fast...
-
- fixed ==> = need to move the graphics subdir URLS to refer to /genex/graphics rather than
- /graphics
-
- fixed ==> = add mergem utility
-
- fixed ==> = note that we need the INSTALLATION GUIDE that is mentioned
- in the 1st splash screen
-
- fixed ==> = submission home directory? [/tmp/submission] (if chose
- /tmp/genex in 1st ?, this should be /tmp/genex/submission
-
- fixed ==> = #### Sorry, user /tmp/submission doesn't work, try again ####
- this should ask whether you want me to create it
- fixed ==> = What DBMS driver should DBI use by default?
- should we give some alternatives at this point?
- fixed ==> = What username should DBI use for the readonly user?
- [add some explanatory text about this - maybe decide on a format for
- allowing each answer to have additional help avialable, as in
- linux kernel config procedure...]
- fixed ==> = What username should DBI use for the super-user account?
- [more help needed]
- = http://cx408397-a.irvn1.occa.home.com/genex/index.html
- [indicated at end as the home URL, isn't installed there]
-
- 11.11.00 - CyberT Ananlyses (from the gxfetchpage) help needs more
- docs in the CyberT help file to explain what the Paired and
- C+E need in terms of minimum number of arrays, etc. should
- really collapse the CyberT form script into 1 - the analytical
- scripts should also be collapsed bu they might be a bit more
- complex to do so.
-
- 11.10.00 - Need to relabel or add help to note that the Current "Retrieve"
- Column in gxfetch_array1.pl indicates to "select for Retrieve or Paired
- Analysis" maybe "Paired / <BR>Retrieve" ? And add matching docs to the
- "What can I do with this Array Table" Should probably rename it to "What do
- the selections allow you to do in the Array Table Below"
-
- 11.01.00 - not going to skip these - might change the GetOrSetGNU() to stop
- only if there's a failure to find one of the GNU Apps; ditto GetOrSet()
-
- 10.31.00 - rationalize how to treat the GeneX-ified stuff to be able to use
- the the regular CyberT files without a huge amount of hand-editing. Talk
- to William about this..? Use Frames and then include other files into the
- frames instead of tables and requireing hand-editing?
-
- what about the samples subdir? on genex??
- referenced in curation-tool/generate-cb.pl
- ? Setting $JobDir in curation-tool/generate-cb.pl
-
- ? htdocs/download dir? bundle with curation-tool? Probably keep separate
- and just cp everything to the right place. Isn;t really related to the
- C-T except as a download access site.
- should use it for all downloads, instead of breaking all the bits up into
- a zillion places...? except that each of the zillion different files are more
- related to the function rather than the download thingie itself... Hmmmmm
-
- still need to be able to skip those stanzas whose vars have been defined
- already. Easy, but tedious. Save til tomorrow.
-
- 10.29.00 - replace all the shebang perl stuff with %%START_PERL%% to make
- sure all the scripts work OK..
- - also have to replace all the substitution var pre/suffixes in the CyberT with
- '%%' instead of '__'
-
-
- 10-28-00 recursion works; now have to edit the .in files to insert the
- correct the !!VARS!! Only have to do the CyberT and gxquery scripts
- (and then mod the query script to allow the addition of the C&E
- script... After that, only have to finish the install-all script
- (rename to install-analyses?) and package.. submit to CVS..
