[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Fri Jul 8 19:03:17 UTC 2005
mwilkinson
Fri Jul 8 15:03:17 EDT 2005
Update of /home/repository/moby/moby-live/Database
In directory pub.open-bio.org:/tmp/cvs-serv24842
Modified Files:
mobycentral.mysql mobynamespace.mysql mobyobject.mysql
mobyrelationship.mysql mobyservice.mysql reset
Added Files:
README mobyobject.data mobyservice.data
Log Message:
all files needed to create a new bootstrapped MOBY Central database
moby-live/Database README,NONE,1.1 mobyobject.data,NONE,1.1 mobyservice.data,NONE,1.1 mobycentral.mysql,1.4,1.5 mobynamespace.mysql,1.5,1.6 mobyobject.mysql,1.8,1.9 mobyrelationship.mysql,1.4,1.5 mobyservice.mysql,1.6,1.7 reset,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Database/mobycentral.mysql 2004/09/14 21:32:35 1.4
+++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2005/07/08 19:03:17 1.5
@@ -1,11 +1,11 @@
--- MySQL dump 8.22
+-- MySQL dump 8.23
--
-- Host: localhost Database: mobycentral
---------------------------------------------------------
--- Server version 3.23.52
+-- Server version 4.1.12-standard
--
--- Table structure for table 'authority'
+-- Table structure for table `authority`
--
CREATE TABLE authority (
@@ -14,16 +14,10 @@
contact_email varchar(255) NOT NULL default '',
authority_id int(10) unsigned NOT NULL auto_increment,
PRIMARY KEY (authority_id)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'authority'
---
-
-
-
---
--- Table structure for table 'collection_input'
+-- Table structure for table `collection_input`
--
CREATE TABLE collection_input (
@@ -31,16 +25,10 @@
article_name varchar(255) default NULL,
service_instance_id int(10) unsigned NOT NULL default '0',
PRIMARY KEY (collection_input_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'collection_input'
---
-
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Table structure for table 'collection_output'
+-- Table structure for table `collection_output`
--
CREATE TABLE collection_output (
@@ -48,42 +36,30 @@
article_name varchar(255) default NULL,
service_instance_id int(10) unsigned NOT NULL default '0',
PRIMARY KEY (collection_output_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'collection_output'
---
-
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Table structure for table 'secondary_input'
+-- Table structure for table `secondary_input`
--
CREATE TABLE secondary_input (
secondary_input_id int(10) unsigned NOT NULL auto_increment,
default_value text,
- maximum_value decimal(10,0) default NULL,
- minimum_value decimal(10,0) default NULL,
+ maximum_value float default NULL,
+ minimum_value float default NULL,
enum_value text,
- datatype enum('INT','FLOAT','STRING') NOT NULL default 'INT',
+ datatype enum('String','Integer','DateTime','Float') default NULL,
article_name varchar(255) default NULL,
service_instance_id int(10) unsigned NOT NULL default '0',
PRIMARY KEY (secondary_input_id)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'secondary_input'
---
-
-
-
---
--- Table structure for table 'service_instance'
+-- Table structure for table `service_instance`
--
CREATE TABLE service_instance (
- category enum('moby','cgi','soap') NOT NULL default 'moby',
+ category enum('moby','soap','wsdl','cgi') default NULL,
servicename varchar(255) NOT NULL default '',
service_type_uri varchar(255) NOT NULL default '',
authority_id int(10) unsigned NOT NULL default '0',
@@ -92,19 +68,25 @@
authoritative enum('1','0') NOT NULL default '0',
description text NOT NULL,
service_instance_id int(10) unsigned NOT NULL auto_increment,
- signatureURL varchar(255),
+ signatureURL varchar(255) default NULL,
+ lsid varchar(255) NOT NULL default '',
PRIMARY KEY (service_instance_id),
UNIQUE KEY servicename (servicename,authority_id)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'service_instance'
+-- Table structure for table `service_validation`
--
-
+CREATE TABLE service_validation (
+ signatureURL varchar(255) NOT NULL default '',
+ error_code int(4) NOT NULL default '0',
+ counter int(1) NOT NULL default '0',
+ PRIMARY KEY (signatureURL)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Table structure for table 'simple_input'
+-- Table structure for table `simple_input`
--
CREATE TABLE simple_input (
@@ -115,16 +97,10 @@
service_instance_id int(10) unsigned default NULL,
collection_input_id int(10) unsigned default NULL,
PRIMARY KEY (simple_input_id)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'simple_input'
---
-
-
-
---
--- Table structure for table 'simple_output'
+-- Table structure for table `simple_output`
--
CREATE TABLE simple_output (
@@ -135,11 +111,5 @@
service_instance_id int(10) unsigned default NULL,
collection_output_id int(10) unsigned default NULL,
PRIMARY KEY (simple_output_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'simple_output'
---
-
