Menu
▾
▴
genex-cvs-commit — CVS commit messages
You can subscribe to this list here.
| 2002 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(267) |
Nov
(344) |
Dec
(119) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2003 |
Jan
(23) |
Feb
(15) |
Mar
(16) |
Apr
(388) |
May
|
Jun
(4) |
Jul
|
Aug
|
Sep
(4) |
Oct
|
Nov
|
Dec
|
|
From: <jas...@us...> - 2003-04-23 21:15:14
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv13555
Modified Files:
Array.xml ArrayDesign.xml Contact.xml ControlledVocab.xml
ExperimentSet.xml ExternalDatabase.xml GroupSec.xml
ParameterValue.xml Parameterizable.xml PhysicalBioAssay.xml
Reporter.xml Sample.xml Species.xml UserSec.xml
Log Message:
* UserSec.xml (Repository):
* Species.xml (Repository):
* Sample.xml (Repository):
* Reporter.xml (Repository):
* PhysicalBioAssay.xml (Repository):
* Parameterizable.xml (Repository):
* ParameterValue.xml (Repository):
* ExperimentSet.xml (Repository):
* ControlledVocab.xml (Repository):
* ExternalDatabase.xml (Repository):
* ArrayDesign.xml (Repository):
* Array.xml (Repository):
added is_securable flag to indicate the table will recieve
ro_groupname, rw_groupname, and audit_fk columns because the
Pymerase group wanted an easier way to know if a table was
going to be given a security view or not.
Index: Array.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Array.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Array.xml 16 Apr 2003 21:22:28 -0000 1.3
--- Array.xml 23 Apr 2003 21:15:00 -0000 1.4
***************
*** 2,8 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Array"
! type="DATA"
! comment="The Array table describes the physical instantiation of
! an ArrayDesign">
<column name="array_pk"
full_name="Accession Number"
--- 2,9 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Array"
! is_securable="true"
! type="DATA"
! comment="The Array table describes the physical instantiation of
! an ArrayDesign">
<column name="array_pk"
full_name="Accession Number"
Index: ArrayDesign.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ArrayDesign.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ArrayDesign.xml 23 Nov 2002 07:57:16 -0000 1.2
--- ArrayDesign.xml 23 Apr 2003 21:15:00 -0000 1.3
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ArrayDesign"
! type="DATA"
! comment="The ArrayDesign table describes the template or model
from which any number of physically distinct (but conceptually
identical) instances of Arrays (e.g. glass slide or chip) are
--- 2,8 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ArrayDesign"
! is_securable="true"
! type="&data_table;"
! comment="The ArrayDesign table describes the template or model
from which any number of physically distinct (but conceptually
identical) instances of Arrays (e.g. glass slide or chip) are
Index: Contact.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Contact.xml,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Contact.xml 23 Nov 2002 07:57:16 -0000 1.7
--- Contact.xml 23 Apr 2003 21:15:00 -0000 1.8
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Contact"
! type="&data_table;"
! comment=" The Contact table provides information that can be
used to contact either data providers or suppliers of particular
technologies, e.g. arrays, hardware and software. The meanings
--- 2,8 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Contact"
! is_securable="true"
! type="&data_table;"
! comment=" The Contact table provides information that can be
used to contact either data providers or suppliers of particular
technologies, e.g. arrays, hardware and software. The meanings
Index: ControlledVocab.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ControlledVocab.xml,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ControlledVocab.xml 23 Nov 2002 07:57:16 -0000 1.7
--- ControlledVocab.xml 23 Apr 2003 21:15:00 -0000 1.8
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ControlledVocab"
! type="&validation_table;"
! comment=" The ControlledVocab table is used to store the vocabularies for the columns of all tables in the DB that are curated by NCGR">
<column name="ro_groupname"
full_name="Read-Only Group Name"
--- 2,10 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ControlledVocab"
! is_securable="true"
! type="&validation_table;"
! comment=" The ControlledVocab table is used to store the
! vocabularies for the columns of all tables in the DB that are
! curated">
<column name="ro_groupname"
full_name="Read-Only Group Name"
Index: ExperimentSet.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ExperimentSet.xml,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** ExperimentSet.xml 23 Nov 2002 07:57:16 -0000 1.8
--- ExperimentSet.xml 23 Apr 2003 21:15:00 -0000 1.9
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ExperimentSet"
! type="&data_table;"
! comment=" The ExperimentSet table groups a set of
PhysicalBioAssay rows into a coherent collection representing a
conceptually related set of treatments (e.g. time series or
--- 2,8 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ExperimentSet"
! is_securable="true"
! type="&data_table;"
! comment=" The ExperimentSet table groups a set of
PhysicalBioAssay rows into a coherent collection representing a
conceptually related set of treatments (e.g. time series or
Index: ExternalDatabase.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ExternalDatabase.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ExternalDatabase.xml 23 Nov 2002 07:57:16 -0000 1.6
--- ExternalDatabase.xml 23 Apr 2003 21:15:01 -0000 1.7
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ExternalDatabase"
! type="&data_table;"
! comment=" The ExternalDatabase table gives information that may be used to access databases outside of GeneX for information about Reporters. The information stored here is used to create hyperlinks in HTML output of various routines.">
<column name="ed_pk"
full_name="Accession Number"
--- 2,11 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="ExternalDatabase"
! is_securable="true"
! type="&data_table;"
! comment=" The ExternalDatabase table gives information that may
! be used to access databases outside of GeneX for information
! about Reporters. The information stored here is used to create
! hyperlinks in HTML output of various routines.">
<column name="ed_pk"
full_name="Accession Number"
Index: GroupSec.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/GroupSec.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** GroupSec.xml 23 Nov 2002 07:57:16 -0000 1.6
--- GroupSec.xml 23 Apr 2003 21:15:01 -0000 1.7
***************
*** 2,8 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="GroupSec"
! type="&data_table;"
! can_self_reference="true"
! comment=" The GroupSec table denotes the groups to which users
may be assigned and with which certain data items
(ExperimentSet, PhysicalBioAssay) may be associated for access
--- 2,9 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="GroupSec"
! is_securable="true"
! type="&data_table;"
! can_self_reference="true"
! comment=" The GroupSec table denotes the groups to which users
may be assigned and with which certain data items
(ExperimentSet, PhysicalBioAssay) may be associated for access
Index: ParameterValue.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ParameterValue.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** ParameterValue.xml 22 Apr 2003 00:47:57 -0000 1.3
--- ParameterValue.xml 23 Apr 2003 21:15:01 -0000 1.4
***************
*** 4,10 ****
]>
<table name="&table_name;"
! type="&data_table;"
! comment=" The &table_name; table contains the values for
! parameters used in any step.">
<column name="param_value_pk"
full_name="Accession Number"
--- 4,11 ----
]>
<table name="&table_name;"
! is_securable="true"
! type="&data_table;"
! comment=" The &table_name; table contains the values for
! parameters used in any step.">
<column name="param_value_pk"
full_name="Accession Number"
Index: Parameterizable.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Parameterizable.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Parameterizable.xml 16 Apr 2003 21:21:47 -0000 1.1
--- Parameterizable.xml 23 Apr 2003 21:15:01 -0000 1.2
***************
*** 4,11 ****
]>
<table name="&table_name;"
! inherits_from="Identifiable"
! type="&data_table;"
! comment="The &table_name; table is an abstract table that other
! tables inherit from. It specifies that things can have parameters">
<column name="param_pk"
full_name="Accession Number"
--- 4,12 ----
]>
<table name="&table_name;"
! is_abstract="true"
! inherits_from="Identifiable"
! type="&data_table;"
