Transcript PerlObjectLayer

The GUS 3.0 Perl Object
Layer
CBIL
Jonathan Schug
June 18 2002
Outline
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Overview
Objects
Using Objects
Superclasses
GA - GusApplication
Plugins
A Programmer's View of GUS3.0
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The application programmer interacts with GUS via the
GusApplication (GA) Perl program.
The GA is a general framework for connecting to GUS30.
Specific tasks are performed by individual plugins.
Plugins use either table-specific classes or SQL access.
Low-level database access is provided by DBI classes.
GusApplication
Plugin
Class
Class
Class
Class
Class
SuperClasses
•
SQL
DBI
Core SRes
DoTS RAD TESS
A GUS3.0 Table
Parents - pointed
to by this table
Primary key
Table-specific attributes
GUS overhead attributes
Children - point to this table
A GUS3.0 Perl Object Layer Class
GUS30/DoTS/Clone.pm
package DoTS::Clone;
use strict;
use GUS30::DoTS::gen::Clone_gen;
use vars qw (@ISA);
@ISA = qw (DoTS::Clone_gen);
1;
• Relies on _gen class for accessor methods.
• This is stub for hand-edited domain-specific methods.
The _gen Class - I
GUS30/DoTS/gen/Clone_gen.pm
package DoTS::Clone_gen;
use strict;
use GUS30::dbiperl_utils::RelationalRow;
use vars qw (@ISA);
@ISA = qw (RelationalRow);
sub setDefaultParams { ... }
• Inherits from RelationalRow
• setDefaultParams to determine if versionable and
updateable.
The _gen Class - II
GUS30/DoTS/gen/Clone_gen.pm
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
setCloneId { ... }
getCloneId { ... }
setLibraryId { ... }
getLibraryId { ... }
setImageId { ... }
getImageId { ... }
setDbestCloneUid { ... }
getDbestCloneUid { ... }
setWashuName { ... }
getWashuName { ... }
setGdbId { ... }
getGdbId { ... }
setMgiId { ... }
getMgiId { ... }
setDbestLength { ... }
getDbestLength { ... }
setWashuLength { ... }
sub getWashuLength { ... }
• There is an
accessor for
each column.
• Note the
case change
and loss of
underscores.
The _gen Class - III
GUS30/DoTS/gen/Clone_gen.pm
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
sub
setModificationDate {
getModificationDate {
setUserRead { ... }
getUserRead { ... }
setUserWrite { ... }
getUserWrite { ... }
setGroupRead { ... }
getGroupRead { ... }
setGroupWrite { ... }
getGroupWrite { ... }
setOtherRead { ... }
getOtherRead { ... }
setOtherWrite { ... }
getOtherWrite { ... }
setRowUserId { ... }
getRowUserId { ... }
setRowGroupId { ... }
getRowGroupId { ... }
setRowProjectId { ...
getRowProjectId { ...
setRowAlgInvocationId
getRowAlgInvocationId
... }
... }
• There is an
accessor for
each column.
• Note the case
change and
loss of
underscores.
}
}
{ ... }
{ ... }
Hand Edited Methods
• Edit main class file, e.g.,
GUS30/DoTS/Clone.pm
• Typically placed in
GUS30/DoTS/hand_edited/
• Symlink in GUS30/DoTS.
• Mostly used in DoTS section.
DoTS/AAFeature.pm:4
DoTS/AASequence.pm:2
DoTS/Assembly.pm:76
DoTS/AssemblySequence.pm:29
DoTS/Evidence.pm:6
DoTS/GeneFeature.pm:4
DoTS/Gene.pm:9
DoTS/IndexWordSimLink.pm:2
DoTS/NAFeature.pm:5
DoTS/NASequence.pm:4
DoTS/RNAFeature.pm:4
DoTS/RNA.pm:3
DoTS/Similarity.pm:9
DoTS/SimilaritySpan.pm:6
DoTS/SplicedNASequence.pm:1
DoTS/TranslatedAAFeature.pm:3
DoTS/TranslatedAAFeatureSegment.pm:2
DoTS/TranslatedAASequence.pm:1
DoTS/VirtualSequence.pm:1
Creating Objects
# get the class
use GUS30::DoTS::Clone;
…
# create new object
my $clone_gus = DoTS::Clone->new({
washu_length => 5,
});
# adjust a column value
$clone_gus->setDbestUid(‘A123456’);
# print some values.
print $clone_gus->getDbestUid, “\n”;
print $clone_gus->toXML, “\n”;
# submit to database
$clone_gus->submit;
Connecting Objects
use GUS30::DoTS::Clone;
use GUS30::DoTS::CloneLibrary;
My $clone_lib_gus = DoTS::CloneLibrary->new({…});
While (<>) {
chomp; my @parts = split /\t/;
my $clone_gus = DoTS::Clone->new({…});
# this
$clone_lib_gus->addChild($clone_gus);
# or this
$clone_gus->setParent($clone_lib_gus);
}
$clone_lib_gus->submit;
Retrieving Objects
Use GUS30::DoTS::CloneLibrary;
My $clone_lib_gus = DoTS::CloneLibrary->new({
clone_library_id => 12345
});
If ($clone_lib_gus->retrieveFromDB) {
$clone_lib_gus->set…(…);
$clone_lib_gus->submit;
print “found it!\n”;
}
Else {
print “did not find any unique row!\n”;
}
Traversing Object Relations - I
Use GUS30::DoTS::CloneLibrary;
Use GUS30::DoTS::Clone;
My $clone_lib_gus = DoTS::CloneLibrary({
clone_library_id => 12345
});
If ($clone_lib_gus->retrieveFromDB) {
my @clones =
$clone_lib_gus->getChildren(‘DoTS.Clone’,1);
foreach (@clones) {
…
}
}
Traversing Object Relations - II
Use GUS30::DoTS::CloneLibrary;
Use GUS30::DoTS::Clone;
My $clone_lib = DoTS::Clone->new({
clone_id => 12345
});
If ($clone_gus->retrieveFromDB) {
my $clone_lib_gus =
$clone_gus->getParent(‘DoTS.CloneLibrary’,1);
. . .