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
===================================================================
RCS file: /home/repository/moby/moby-live/Database/mobynamespace.mysql,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Database/mobynamespace.mysql 2003/05/24 20:22:15 1.5
+++ /home/repository/moby/moby-live/Database/mobynamespace.mysql 2005/07/08 19:03:17 1.6
@@ -1,11 +1,11 @@
--- MySQL dump 8.22
+-- MySQL dump 8.23
--
-- Host: localhost Database: mobynamespace
---------------------------------------------------------
--- Server version 3.23.52
+-- Server version 4.1.12-standard
--
--- Table structure for table 'namespace'
+-- Table structure for table `namespace`
--
CREATE TABLE namespace (
@@ -15,18 +15,20 @@
description text NOT NULL,
authority varchar(255) NOT NULL default '',
contact_email varchar(255) NOT NULL default '',
+ object text,
+ generic_url tinytext,
+ synonym text,
+ url_syntax text,
+ url_example text,
+ shorthand_name varchar(255) default NULL,
+ example_id varchar(255) default NULL,
+ note mediumtext,
PRIMARY KEY (namespace_id),
UNIQUE KEY namespace_type (namespace_type)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'namespace'
---
-
-
-
---
--- Table structure for table 'namespace_term2term'
+-- Table structure for table `namespace_term2term`
--
CREATE TABLE namespace_term2term (
@@ -35,11 +37,5 @@
namespace1_id int(11) NOT NULL default '0',
namespace2_id int(11) NOT NULL default '0',
PRIMARY KEY (assertion_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'namespace_term2term'
---
-
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
===================================================================
RCS file: /home/repository/moby/moby-live/Database/mobyobject.mysql,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Database/mobyobject.mysql 2003/06/10 23:01:26 1.8
+++ /home/repository/moby/moby-live/Database/mobyobject.mysql 2005/07/08 19:03:17 1.9
@@ -1,11 +1,11 @@
--- MySQL dump 8.22
+-- MySQL dump 8.23
--
-- Host: localhost Database: mobyobject
---------------------------------------------------------
--- Server version 3.23.52
+-- Server version 4.1.12-standard
--
--- Table structure for table 'object'
+-- Table structure for table `object`
--
CREATE TABLE object (
@@ -17,21 +17,10 @@
contact_email varchar(255) NOT NULL default '',
PRIMARY KEY (object_id),
UNIQUE KEY object_type (object_type)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'object'
---
-
-
-INSERT INTO object VALUES (1,'urn:lsid:biomoby.org:objectclass:object','Object','an object','openinformatics.com','jason at openinformatics.com');
-INSERT INTO object VALUES (2,'urn:lsid:biomoby.org:objectclass:integer','Integer','an int','openinformatics.com','jason at openinformatics.com');
-INSERT INTO object VALUES (3,'urn:lsid:biomoby.org:objectclass:string','String','a string','openinformatics.com','jason at openinformatics.com');
-INSERT INTO object VALUES (4,'urn:lsid:biomoby.org:objectclass:float','Float','a floating point number','openinformatics.com','jason at openinformatics.com');
-INSERT INTO object VALUES (5,'urn:lsid:biomoby.org:objectclass:datetime','DateTime','a date or time in ISO-8601 format','openinformatics.com','jason at openinformatics.com');
-
---
--- Table structure for table 'object_term2term'
+-- Table structure for table `object_term2term`
--
CREATE TABLE object_term2term (
@@ -41,14 +30,5 @@
object2_id int(11) NOT NULL default '0',
object2_articlename varchar(255) default NULL,
PRIMARY KEY (assertion_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'object_term2term'
---
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-INSERT INTO object_term2term VALUES (1,'urn:lsid:biomoby.org:objectrelation:isa',2,1,NULL);
-INSERT INTO object_term2term VALUES (2,'urn:lsid:biomoby.org:objectrelation:isa',3,1,NULL);
-INSERT INTO object_term2term VALUES (3,'urn:lsid:biomoby.org:objectrelation:isa',4,1,NULL);
-INSERT INTO object_term2term VALUES (4,'urn:lsid:biomoby.org:objectrelation:isa',5,3,NULL);
===================================================================
RCS file: /home/repository/moby/moby-live/Database/mobyrelationship.mysql,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Database/mobyrelationship.mysql 2003/05/24 20:26:07 1.4
+++ /home/repository/moby/moby-live/Database/mobyrelationship.mysql 2005/07/08 19:03:17 1.5
@@ -1,11 +1,11 @@
--- MySQL dump 8.22
+-- MySQL dump 8.23
--
-- Host: localhost Database: mobyrelationship
---------------------------------------------------------
--- Server version 3.23.52
+-- Server version 4.1.12-standard
--
--- Table structure for table 'relationship'
+-- Table structure for table `relationship`
--
CREATE TABLE relationship (
@@ -19,20 +19,10 @@
ontology varchar(200) NOT NULL default '',
PRIMARY KEY (relationship_id),
UNIQUE KEY LSID (relationship_lsid)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'relationship'