! comment="The &table_name; table is an abstract table that other
! tables inherit from. It specifies that things can have parameters">
<column name="param_pk"
full_name="Accession Number"
Index: PhysicalBioAssay.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/PhysicalBioAssay.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** PhysicalBioAssay.xml 23 Nov 2002 07:57:16 -0000 1.4
--- PhysicalBioAssay.xml 23 Apr 2003 21:15:01 -0000 1.5
***************
*** 2,6 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="PhysicalBioAssay"
! type="&data_table;"
comment=" The PhysicalBioAssay table is used in two related, but
distinct fashions: to represent the primary data for gene
--- 2,7 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="PhysicalBioAssay"
! is_securable="true"
! type="&data_table;"
comment=" The PhysicalBioAssay table is used in two related, but
distinct fashions: to represent the primary data for gene
Index: Reporter.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Reporter.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Reporter.xml 23 Nov 2002 07:57:16 -0000 1.2
--- Reporter.xml 23 Apr 2003 21:15:01 -0000 1.3
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Reporter"
! type="&data_table;"
! comment=" The Reporter table describes the genetic elements that are used as probes in gene expression experiments (e.g. the cDNA elements that are immobilized on a glass slide). They can be cloned genes, ESTs, etc.">
<column name="rep_pk"
full_name="Accession Number"
--- 2,11 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Reporter"
! is_securable="true"
! type="&data_table;"
! comment=" The Reporter table describes the genetic elements
! that are used as probes in gene expression experiments
! (e.g. the cDNA elements that are immobilized on a glass
! slide). They can be cloned genes, ESTs, etc.">
<column name="rep_pk"
full_name="Accession Number"
Index: Sample.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Sample.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Sample.xml 23 Nov 2002 07:57:16 -0000 1.6
--- Sample.xml 23 Apr 2003 21:15:01 -0000 1.7
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Sample"
! type="&data_table;"
! comment=" The Sample table gives detailed information concerning the derivation of the DNA used to hybridize with an instance of an Array. ">
<column name="smp_pk"
full_name="Accession Number"
--- 2,10 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Sample"
! is_securable="true"
! type="&data_table;"
! comment=" The Sample table gives detailed information
! concerning the derivation of the DNA used to hybridize with an
! instance of an Array. ">
<column name="smp_pk"
full_name="Accession Number"
Index: Species.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Species.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Species.xml 23 Nov 2002 07:57:16 -0000 1.5
--- Species.xml 23 Apr 2003 21:15:01 -0000 1.6
***************
*** 2,7 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Species"
! type="&data_table;"
! comment=" The Species table characterizes primary taxonomic information concerning the organisms being researched. It can be used to obtain further taxonomic data for the species in question.">
<column name="spc_pk"
full_name="Accession Number"
--- 2,11 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="Species"
! is_securable="true"
! type="&data_table;"
! comment=" The Species table characterizes primary taxonomic
! information concerning the organisms being researched. It can
! be used to obtain further taxonomic data for the species in
! question.">
<column name="spc_pk"
full_name="Accession Number"
Index: UserSec.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/UserSec.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** UserSec.xml 23 Nov 2002 07:57:16 -0000 1.5
--- UserSec.xml 23 Apr 2003 21:15:01 -0000 1.6
***************
*** 2,9 ****
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="UserSec"
! type="&data_table;"
! comment=" The UserSec is now a mirror of the system user table
! (pg_user for Postgres), and mainly exists to store a reference
! to the contact information for the user.">
<column name="username"
full_name="User Name"
--- 2,10 ----
<!DOCTYPE table SYSTEM "../../DTD/table.dtd">
<table name="UserSec"
! is_securable="true"
! type="&data_table;"
! comment=" The UserSec is now a mirror of the system user table
! (pg_user for Postgres), and mainly exists to store a reference
! to the contact information for the user.">
<column name="username"
full_name="User Name"
|
|
From: <jas...@us...> - 2003-04-23 21:12:44
|
Update of /cvsroot/genex/genex-server/DB/xml In directory sc8-pr-cvs1:/tmp/cvs-serv13178 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/DB/xml/ChangeLog,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ChangeLog 23 Apr 2003 21:00:06 -0000 1.1 --- ChangeLog 23 Apr 2003 21:12:41 -0000 1.2 *************** *** 1,4 **** --- 1,28 ---- 2003-04-23 Jason E. Stewart <ja...@op...> + * UserSec.xml (Repository): + * Species.xml (Repository): + * Sample.xml (Repository): + * Reporter.xml (Repository): + * PhysicalBioAssay.xml (Repository): + * Parameterizable.xml (Repository): + * ParameterValue.xml (Repository): + * ExperimentSet.xml (Repository): + * ControlledVocab.xml (Repository): + * ExternalDatabase.xml (Repository): + * ArrayDesign.xml (Repository): + * Array.xml (Repository): + added is_securable flag to indicate the table will recieve + ro_groupname, rw_groupname, and audit_fk columns because the + Pymerase group wanted an easier way to know if a table was + going to be given a security view or not. + + * ProtocolStep.xml (Repository): + added UNIQUE index on "order protocol_fk" because a protocol + should not have two steps that have the same order. + + * Identifiable.xml (Repository): + moved ro_groupname, rw_groupname, and audit_fk columns to Securable + * Securable.xml (Repository): * ProtocolStepApplication.xml (Repository): |
|
From: <jas...@us...> - 2003-04-23 21:12:24
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv13047
Modified Files:
Identifiable.xml
Log Message:
* Identifiable.xml (Repository):
moved ro_groupname, rw_groupname, and audit_fk columns to Securable
Index: Identifiable.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Identifiable.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Identifiable.xml 23 Nov 2002 07:57:16 -0000 1.4
--- Identifiable.xml 23 Apr 2003 21:12:20 -0000 1.5
***************
*** 1,9 ****
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd">
! <table name="Identifiable"
! type="&data_table;" comment=" The Identifiable table is an
! abstract table that provides two columns to its subclasses: name
! and identifier, as well as security information, and audit
! tracking information">
<column name="name"
full_name="Name"
--- 1,14 ----
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
! <!ENTITY table_name "Identifiable">
! ]>
! <table name="&table_name;"
! type="&data_table;"
! is_abstract="true"
! inherits_from="Securable"
! comment="The &table_name; table is an abstract table that
! provides two columns to its subclasses: name and identifier, as
! well as security information, and audit tracking information
! through Securable">
<column name="name"
full_name="Name"
***************
*** 15,50 ****
type="varchar(128)"
comment="an unambiguous identifier"/>
- <column name="ro_groupname"
- full_name="Read-Only Group Name"
- not_null="true"
- type="name"
- comment="The group with permission to view this data"/>
- <foreign_key column_id="ro_groupname"
- foreign_table ="GroupSec"
- foreign_table_pkey ="name"
- fkey_type ="&fkey_oto;"/>
- <column name="rw_groupname"
- full_name="Read/Write Group Name"
- not_null="true"
- type="name"
- comment="The group with permission to modify this data"/>
- <foreign_key column_id="rw_groupname"
- foreign_table ="GroupSec"
- foreign_table_pkey ="name"
- fkey_type ="&fkey_oto;"/>
- <column name="audit_fk"
- full_name="Audit"
- not_null="true"
- type="int4"
- comment="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. "/>
- <foreign_key column_id="audit_fk"
- write_sql="false"
- foreign_table ="Audit"
- foreign_table_pkey ="audit_pk"
- fkey_type ="&fkey_oto;"/>
<unique column_ids="identifier"/>
</table>
--- 20,23 ----
|
|
From: <jas...@us...> - 2003-04-23 21:09:38
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv11771
Modified Files:
ProtocolStep.xml
Log Message:
* ProtocolStep.xml (Repository):
added UNIQUE index on "order protocol_fk" because a protocol
should not have two steps that have the same order.