}
Deleting Objects
Use GUS30::DoTS::CloneLibrary;
Use GUS30::DoTS::Clone;
My $clone_lib_gus = DoTS::CloneLibrary({
clone_library_id => 12345
});
If ($clone_lib_gus->retrieveFromDB) {
$clone_lib_gus->markDeleted;
my @clones =
$clone_lib_gus->getChildren(‘DoTS.Clone’,1);
foreach (@clones) {
$_->markDeleted;
}
$clone_lib_gus->submit;
}
• Recursively deletes children as well.
The Object Cache
• A cache of objects is maintained so that
getParents and getChildren always return the
same instance of a row.
• Cache is limited in size to avoid large
memory requirements.
• Cache is cleared with undefPointerCache
method on object or plugin
• Cache size is increased with
setMaximumNumberOfObjects method.
Dbiperl_utils
Support and base classes for object
classes.
• RelationalRow
• DbiRow
• DbiTable
• DbiDatabase
RelationalRow.pm
• Contains 176 methods in these categories:
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–
–
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–
–
–
Accessors for default overhead values
Accessors for debugging and verbose modes
Pointer cache maintenance
Class information
Parent/child information
XML management
Deletion marking
Submission management
Similarity and Evidence management
• Isa DbiRow
DbiRow.pm
• Contains 43 methods in these categories:
– Get/Set methods to support class-specific
accessors
– Accessors for table and class names
– Attribute information
– Tracking attribute value changes
– retrieveFromDB
– IdentityInsert management
– Get DbHandle, MetaHandle, and Database
DbiTable.pm
• 76 methods for
– Various table names
– Attribute information
– Relations information
– Primary keys and ids
– Others
DbiDatabase.pm
• 103 methods covering these areas:
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Database handles
Login information
Database and section names
Transaction management
Table and view names
Object cache
Counters
Overhead Columns
Contain information about:
•History
•Ownership
•Access permissions
•Data provenance
Who manages these columns?
GusApplication (GA)
• Purpose is to standardize database
access application
• Provides:
– Database login
– Default ownership and permissions
– Algorithm and parameter tracking
– Command line access
Algorithms & Stuff
Algorithm
AlgorithmParamKeyType
AlgorithmImplementation
AlgorithmParamKey
AlgorithmInvocation
AlgorithmParam
Tracks what programs implementing what algorithms were
run with what parameters.
GA populates these tables.
GA Usage
ga [<mode>] [<plugin_class>] <plugin_class_options>
• <mode> is one of
– +create : creates Algorithm, AlgorithmImplementation, and
AlgorithmParamKey
– +update : creates AlgorithmImplementation and
AlgorithmParamKey
– +history : lists invocations
– +run : runs the plugin (default)
• <plugin_class>
– From hierarchical namespace, e.g., Utils::UpdateGusFromXML
• <plugin_class_options>
– Defined by plugin plus some generic GA options.
– E.g., --file data.tab --commit --verbose
Plugins
• A plugin is just a package that inherits from
GUS30::GA_plugins::Plugin.
package GUS30::GA_plugins::Utils::UpdateGusFromXML;
@ISA = qw(GUS30::GA_plugins::Plugin);
• It must have two methods:
– new - to create and initialize the plugin object
– run - perform actions of plugin
The new Method
• Must initialize certain important plugin
attributes:
sub new {
my $Class = shift;
my $m = bless {}, $Class;
$m->setUsage(‘what this algorithm does’);
$m->setVersion('2.0');
$m->setRequiredDbVersion({ Core => ‘3’, DoTS => ‘3’ });
$m->setDescription(‘what is new in implementation);
$m->setEasyCspOptions(…); # command line options
return $m
}
Command Line Options
• A hash describing a parameter:
–
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–
–
–
–
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h => hint for user
t => parameter data type (boolean, string, integer, float)
d => default value
l => is a list if true
e => list of legal reg-exps
r => required if true
o => command line flag
• E.g.,
{ h
t
d
o
},
=>
=>
=>
=>
'start label ordinals with this value',
'integer',
0,
'FirstOrdinal',
GA-Supplied Comand-line Options
• GA adds these options:
–
–
–
–
–
–
–
–
–
–
–
commit
verbose
debug
user
group
project
comment
database
server
implementation
algoinvo
• Pink ones also read from config file .gus30.cfg
Example: TESS::LoadMultinomialLabelSet
TESS::MultinomialLabelSet
TESS::MultinomialLabel
•Task is to maintain entries in these two tables
•MultinomialLabelSet stores sets of labels for
multinomial observations, e.g., DNA, AA, or dimer
gaps.
•Can also be DNA or AA dimers, trimers, etc.
•MultinomialLabel stores individual names.