---
-
-
-INSERT INTO relationship VALUES (1,'urn:lsid:biomoby.org:objectrelation:hasa','hasa','1','Describes a container relationship where the predicate object is contained within the subject object in one copy only','www.biomoby.org','markw at illuminae.com','object');
-INSERT INTO relationship VALUES (2,'urn:lsid:biomoby.org:objectrelation:has','has','1','Describes a container relationship where the predicate object is contained within the subject object in one or more copies','www.biomoby.org','markw at illuminae.com','object');
-INSERT INTO relationship VALUES (3,'urn:lsid:biomoby.org:objectrelation:isa','isa','0','Describes an inheritence relationship where all attributes of the parent must be in the child','www.biomoby.org','markw at illuminae.com','object');
-INSERT INTO relationship VALUES (4,'urn:lsid:biomoby.org:servicerelation:isa','isa','0','Describes an inheritence relationship where the predicate service performs a more specific operation compared to the subject service','www.biomoby.org','markw at illuminae.com','service');
-
---
--- Table structure for table 'relationship_term2term'
+-- Table structure for table `relationship_term2term`
--
CREATE TABLE relationship_term2term (
@@ -42,9 +32,5 @@
relationship2_id int(10) unsigned NOT NULL default '0',
object2_articlename varchar(255) default NULL,
PRIMARY KEY (assertion_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'relationship_term2term'
---
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
===================================================================
RCS file: /home/repository/moby/moby-live/Database/mobyservice.mysql,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Database/mobyservice.mysql 2003/06/10 23:01:26 1.6
+++ /home/repository/moby/moby-live/Database/mobyservice.mysql 2005/07/08 19:03:17 1.7
@@ -1,11 +1,11 @@
--- MySQL dump 8.22
+-- MySQL dump 8.23
--
-- Host: localhost Database: mobyservice
---------------------------------------------------------
--- Server version 3.23.52
+-- Server version 4.1.12-standard
--
--- Table structure for table 'service'
+-- Table structure for table `service`
--
CREATE TABLE service (
@@ -17,22 +17,10 @@
contact_email varchar(255) NOT NULL default '',
PRIMARY KEY (service_id),
UNIQUE KEY service_type (service_type)
-) TYPE=MyISAM;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
--
--- Dumping data for table 'service'
---
-
-
-INSERT INTO service VALUES (1,'urn:lsid:biomoby.org:servicetype:service','Service','The base type','openinformatics.com','email');
-INSERT INTO service VALUES (2,'urn:lsid:biomoby.org:servicetype:retrieval','Retrieval','The base retrieval type','openinformatics.com','email');
-INSERT INTO service VALUES (3,'urn:lsid:biomoby.org:servicetype:resolution','Resolution','resolve data','openinformatics.com','email');
-INSERT INTO service VALUES (4,'urn:lsid:biomoby.org:servicetype:parsing','Parsing','parse data','openinformatics.com','email');
-INSERT INTO service VALUES (5,'urn:lsid:biomoby.org:servicetype:registration','Registration','register data','openinformatics.com','email');
-INSERT INTO service VALUES (6,'urn:lsid:biomoby.org:servicetype:analysis','Analysis','analyze data','openinformatics.com','email');
-
---
--- Table structure for table 'service_term2term'
+-- Table structure for table `service_term2term`
--
CREATE TABLE service_term2term (
@@ -41,15 +29,5 @@
service1_id int(11) NOT NULL default '0',
service2_id int(11) NOT NULL default '0',
PRIMARY KEY (assertion_id)
-) TYPE=MyISAM;
-
---
--- Dumping data for table 'service_term2term'
---
-
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-INSERT INTO service_term2term VALUES (8,'urn:lsid:biomoby.org:servicerelation:isa',2,1);
-INSERT INTO service_term2term VALUES (4,'urn:lsid:biomoby.org:servicerelation:isa',3,1);
-INSERT INTO service_term2term VALUES (5,'urn:lsid:biomoby.org:servicerelation:isa',4,1);
-INSERT INTO service_term2term VALUES (6,'urn:lsid:biomoby.org:servicerelation:isa',5,1);
-INSERT INTO service_term2term VALUES (7,'urn:lsid:biomoby.org:servicerelation:isa',6,1);
===================================================================
RCS file: /home/repository/moby/moby-live/Database/reset,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Database/reset 2003/05/24 20:41:44 1.1
+++ /home/repository/moby/moby-live/Database/reset 2005/07/08 19:03:17 1.2
@@ -1,6 +1,7 @@
+#!/bin/bash
mysql -u root -p < reset2
mysql -u root -p mobycentral < mobycentral.mysql
-mysql -u root -p mobyobject < mobyobject.mysql
-mysql -u root -p mobyservice < mobyservice.mysql
+mysql -u root -p mobyobject < mobyobject.data
+mysql -u root -p mobyservice < mobyservice.data
mysql -u root -p mobynamespace < mobynamespace.mysql
mysql -u root -p mobyrelationship < mobyrelationship.mysql
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