Index: ProtocolStep.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ProtocolStep.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ProtocolStep.xml 17 Apr 2003 18:03:24 -0000 1.2
--- ProtocolStep.xml 23 Apr 2003 21:09:34 -0000 1.3
***************
*** 34,37 ****
--- 34,38 ----
foreign_table_pkey ="proc_pk"
fkey_type ="&fkey_oto;"/>
+ <unique column_ids="order protocol_fk"/>
<primary_key column_id="proto_step_pk"/>
</table>
|
|
From: <jas...@us...> - 2003-04-23 21:00:18
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv8029
Added Files:
ChangeLog ProtocolStepApplication.xml Securable.xml
Log Message:
* Securable.xml (Repository):
* ProtocolStepApplication.xml (Repository):
new table
--- NEW FILE: ChangeLog ---
2003-04-23 Jason E. Stewart <ja...@op...>
* Securable.xml (Repository):
* ProtocolStepApplication.xml (Repository):
new table
2003-04-21 Jason E. Stewart <ja...@op...>
* ParameterValue.xml (Repository):
fixed the broken foreign key constraint on parameter_fk
--- NEW FILE: ProtocolStepApplication.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "ProtocolStepApplication">
]>
<table name="&table_name;"
inherits_from="Securable"
type="&data_table;"
comment=" The &table_name; table describes the concrete use in
time by a person of a protocol step.">
<column name="proto_step_app_pk"
full_name="Accession Number"
type="serial"
comment=""/>
<column name="activity_date"
full_name="Activity Date"
not_null="true"
type="datetime"
comment=" the date when the protocol step was performed"/>
<column name="performer_con_fk"
full_name="Protocol Step Performer"
not_null="true"
type="int4"
comment=" the person who performed the protocol step"/>
<foreign_key column_id="performer_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
<column name="protocol_step_fk"
full_name="Protocol Step"
not_null="true"
type="int4"
comment="The protocol step that was performed"/>
<foreign_key column_id="protocol_step_fk"
foreign_table ="ProtocolStep"
foreign_table_pkey ="protocol_step_pk"
fkey_type ="&fkey_oto;"/>
<column name="proto_app_fk"
full_name="Protocol Application"
not_null="true"
type="int4"
comment="The protocol application that this step is part of"/>
<foreign_key column_id="proto_app_fk"
foreign_table ="ProtocolApplication"
foreign_table_pkey ="proto_app_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="proto_step_app_pk"/>
<unique column_ids="proto_app_fk proto_step_fk"/>
</table>
--- NEW FILE: Securable.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "Securable">
]>
<table name="&table_name;"
is_securable="true"
is_abstract="true"
type="&data_table;"
comment=" The &table_name; table is an abstract table that
provides security information, and audit tracking information">
<column name="ro_groupname"
full_name="Read-Only Group Name"
not_null="true"
type="name"
comment="The group with permission to view this data"/>
<foreign_key column_id="ro_groupname"
foreign_table ="GroupSec"
foreign_table_pkey ="name"
fkey_type ="&fkey_oto;"/>
<column name="rw_groupname"
full_name="Read/Write Group Name"
not_null="true"
type="name"
comment="The group with permission to modify this data"/>
<foreign_key column_id="rw_groupname"
foreign_table ="GroupSec"
foreign_table_pkey ="name"
fkey_type ="&fkey_oto;"/>
<column name="audit_fk"
full_name="Audit"
not_null="true"
type="int4"
comment="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. "/>
<foreign_key column_id="audit_fk"
write_sql="false"
foreign_table ="Audit"
foreign_table_pkey ="audit_pk"
fkey_type ="&fkey_oto;"/>
</table>
|
|
From: <ki...@us...> - 2003-04-23 17:40:39
|
Update of /cvsroot/genex/genex-www In directory sc8-pr-cvs1:/tmp/cvs-serv5447 Modified Files: index.shtml Log Message: swaped menu and tracker positions Index: index.shtml =================================================================== RCS file: /cvsroot/genex/genex-www/index.shtml,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** index.shtml 23 Apr 2003 17:03:31 -0000 1.6 --- index.shtml 23 Apr 2003 17:40:35 -0000 1.7 *************** *** 14,19 **** <td width="25%" valign="top"> ! <!--#include virtual="content/menu.ssi"--> ! <!--#include virtual="genex_tracker.cache"--> </td> --- 14,19 ---- <td width="25%" valign="top"> ! <!--#include virtual="genex_tracker.cache"--> ! <!--#include virtual="content/menu.ssi"--> </td> |
|
From: <ki...@us...> - 2003-04-23 17:03:35
|
Update of /cvsroot/genex/genex-www In directory sc8-pr-cvs1:/tmp/cvs-serv18724 Modified Files: index.shtml Log Message: added sf.net new export Index: index.shtml =================================================================== RCS file: /cvsroot/genex/genex-www/index.shtml,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** index.shtml 22 Apr 2003 22:15:11 -0000 1.5 --- index.shtml 23 Apr 2003 17:03:31 -0000 1.6 *************** *** 19,23 **** </td> <td align="LEFT" VALIGN="top"> ! <!--#include virtual="content/main.ssi"--> --- 19,32 ---- </td> <td align="LEFT" VALIGN="top"> ! <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5"\> ! <tr valign="top" bgcolor="#FFD78F"> ! <th><big>Recent News</big></th> ! </tr> ! <tr bgcolor="#FFD78F"> ! <td> ! <!--#include virtual="genex_news.cache"--> ! </td> ! </tr> ! </table> <!--#include virtual="content/main.ssi"--> |
|
From: <ki...@us...> - 2003-04-23 17:03:04
|
Update of /cvsroot/genex/genex-www/content
In directory sc8-pr-cvs1:/tmp/cvs-serv17934/content
Modified Files:
main.ssi
Log Message:
Changed Recent News to Old news
Index: main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/main.ssi,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** main.ssi 10 Nov 2002 02:22:24 -0000 1.9
--- main.ssi 23 Apr 2003 17:02:58 -0000 1.10
***************
*** 3,7 ****
<table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
<tr valign="top" bgcolor="#FFD78F">
! <th><big>Recent News</big></th>
</tr>
<tr bgcolor="#FFD78F">
--- 3,7 ----
<table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
<tr valign="top" bgcolor="#FFD78F">
! <th><big>Old News</big></th>
</tr>
<tr bgcolor="#FFD78F">
|
|
From: <ki...@us...> - 2003-04-22 22:15:16
|
Update of /cvsroot/genex/genex-www In directory sc8-pr-cvs1:/tmp/cvs-serv10381 Modified Files: index.shtml Log Message: added tracker export Index: index.shtml =================================================================== RCS file: /cvsroot/genex/genex-www/index.shtml,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** index.shtml 18 Feb 2002 21:30:36 -0000 1.4 --- index.shtml 22 Apr 2003 22:15:11 -0000 1.5 *************** *** 15,18 **** --- 15,19 ---- <!--#include virtual="content/menu.ssi"--> + <!--#include virtual="genex_tracker.cache"--> </td> |
|
From: <ki...@us...> - 2003-04-22 22:14:15
|
Update of /cvsroot/genex/genex-www/content
In directory sc8-pr-cvs1:/tmp/cvs-serv9768/content
Modified Files:
menu.ssi
Log Message:
menu.ssi is not being processed on server, have to put into index.shtml file.
Index: menu.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/menu.ssi,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** menu.ssi 22 Apr 2003 21:58:31 -0000 1.16
--- menu.ssi 22 Apr 2003 22:14:08 -0000 1.17
***************
*** 122,130 ****
</td>
</tr>
! <tr>
! <td>
! <!--#include virtual="/genex_tracker.cache"-->
! </td>
! </tr>
! </table>
<!-- End Nav Bar Table -->
--- 122,126 ----
</td>
</tr>
! </table>
!