-
### *** emacs file mode definition ***
--- 74,77 ----
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.128
retrieving revision 1.129
diff -C2 -d -r1.128 -r1.129
*** ChangeLog 20 Apr 2003 02:10:56 -0000 1.128
--- ChangeLog 26 Apr 2003 23:28:20 -0000 1.129
***************
*** 1,2 ****
--- 1,84 ----
+ 2003-04-26 Jason E. Stewart <ja...@op...>
+
+ * Install (Repository):
+ now copies the genex-2.conf file to LOCAL_ETC
+ added creation of LOCAL_ETC *before* installing MANIFEST files
+
+ * Configure (Repository):
+ Added LOCAL_ETC, GENEX_MASON_HANDLER, PRIVATE_PERL_API
+ renamed GENEX_MASON_DIR => GENEX_MASON_COMP_ROOT
+ brought back the ability to install the Perl API to a private
+ location, but like modifying the default name of the genex
+ installation, it can only be indicated by runing the script as:
+ /usr/bin/perl Configure --PRIVATE_PERL_API
+ Changed how GENEX_EXTRALIBS is used, it no longer includes the
+ 'use lib' portion, and is instead a list of directory names
+ that must be wrapped like: 'use lib qw(%%GENEX_EXTRALIBS%%')
+
+ * Mason/workspace/protocol-step-insert.html.in (Repository):
+ fixed 'order' => 'protocol_order'
+
+ * Mason/workspace/comps/contacts.mason (Repository):
+ * Mason/workspace/comps/authenticate.mason.in (Repository):
+ * Mason/workspace/add_user_to_group.html.in (Repository):
+ * Mason/workspace/array-design.html.in (Repository):
+ * Mason/workspace/authenticate.html.in (Repository):
+ * Mason/workspace/autohandler.in (Repository):
+ * Mason/workspace/bioassay.html.in (Repository):
+ * Mason/workspace/contact-insert.html.in (Repository):
+ * Mason/workspace/data-loader.html.in (Repository):
+ * Mason/workspace/data-sources.html.in (Repository):
+ * Mason/workspace/experiments.html.in (Repository):
+ * Mason/workspace/experimentset-create.html.in (Repository):
+ * Mason/workspace/generate_group.html.in (Repository):
+ * Mason/workspace/generate_user.html.in:
+ * Mason/workspace/group-create.html.in:
+ * Mason/workspace/group-maint.html.in:
+ * Mason/workspace/kill-cookie.html.in:
+ * Mason/workspace/noauth-autohandler.in:
+ * Mason/workspace/query.html.in:
+ * Mason/workspace/sample-insert.html.in:
+ * Mason/workspace/user-insert.html.in:
+ * Mason/workspace/workspace.html.in:
+ added GENEX_EXTRALIBS
+
+ * apache/genex-2.conf.in (Message):
+ seperated out the MasonCompRoot and MasonDataDir from the
+ substitution
+ added the handler.pl
+ removed the importing of modules, hopefully having it in the
+ handler script will work better for Apache
+
+ * apache/genex-2-handler.pl.in:
+ A first shot at using a handler.pl file to run Mason
+
+ 2003-04-23 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/parameter-value-insert.html (Repository):
+ replaced repetitive code with new components
+
+ * Mason/workspace/comps/ro_rw_group.mason (Repository):
+ added the ability to set default groups for each menu
+
+ * Mason/workspace/protocol-application-insert.html (Repository):
+ Added a better introduction message
+
+ 2003-04-21 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/sample-insert.html.in (Repository):
+ * Mason/workspace/protocol-step-insert.html (Repository):
+ * Mason/workspace/protocol-insert.html (Repository):
+ * Mason/workspace/procedure-insert.html (Repository):
+ * Mason/workspace/parameter-insert.html (Repository):
+ * Mason/workspace/group-create.html.in (Repository):
+ * Mason/workspace/data-loader.html.in (Repository):
+ * Mason/workspace/array-design.html.in (Repository):
+ all command line args are quoted
+
+ 2003-04-20 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/index.html (Repository):
+ reorganized
+
2003-04-19 Jason E. Stewart <ja...@op...>
|
|
From: <jas...@us...> - 2003-04-26 23:26:51
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv29301
Modified Files:
Install
Log Message:
now copies the genex-2.conf file to LOCAL_ETC
added creation of LOCAL_ETC *before* installing MANIFEST files
Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Install 25 Nov 2002 21:49:24 -0000 1.18
--- Install 26 Apr 2003 23:26:46 -0000 1.19
***************
*** 476,479 ****
--- 476,487 ----
+
+ ######################################################################
+ #
+ # the etc dir
+ #
+ $DIR = $VARS{LOCAL_ETC};
+ genex_mkdir($DIR,755) unless -d $DIR;
+
######################################################################
#
***************
*** 812,820 ****
#############################################################################
! # Copy the genex-2.conf file to $APACHE_CONF_DIR
#############################################################################
! $DIR = $APACHE_CONF_DIR;
my $file = 'genex-2.conf';
- # genex_system("cp $MOTHERDIR/apache/$file $DIR");
print STDERR <<EOT;
--- 820,827 ----
#############################################################################
! # Let the user know about including the apache config file
#############################################################################
! $DIR = $VARS{LOCAL_ETC};
my $file = 'genex-2.conf';
print STDERR <<EOT;
|