<!-- End Nav Bar Table -->
|
|
From: <ki...@us...> - 2003-04-22 21:58:36
|
Update of /cvsroot/genex/genex-www/content In directory sc8-pr-cvs1:/tmp/cvs-serv3517 Modified Files: menu.ssi Log Message: added sf.net tracker Index: menu.ssi =================================================================== RCS file: /cvsroot/genex/genex-www/content/menu.ssi,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** menu.ssi 7 Mar 2003 23:29:37 -0000 1.15 --- menu.ssi 22 Apr 2003 21:58:31 -0000 1.16 *************** *** 122,125 **** --- 122,130 ---- </td> </tr> + <tr> + <td> + <!--#include virtual="/genex_tracker.cache"--> + </td> + </tr> </table> <!-- End Nav Bar Table --> |
|
From: <jas...@us...> - 2003-04-22 01:37:18
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv31148 Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/Mason/workspace/.cvsignore,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** .cvsignore 16 Apr 2003 23:29:41 -0000 1.4 --- .cvsignore 22 Apr 2003 01:37:14 -0000 1.5 *************** *** 17,20 **** --- 17,21 ---- noauth-autohandler query.html + sample-insert.html user-insert.html workspace.html |
|
From: <jas...@us...> - 2003-04-22 01:29:34
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv27850
Modified Files:
array-design.html.in data-loader.html.in group-create.html.in
parameter-insert.html procedure-insert.html
protocol-insert.html protocol-step-insert.html
sample-insert.html.in
Log Message:
* 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
Index: array-design.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/array-design.html.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** array-design.html.in 20 Apr 2003 02:00:39 -0000 1.4
--- array-design.html.in 22 Apr 2003 01:29:29 -0000 1.5
***************
*** 136,144 ****
} else {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/array-design-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
);
foreach my $file (@files) {
--- 136,144 ----
} else {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/array-design-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
);
foreach my $file (@files) {
Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** data-loader.html.in 20 Apr 2003 02:01:24 -0000 1.8
--- data-loader.html.in 22 Apr 2003 01:29:29 -0000 1.9
***************
*** 207,218 ****
} else {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/mbad-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
! "--es_pk=$es_pk",
! "--ad_pk=$ad_pk",
! "--fe_sw_pk=$fe_sw_pk",
);
--- 207,218 ----
} else {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/mbad-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
! "--es_pk='$es_pk'",
! "--ad_pk='$ad_pk'",
! "--fe_sw_pk='$fe_sw_pk'",
);
Index: group-create.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/group-create.html.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** group-create.html.in 21 Apr 2003 00:29:37 -0000 1.3
--- group-create.html.in 22 Apr 2003 01:29:29 -0000 1.4
***************
*** 128,136 ****
$group_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/group-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--group='$group_name'",
);
--- 128,136 ----
$group_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/group-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--group='$group_name'",
);
Index: parameter-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/parameter-insert.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** parameter-insert.html 17 Apr 2003 17:56:50 -0000 1.1
--- parameter-insert.html 22 Apr 2003 01:29:29 -0000 1.2
***************
*** 182,190 ****
if ($submit) {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/parameter-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--type='$parameter_type'",
"--default='$default'",
--- 182,190 ----
if ($submit) {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/parameter-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--type='$parameter_type'",
"--default='$default'",
Index: procedure-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/procedure-insert.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** procedure-insert.html 17 Apr 2003 17:57:40 -0000 1.2
--- procedure-insert.html 22 Apr 2003 01:29:29 -0000 1.3
***************
*** 164,172 ****
$proc_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/procedure-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--name='$proc_name'",
);
--- 164,172 ----
$proc_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/procedure-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--name='$proc_name'",
);
***************
*** 176,180 ****
}
if ($procedure_type ne $no_type) {
! push(@args,"--type=$procedure_type");
}
--- 176,180 ----
}
if ($procedure_type ne $no_type) {
! push(@args,"--type='$procedure_type'");
}
Index: protocol-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/protocol-insert.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** protocol-insert.html 17 Apr 2003 17:58:22 -0000 1.2
--- protocol-insert.html 22 Apr 2003 01:29:29 -0000 1.3
***************
*** 207,215 ****
$proto_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--name='$proto_name'",
);
--- 207,215 ----
$proto_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--name='$proto_name'",
);
***************
*** 223,230 ****
}
if ($protocol_type ne $no_type) {
! push(@args,"--type=$protocol_type");
}
if ($provider ne $no_type) {
! push(@args,"--provider=$provider");
}
--- 223,230 ----
}
if ($protocol_type ne $no_type) {
! push(@args,"--type='$protocol_type'");
}
if ($provider ne $no_type) {
! push(@args,"--provider='$provider'");
}
Index: protocol-step-insert.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/protocol-step-insert.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-step-insert.html 17 Apr 2003 17:56:50 -0000 1.1
--- protocol-step-insert.html 22 Apr 2003 01:29:29 -0000 1.2
***************
*** 9,51 ****
% } else {
! <h2>Read Group</h2>
! <p>Choose the <b>read group</b> that will be given to the
! protocol step 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 step 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>
--- 9,13 ----
% } else {
! <& comps/ro_rw_group.mason, type=>"ParameterValue" &>
<hr noshade size=5>
***************
*** 144,148 ****
use Bio::Genex::Connect;
use Bio::Genex::Config;
- use Bio::Genex::GroupSec;
use Bio::Genex::Protocol;
use Bio::Genex::Procedure;
--- 106,109 ----
***************
*** 162,174 ****
my @protocols;
my @procs;
! my @contacts = ([$no_type,$no_type]);
my $data = '';
if ($submit) {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-step-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--order='$order'",
"--proto_fk='$proto_fk'",
--- 123,135 ----
my @protocols;
my @procs;
!
my $data = '';
if ($submit) {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-step-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--order='$order'",
"--proto_fk='$proto_fk'",
Index: sample-insert.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/sample-insert.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** sample-insert.html.in 21 Apr 2003 00:26:29 -0000 1.1
--- sample-insert.html.in 22 Apr 2003 01:29:29 -0000 1.2
***************
*** 485,493 ****
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/sample-insert.pl";
! my @args = ("--user=$session->{username}",
! "--password=$session->{password}",
! "--dbname=$session->{dbname}",
! "--ro_group=$read_group",
! "--rw_group=$write_group",
"--name='$sample_name'",
"--spc_fk='$spc_fk'",
--- 485,493 ----
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/sample-insert.pl";
! my @args = ("--user='$session->{username}'",
! "--password='$session->{password}'",
! "--dbname='$session->{dbname}'",
! "--ro_group='$read_group'",
! "--rw_group='$write_group'",
"--name='$sample_name'",
"--spc_fk='$spc_fk'",
***************
*** 495,513 ****
);
! push(@args,'--description'=>$sample_description)
if $sample_description;
! push(@args,'--seed_supplier_cat_num'=>$sample_seed_supplier_cat_num)
if $sample_seed_supplier_cat_num;
! push(@args,'--cultivar_name'=>$sample_cultivar_name)
if $sample_cultivar_name;
! push(@args,'--variety'=>$sample_variety)
if $sample_variety;
! push(@args,'--strain'=>$sample_strain)
if $sample_strain;
! push(@args,'--cell_line'=>$sample_cell_line)
if $sample_cell_line;
! push(@args,'--genotype'=>$sample_genotype)
if $sample_genotype;
! push(@args,'--phenotype_name'=>$sample_phenotype_name)
if $sample_phenotype_name;
--- 495,513 ----
);
! push(@args,"--description='$sample_description'")
if $sample_description;
! push(@args,"--seed_supplier_cat_num='$sample_seed_supplier_cat_num'")
if $sample_seed_supplier_cat_num;
! push(@args,"--cultivar_name='$sample_cultivar_name'")
if $sample_cultivar_name;
! push(@args,"--variety='$sample_variety'")
if $sample_variety;
! push(@args,"--strain='$sample_strain'")
if $sample_strain;
! push(@args,"--cell_line='$sample_cell_line'")
if $sample_cell_line;
! push(@args,"--genotype='$sample_genotype'")
if $sample_genotype;
! push(@args,"--phenotype_name='$sample_phenotype_name'")
if $sample_phenotype_name;
***************
*** 518,523 ****
goto FINISHED;
} else {
! push(@args,'--age'=>$sample_age);
! push(@args,'--age_units'=>$sample_age_units);
}
}
--- 518,523 ----
goto FINISHED;
} else {
! push(@args,"--age='$sample_age'");
! push(@args,"--age_units='$sample_age_units'");
}
}
***************
*** 529,564 ****
goto FINISHED;
} else {
! push(@args,'--dev_stage_time'=>$sample_dev_stage_time);
! push(@args,'--dev_stage_units'=>$sample_dev_stage_units);
}
}
! push(@args,'--sex_mating_type'=>$sample_sex_mating_type)
if $sample_sex_mating_type and $sample_sex_mating_type ne $no_type;
! push(@args,'--dev_stage_name'=>$sample_dev_stage_name)
if $sample_dev_stage_name and $sample_dev_stage_name ne $no_type;
! push(@args,'--organ_type'=>$sample_organ_type)
if $sample_organ_type and $sample_organ_type ne $no_type;
! push(@args,'--tissue_type'=>$sample_tissue_type)
if $sample_tissue_type and $sample_tissue_type ne $no_type;
! push(@args,'--atcc_cell_type'=>$sample_atcc_cell_type)
if $sample_atcc_cell_type and $sample_atcc_cell_type ne $no_type;
! push(@args,'--primary_cell_type'=>$sample_primary_cell_type)
if $sample_primary_cell_type and $sample_atcc_cell_type ne $no_type;
! push(@args,'--organism_intactness'=>$sample_organism_intactness)
if $sample_organism_intactness and $sample_organism_intactness ne $no_type;
! push(@args,'--genetic_status'=>$sample_genetic_status)
if $sample_genetic_status and $sample_genetic_status ne $no_type;
! push(@args,'--genetic_status_comment'=>$sample_genetic_status_comment)
if $sample_genetic_status_comment;
! push(@args,'--growth_cond'=>$sample_growth_cond)
if $sample_growth_cond;
! push(@args,'--pathology_descr'=>$sample_pathology_descr)
if $sample_pathology_descr;
! push(@args,'--common_acc_num'=>$sample_common_acc_num)
if $sample_common_acc_num;
! push(@args,'--abrc_acc_num'=>$sample_abrc_acc_num)
if $sample_abrc_acc_num;
! push(@args,'--nottingham_acc_num'=>$sample_nottingham_acc_num)
if $sample_nottingham_acc_num;
--- 529,564 ----
goto FINISHED;
} else {
! push(@args,"--dev_stage_time='$sample_dev_stage_time'");
! push(@args,"--dev_stage_units='$sample_dev_stage_units'");
}
}
! push(@args,"--sex_mating_type='$sample_sex_mating_type'")
if $sample_sex_mating_type and $sample_sex_mating_type ne $no_type;
! push(@args,"--dev_stage_name='$sample_dev_stage_name'")
if $sample_dev_stage_name and $sample_dev_stage_name ne $no_type;
! push(@args,"--organ_type='$sample_organ_type'")
if $sample_organ_type and $sample_organ_type ne $no_type;
! push(@args,"--tissue_type='$sample_tissue_type'")
if $sample_tissue_type and $sample_tissue_type ne $no_type;
! push(@args,"--atcc_cell_type='$sample_atcc_cell_type'")
if $sample_atcc_cell_type and $sample_atcc_cell_type ne $no_type;
! push(@args,"--primary_cell_type='$sample_primary_cell_type'")
if $sample_primary_cell_type and $sample_atcc_cell_type ne $no_type;
! push(@args,"--organism_intactness='$sample_organism_intactness'")
if $sample_organism_intactness and $sample_organism_intactness ne $no_type;
! push(@args,"--genetic_status='$sample_genetic_status'")
if $sample_genetic_status and $sample_genetic_status ne $no_type;
! push(@args,"--genetic_status_comment='$sample_genetic_status_comment'")
if $sample_genetic_status_comment;
! push(@args,"--growth_cond='$sample_growth_cond'")
if $sample_growth_cond;
! push(@args,"--pathology_descr='$sample_pathology_descr'")
if $sample_pathology_descr;
! push(@args,"--common_acc_num='$sample_common_acc_num'")
if $sample_common_acc_num;
! push(@args,"--abrc_acc_num='$sample_abrc_acc_num'")
if $sample_abrc_acc_num;
! push(@args,"--nottingham_acc_num='$sample_nottingham_acc_num'")
if $sample_nottingham_acc_num;
|
|
From: <jas...@us...> - 2003-04-22 01:22:31
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv25372
Modified Files:
parameter-insert.pl.in protocol-step-insert.pl.in
Log Message:
now returns pkey
Index: parameter-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/parameter-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** parameter-insert.pl.in 17 Apr 2003 17:55:14 -0000 1.1
--- parameter-insert.pl.in 22 Apr 2003 01:22:26 -0000 1.2
***************
*** 125,130 ****
if exists $OPTIONS{default};
! print "Adding Parameter info\n";
! $param_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert Parameter",
--- 125,131 ----
if exists $OPTIONS{default};
! print STDERR "Adding Parameter info\n";
!
! my $pk = $param_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert Parameter",
***************
*** 132,135 ****
--- 133,137 ----
+ print STDOUT "$pk\n";
print STDERR "Finished\n";
Index: protocol-step-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-step-insert.pl.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** protocol-step-insert.pl.in 17 Apr 2003 17:55:14 -0000 1.1
--- protocol-step-insert.pl.in 22 Apr 2003 01:22:26 -0000 1.2
***************
*** 130,135 ****
$ps_db->proc_obj($proc_db);
! print "Adding ProtocolStep info\n";
! $ps_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert ProtocolStep",
--- 130,135 ----
$ps_db->proc_obj($proc_db);
! print STDERR "Adding ProtocolStep info\n";
! my $pk = $ps_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert ProtocolStep",
***************
*** 137,140 ****
--- 137,141 ----
+ print STDOUT "$pk\n";
print STDERR "Finished\n";
|
|
From: <jas...@us...> - 2003-04-22 01:19:43
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv24442
Added Files:
objs2table.mason tableize.mason radio-group.mason
Log Message:
new
--- NEW FILE: objs2table.mason ---
% foreach my $row (@rows) {
<tr><% $row %></tr>
% }
<%args>
$objects
</%args>
<%once>
use CGI;
</%once>
<%init>;
my @rows;
my $cgi = CGI->new('');
my %name2column = %{$objects->[0]->name2column()};
my @column_names = @{$objects->[0]->column_names()};
#
# sort the names so the output is in a determined order
my @column_copy = sort keys %name2column;
# make a header element.
push(@rows,$cgi->th(\@column_copy));
foreach my $object (@{$objects}) {
my %tmp_values;
# now extract the data from the object
foreach (@column_names) {
no strict 'refs';
$tmp_values{$_} = $object->$_();
}
my @values;
foreach (@column_copy) {
push(@values, $tmp_values{$name2column{$_}});
}
push(@rows,$cgi->td([map {!defined $_ ? ' ' : $_} @values]));
}
</%init>
--- NEW FILE: tableize.mason ---
<table>
<% $result %>
</table>
<%args>
$rows => 1
$columns => 1
$rowheaders => undef
$colheaders => undef
$array_ref
</%args>
<%init>;
my @elements = @{$array_ref};
#
# code stolen from CGI.pm version 2.81, thanks Lincoln!
#
$rowheaders = [] unless defined $rowheaders;
$colheaders = [] unless defined $colheaders;
my($result);
if (defined($columns)) {
$rows = int(0.99 + @elements/$columns) unless defined($rows);
}
if (defined($rows)) {
$columns = int(0.99 + @elements/$rows) unless defined($columns);
}
# rearrange into a pretty table
my($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++) {
$result .= "<td>" . $elements[$column*$rows + $row] . "</td>"
if defined($elements[$column*$rows + $row]);
}
$result .= "</tr>";
}
</%init>
--- NEW FILE: radio-group.mason ---
<& tableize.mason, array_ref=>\@elements, columns=>$cols, rows=>$rows &>
<%args>
$name
$cols => undef
$rows => undef
$array_ref
</%args>
<%init>;
my @elements;
foreach my $val (@{$array_ref}) {
push(@elements,qq[<input type="radio" name="$name" value="$val"></input>$val]);
}
</%init>
|
|
From: <jas...@us...> - 2003-04-22 01:16:49
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv23369
Modified Files:
index.html
Log Message:
new files
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** index.html 21 Apr 2003 00:27:23 -0000 1.7
--- index.html 22 Apr 2003 01:16:46 -0000 1.8
***************
*** 26,29 ****
--- 26,30 ----
<li><a href="workspace.html">workspace.html</a></li>
<li><a href="bioassay.html">bioassay.html</a></li>
+ <li><a href="list-tables.html">list-tables.html</a></li>
<h2>Utilities for loading Data and Annotations</h2>
***************
*** 32,35 ****
--- 33,37 ----
<li><a href="experimentset-create.html">experimentset-create.html</a></li>
<li><a href="parameter-insert.html">parameter-insert.html</a></li>
+ <li><a href="parameter-value-insert.html">parameter-value-insert.html</a></li>
<li><a href="protocol-insert.html">protocol-insert.html</a></li>
<li><a href="protocol-step-insert.html">protocol-step-insert.html</a></li>
|
|
From: <jas...@us...> - 2003-04-22 01:16:14
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv23144
Added Files:
fetch-table.html list-tables.html parameter-value-insert.html
Log Message:
new
--- NEW FILE: fetch-table.html ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($error) {
<font color="red"><b><% $error %></b></font>
% } else {
<table bgcolor="#D8E4F7" width="444" border="1">
<theader>
<th colspan="100"><b><% $result %></b></th>
</theader>
<& comps/objs2table.mason, objects=>\@objects &>
</table>
% }
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
</div>
</form>
<%args>
$debug => 0
$all => 0
$pkey => undef
$pkey_link => undef
$table_name
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/fetch-table.html"
name=>'GeneX DB Data Browser Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/fetch-table.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::HTMLUtils;
# use Apache::DB ();
</%once>
<%init>;
# $table_name = $Bio::Genex::TABLE2CLASS{$table_name};
my $name = $m->current_comp->attr('name') . " for Table $table_name";
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $result;
my $error;
my $count;
# Apache::DB->init;
# Apache::DB->handler;
my $class = "Bio::Genex::$table_name";
eval "require $class";
if ($@) {
# the eval didn't work, so we'll do something nice
$error = "class: $class for table: $table_name not found, please try a different table";
goto FINISH;
}
my @objects;
if (defined $pkey) {
my @args = (dbh=>$dbh,id=>$pkey);
if ($class->linking_table) {
unless (defined $pkey_link) {
$error = "$class is a linking table.\n";
$error .= "You must specify a PKEY_LINK parameter to view an individual row in this table";
goto FINISH;
}
push(@args,pkey_link=>$pkey_link);
}
push(@objects, $class->new(@args));
} else {
no strict 'refs';
$ {$class . '::LIMIT'} = 100; # an upper bound for the table length
push(@objects, $class->get_all_objects($dbh));
}
$count = scalar @objects;
if ($count) {
$result = "Found $count $table_name objects";
} else {
$error = "No objects found\n";
}
FINISH : {
; # do nothing
}
</%init>
--- NEW FILE: list-tables.html ---
<h1 align="center"><% $name %></h1>
<h2>Choose a table to investigate</h2>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
<& comps/tableize.mason, array_ref=>\@tables, columns=>4, rows=>undef &>
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
</div>
</form>
<%args>
$debug => 0
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/fetch-table.html"
name=>'GeneX DB Table Listing Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/list-tables.html"
</%attr>
<%once>
use Bio::Genex;
# 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');
# Apache::DB->init;
# Apache::DB->handler;
my $sth = $dbh->table_info || die $DBI::errstr;
my @tables;
while (my ($table_name,$type) = ($sth->fetchrow_array)[2..3]) {
die $DBI::errstr if $sth->err;
# we only want tables
next unless $type eq 'TABLE';
# skip postgres system tables
next if $table_name =~ /^pga?_/;
# skip tables that have no classes (e.g. MBA Data tables
next unless exists $Bio::Genex::TABLE2CLASS{$table_name};
push(@tables,$Bio::Genex::TABLE2CLASS{$table_name});
}
@tables = map {qq[<input type="submit" name="table_name" size="33" value="$_">]} @tables;
</%init>
--- NEW FILE: parameter-value-insert.html ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($submit) {
<h2><% $data %></h2>
% } else {
<& comps/ro_rw_group.mason, type=>"ParameterValue" &>
<hr noshade size=5>
<h2>Value</h2>
<p>Indicates the value of this parameter in the protocol
step. If no value is specified, the default value from the
parameter (if any) will be used.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Value</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<input type="text" name="value" size="65" maxlength="128">
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Protocol Step</h2>
<p>Choose the <b>Protocol Step</b> to which this parameter
value belongs.</p>
<p>The entry must exist in the DB first, click
<a href="protocol-step-insert.html">here</a> if you need to
enter the protocol step info, then return to this page and hit
your browsers <b>Reload</b> button.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Protocol Step</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"proto_step_fk",
array_ref=>\@protocol_steps &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Parameter</h2>
<p>Choose the <b>Parameter</b> to which this step belongs.</p>
<p>The entry must exist in the DB first, click
<a href="Parameter-insert.html">here</a> if you need to
enter the Parameter info, then return to this page and
hit your browsers <b>Reload</b> button.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Parameter</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"parameter_fk",
array_ref=>\@parameters &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Create Parameter Value" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$read_group => ''
$write_group => ''
$value => ''
$proto_step_fk => ''
$parameter_fk => ''
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/parameter-value-insert.html"
name=>'GeneX DB Parameter Value Creation Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/parameter-value-insert.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Config;
use Bio::Genex::ProtocolStep;
use Bio::Genex::Parameter;
# 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');
# Apache::DB->init;
# Apache::DB->handler;
my $no_type = 'NONE';
my @protocol_steps;
my @parameters;
my $data = '';
if ($submit) {
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/parameter-value-insert.pl";
my @args = ("--user='$session->{username}'",
"--password='$session->{password}'",
"--dbname='$session->{dbname}'",
"--ro_group='$read_group'",
"--rw_group='$write_group'",
"--proto_step_fk='$proto_step_fk'",
"--parameter_fk='$parameter_fk'",
);
push(@args,"--value='$value'")
if defined $value;
my $command = join(' ', $cmd, @args);
my $pk = `$command`;
if ($?) {
$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = <$!></p>
EOE
} else {
$data = "Parameter Value Successfully Created, with primary key: $pk";
}
} else {
my @ps_dbs = Bio::Genex::ProtocolStep->get_all_objects($dbh);
foreach my $ps_db (@ps_dbs) {
push(@protocol_steps,[$ps_db->proto_step_pk,
join(':',
$ps_db->protocol_obj->name,
$ps_db->order)
]);
}
my @param_dbs = Bio::Genex::Parameter->get_all_objects($dbh);
foreach my $param_db (@param_dbs) {
push(@parameters,[$param_db->parameter_pk,
join(':',
$param_db->name,
$param_db->type,
$param_db->default_value)
]);
}
}
</%init>
|
|
From: <jas...@us...> - 2003-04-22 01:09:13
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv20598 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** MANIFEST.in 21 Apr 2003 00:30:05 -0000 1.11 --- MANIFEST.in 22 Apr 2003 01:09:10 -0000 1.12 *************** *** 60,66 **** --- 60,72 ---- 'Mason/workspace/protocol-step-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/procedure-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/parameter-value-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/sample-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/list-tables.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/fetch-table.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/comps/ro_rw_group.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/tableize.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/objs2table.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/htmlize-fkey.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/contacts.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', *************** *** 70,73 **** --- 76,80 ---- 'Mason/workspace/comps/hiddenlist.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/query-checkboxes.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/radio-group.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/query-drop-down.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/query-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', *************** *** 95,98 **** --- 102,106 ---- 'Genex/scripts/sample-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/parameter-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/parameter-value-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/protocol-step-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/procedure-insert.pl' => '%%GENEX_BIN_DIR%%', |
|
From: <jas...@us...> - 2003-04-22 00:58:55
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv17125/Genex/scripts
Added Files:
parameter-value-insert.pl.in
Log Message:
new GUI
--- NEW FILE: parameter-value-insert.pl.in ---
%%START_PERL%%
#
# parameter-value-insert.pl.in
# first version Tue Oct 24 14:13:45 MST 2000
# script for inserting parameter value entries into genex DB
#
# author: Jason E. Stewart (ja...@op...)
# Copyright 2003 Jason E. Stewart
#
my $VERSION = '$Id: parameter-value-insert.pl.in,v 1.1 2003/04/22 00:58:50 jason_e_stewart Exp $ ';
use strict;
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
# use blib;
use Bio::Genex qw(error);
use Bio::Genex::XMLUtils;
use Bio::Genex::ParameterValue;
use Bio::Genex::Parameter;
use Bio::Genex::ProtocolStep;
use Bio::Genex::Contact;
use Bio::Genex::Config;
use Bio::Genex::GenexAdmin;
$Bio::Genex::GenexAdmin::DEBUG = 1;
$Bio::Genex::ParameterValue::DEBUG = 1;
my $infile;
my %OPTIONS;
$OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
$OPTIONS{ro_groupname} = 'public';
$OPTIONS{rw_groupname} = 'superuser';
my $rc = GetOptions(\%OPTIONS,
'dbname=s',
'value=s',
'proto_step_fk=i',
'parameter_fk=i',
'ro_groupname=s',
'rw_groupname=s',
'username=s',
'password=s',
'help',
'debug',
);
my $USAGE = <<"EOU";
usage: $0 [required flags] [options]
required flags:
--proto_step_fk=num : the protocol step foreign key
--parameter_fk=num : the parameter foreign key
--username=name : the DB username to login as
--password=word : the DB password to login with
optional parameters:
--value=string : the value of this parameter in the protocol step
--dbname=name : the name of the DB to create
--ro_groupname=name : the name of the read-only group to use
--rw_groupname=name : the name of the read-write group to use
--debug : rollback instead of commit
--help : print this message
EOU
die "Bad option\n$USAGE" unless $rc;
die $USAGE if exists $OPTIONS{help};
die "Must specify --username\n$USAGE"
unless exists $OPTIONS{username};
die "Must specify --password\n$USAGE"
unless exists $OPTIONS{password};
# open up a writeable connection
my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
USER => $OPTIONS{username},
PASSWORD => $OPTIONS{password},
TRANSACTION => 1,
);
my @error_args = (caller=>$0);
die "Must specify --proto_step_fk\n$USAGE"
unless exists $OPTIONS{proto_step_fk};
die "Must specify --parameter_fk\n$USAGE"
unless exists $OPTIONS{parameter_fk};
my ($ro_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
column=>'name',
value=>$OPTIONS{ro_groupname},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate $OPTIONS{ro_groupname} group")
unless defined $ro_group_db;
my ($rw_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
column=>'name',
value=>$OPTIONS{rw_groupname},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate $OPTIONS{rw_groupname} group")
unless defined $rw_group_db;
my $pv_db = Bio::Genex::ParameterValue->new(ro_groupname_obj=>$ro_group_db,
rw_groupname_obj=>$rw_group_db,
);
# handle the required fkeys
my ($ps_db) = Bio::Genex::ProtocolStep->get_all_objects($dbh,
column=>'proto_step_pk',
value=>$OPTIONS{proto_step_fk},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate ProtocolStep entry for value: $OPTIONS{proto_step_fk}")
unless defined $ps_db;
$pv_db->proto_step_obj($ps_db);
my ($param_db) = Bio::Genex::Parameter->get_all_objects($dbh,
column=>'parameter_pk',
value=>$OPTIONS{parameter_fk},
);
$dbh->error(@error_args,
no_errstr=>1,
message=>"Couldn't locate Parameter entry for value: $OPTIONS{parameter_fk}")
unless defined $param_db;
$pv_db->parameter_obj($param_db);
# handle the optional values
$pv_db->value($OPTIONS{value})
if exists $OPTIONS{value};
print STDERR "Adding ParameterValue info\n";
my $pk = $pv_db->insert_db($dbh);
$dbh->error(@error_args,
message=>"Couldn't insert ParameterValue",
) if $dbh->err;
print STDOUT "$pk\n";
print STDERR "Finished\n";
if (exists $OPTIONS{debug}) {
$dbh->rollback();
} else {
$dbh->commit();
}
$dbh->disconnect();
exit(0);
|
|
From: <jas...@us...> - 2003-04-22 00:50:27
|
Update of /cvsroot/genex/genex-server/Genex/ParameterValue
In directory sc8-pr-cvs1:/tmp/cvs-serv14226/Genex/ParameterValue
Modified Files:
ParameterValue.pm
Log Message:
fixed the broken foreign key constraint on parameter_fk
Index: ParameterValue.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ParameterValue/ParameterValue.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ParameterValue.pm 17 Apr 2003 18:00:34 -0000 1.2
--- ParameterValue.pm 22 Apr 2003 00:50:24 -0000 1.3
***************
*** 20,23 ****
--- 20,24 ----
use Bio::Genex::GroupSec;
use Bio::Genex::Audit;
+ use Bio::Genex::Parameter;
use Bio::Genex::ProtocolStep;
***************
*** 76,79 ****
--- 77,87 ----
'table_name' => 'GroupSec'
}, 'Bio::Genex::Fkey' ),
+ 'parameter_obj' => bless( {
+ 'fkey_name' => 'parameter_obj',
+ 'can_self_reference' => 'false',
+ 'pkey_name' => 'parameter_pk',
+ 'fkey_type' => 'ONE_TO_ONE_OO',
+ 'table_name' => 'Parameter'
+ }, 'Bio::Genex::Fkey' ),
'proto_step_obj' => bless( {
'fkey_name' => 'proto_step_obj',
***************
*** 110,113 ****
--- 118,122 ----
'rw_groupname_obj' => 'rw_groupname',
'ro_groupname_obj' => 'ro_groupname',
+ 'parameter_obj' => 'parameter_fk',
'proto_step_obj' => 'proto_step_fk'
}
***************
*** 325,329 ****
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['param_value_pk', 'value', 'proto_step_fk', 'parameter_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'proto_step_obj', 'proto_step_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj']);
--- 334,338 ----
# this calls the Class::ObjectTemplate::attributes() method
# to initialize all the class attributes
! attributes (no_lookup=>['fetched', 'fetch_all', 'fetched_attr', 'id', 'dbh'], lookup=>['param_value_pk', 'value', 'proto_step_fk', 'parameter_fk', 'ro_groupname', 'rw_groupname', 'audit_fk', 'proto_step_obj', 'parameter_obj', 'ro_groupname_obj', 'rw_groupname_obj', 'audit_obj']);
|
|
From: <jas...@us...> - 2003-04-22 00:49:01
|
Update of /cvsroot/genex/genex-server/Genex
In directory sc8-pr-cvs1:/tmp/cvs-serv13982/Genex
Modified Files:
Genex.pm.in
Log Message:
* Genex.pm.in (Repository):
new version (2.7.20030421)
Index: Genex.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Genex.pm.in,v
retrieving revision 1.54
retrieving revision 1.55
diff -C2 -d -r1.54 -r1.55
*** Genex.pm.in 17 Apr 2003 18:01:12 -0000 1.54
--- Genex.pm.in 22 Apr 2003 00:48:57 -0000 1.55
***************
*** 58,62 ****
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20030417';
# Preloaded methods go here.
--- 58,62 ----
Exporter::export_ok_tags('ASSERT');
! $VERSION = '2.7.20030421';
# Preloaded methods go here.
***************
*** 123,193 ****
%TABLE2CLASS = (
! al_coating => 'AL_Coating',
! al_defaultspotconcunits => 'AL_DefaultSpotConcUnits',
! al_identifiercode => 'AL_IdentifierCode',
! al_medium => 'AL_Medium',
! feature => 'Feature',
! al_technologytype => 'AL_TechnologyType',
! als_spottype => 'ALS_SpotType',
! am_equationtype => 'AM_EquationType',
! am_factorvalues => 'AM_FactorValues',
! am_spotmeasurementunits => 'AM_SpotMeasurementUnits',
! am_spots => 'AM_Spots',
! am_suspectspots => 'AM_SuspectSpots',
! am_type => 'AM_Type',
! arraylayout => 'ArrayLayout',
! arraymeasurement => 'ArrayMeasurement',
! blasthits => 'BlastHits',
! canonicalsequencefeature => 'CanonicalSequenceFeature',
! chromosome => 'Chromosome',
! citation => 'Citation',
! citationlink => 'CitationLink',
! contact => 'Contact',
! contacttype => 'ContactType',
! csf_type => 'CSF_Type',
! ef_majorcategory => 'EF_MajorCategory',
! ef_minorcategory => 'EF_MinorCategory',
! es_quantityseriestype => 'ES_QuantitySeriesType',
! es_treatmenttype => 'ES_TreatmentType',
! experimentfactors => 'ExperimentFactors',
! experimentset => 'ExperimentSet',
! externaldatabase => 'ExternalDatabase',
! grouplink => 'GroupLink',
! groupsec => 'GroupSec',
! hotspots => 'HotSpots',
! hs_thresholdtype => 'HS_ThresholdType',
! protocol => 'Protocol',
! prt_type => 'PRT_Type',
! relatedcsf => 'RelatedCSF',
! sample => 'Sample',
! sampleprotocols => 'SampleProtocols',
! scanner => 'Scanner',
! scn_modeldescription => 'SCN_ModelDescription',
! smp_ageunits => 'SMP_AgeUnits',
! smp_developmentstagename => 'SMP_DevelopmentStageName',
! smp_developmentstageunits => 'SMP_DevelopmentStageUnits',
! smp_geneticstatus => 'SMP_GeneticStatus',
! smp_organismintactness => 'SMP_OrganismIntactness',
! smp_organtype => 'SMP_OrganType',
! smp_primarycelltype => 'SMP_PrimaryCellType',
! smp_sexmatingtype => 'SMP_SexMatingType',
! smp_tissuetype => 'SMP_TissueType',
! software => 'Software',
! spc_cellstructure => 'SPC_CellStructure',
! spc_generalclassification => 'SPC_GeneralClassification',
! species => 'Species',
! spotlink => 'SpotLink',
! spotter => 'Spotter',
! spt_modeldescription => 'SPT_ModelDescription',
! sw_name => 'SW_Name',
! sw_type => 'SW_Type',
! tl_factorvalues => 'TL_FactorValues',
! treatment_ams => 'Treatment_AMs',
! treatmentlevel => 'TreatmentLevel',
! usercanonicallink => 'UserCanonicalLink',
! usersec => 'UserSec',
! usersequencefeature => 'UserSequenceFeature',
! usf_externaldblink => 'USF_ExternalDBLink',
! usf_type => 'USF_Type',
);
--- 123,172 ----
%TABLE2CLASS = (
! 'am_factorvalues'=>'AM_FactorValues',
! 'array'=>'Array',
! 'arraydesign'=>'ArrayDesign',
! 'audit'=>'Audit',
! 'blasthits'=>'BlastHits',
! 'channel'=>'Channel',
! 'chromosome'=>'Chromosome',
! 'citation'=>'Citation',
! 'contact'=>'Contact',
! 'contacttype'=>'ContactType',
! 'controlledvocab'=>'ControlledVocab',
! 'experimentfactors'=>'ExperimentFactors',
! 'experimentset'=>'ExperimentSet',
! 'externaldatabase'=>'ExternalDatabase',
! 'feature'=>'Feature',
! 'featureextractionsoftware'=>'FeatureExtractionSoftware',
! 'g2g'=>'G2G',
! 'genexadmin'=>'GenexAdmin',
! 'grouplink'=>'GroupLink',
! 'groupsec'=>'GroupSec',
! 'hardware'=>'Hardware',
! 'hotspots'=>'HotSpots',
! 'identifiable'=>'Identifiable',
! 'measuredbioassay'=>'MeasuredBioAssay',
! 'parameter'=>'Parameter',
! 'parametervalue'=>'ParameterValue',
! 'parameterizable'=>'Parameterizable',
! 'physicalbioassay'=>'PhysicalBioAssay',
! 'procedure'=>'Procedure',
! 'protocol'=>'Protocol',
! 'protocolapplication'=>'ProtocolApplication',
! 'protocolapplicationlink'=>'ProtocolApplicationLink',
! 'protocolstep'=>'ProtocolStep',
! 'quantitationlink'=>'QuantitationLink',
! 'quantitationtype'=>'QuantitationType',
! 'quantitationtypedimension'=>'QuantitationTypeDimension',
! 'reporter'=>'Reporter',
! 'sf_externaldblink'=>'SF_ExternalDBLink',
! 'sample'=>'Sample',
! 'samplelink'=>'SampleLink',
! 'software'=>'Software',
! 'species'=>'Species',
! 'tl_factorvalues'=>'TL_FactorValues',
! 'treatmentlevel'=>'TreatmentLevel',
! 'treatment_ams'=>'Treatment_AMs',
! 'usersec'=>'UserSec',
);
|
|
From: <jas...@us...> - 2003-04-22 00:48:00
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv13782/DB/xml
Modified Files:
ParameterValue.xml
Log Message:
* ParameterValue.xml (Repository):
fixed the broken foreign key constraint on parameter_fk
Index: ParameterValue.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ParameterValue.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ParameterValue.xml 17 Apr 2003 18:02:49 -0000 1.2
--- ParameterValue.xml 22 Apr 2003 00:47:57 -0000 1.3
***************
*** 30,36 ****
type="int4"
comment="the procedure parameter this parameter value applies to"/>
! <foreign_key column_id="proto_step_fk"
! foreign_table ="ProtocolStep"
! foreign_table_pkey ="proto_step_pk"
fkey_type ="&fkey_oto;"/>
<column name="ro_groupname"
--- 30,36 ----
type="int4"
comment="the procedure parameter this parameter value applies to"/>
! <foreign_key column_id="parameter_fk"
! foreign_table ="Parameter"
! foreign_table_pkey ="parameter_pk"
fkey_type ="&fkey_oto;"/>
<column name="ro_groupname"
|
|
From: <jas...@us...> - 2003-04-22 00:46:06
|
Update of /cvsroot/genex/genex-server/DB/xml In directory sc8-pr-cvs1:/tmp/cvs-serv13243/DB/xml Removed Files: QuantitationDimension.xml Log Message: cruft --- QuantitationDimension.xml DELETED --- |
|
From: <jas...@us...> - 2003-04-22 00:45:22
|
Update of /cvsroot/genex/genex-server/Genex/samples In directory sc8-pr-cvs1:/tmp/cvs-serv13081/Genex/samples Removed Files: control-bundle.pl.in curation-tool-login.pl.in pass-auth-login.pl.in pass-invalid-login.pl.in pass-mod-invalid.pl.in pass-mod.pl.in session-login.pl.in Log Message: cruft --- control-bundle.pl.in DELETED --- --- curation-tool-login.pl.in DELETED --- --- pass-auth-login.pl.in DELETED --- --- pass-invalid-login.pl.in DELETED --- --- pass-mod-invalid.pl.in DELETED --- --- pass-mod.pl.in DELETED --- --- session-login.pl.in DELETED --- |
|
From: <jas...@us...> - 2003-04-21 00:30:09
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv25571 Modified Files: MANIFEST.in Log Message: new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** MANIFEST.in 20 Apr 2003 01:48:44 -0000 1.10 --- MANIFEST.in 21 Apr 2003 00:30:05 -0000 1.11 *************** *** 60,64 **** --- 60,67 ---- 'Mason/workspace/protocol-step-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/procedure-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/sample-insert.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/comps/ro_rw_group.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', + 'Mason/workspace/comps/contacts.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', 'Mason/workspace/comps/data-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', *************** *** 90,93 **** --- 93,97 ---- 'Genex/scripts/priveleges.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/protocol-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/sample-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/parameter-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/protocol-step-insert.pl' => '%%GENEX_BIN_DIR%%', |
