Ace - Object-Oriented Access to ACEDB Databases
use Ace;
# open a remote database connection
$db = Ace->connect(-host => 'beta.crbm.cnrs-mop.fr',
-port => 20000100);
# open a local database connection
$local = Ace->connect(-path=>'~acedb/my_ace');
# simple queries
$sequence = $db->fetch(Sequence => 'D12345');
$count = $db->count(Sequence => 'D*');
@sequences = $db->fetch(Sequence => 'D*');
$i = $db->fetch_many(Sequence=>'*'); # fetch a cursor
while ($obj = $i->next) {
print $obj->asTable;
}
# complex queries
$query = <<END;
find Annotation Ready_for_submission ; follow gene ;
follow derived_sequence ; >DNA
END
@ready_dnas= $db->fetch(-query=>$query);
$ready = $db->fetch_many(-query=>$query);
while ($obj = $ready->next) {
# do something with obj
}
# database cut and paste
$sequence = $db->fetch(Sequence => 'D12345');
$local_db->put($sequence);
@sequences = $db->fetch(Sequence => 'D*');
$local_db->put(@sequences);
# Get errors
print Ace->error;
print $db->error;
AcePerl provides an interface to the ACEDB object-oriented database. Both read
and write access is provided, and ACE objects are returned as
similarly-structured Perl objects. Multiple databases can be opened
simultaneously.
You will interact with several Perl classes:
Ace,
Ace::Object,
Ace::Iterator,
Ace::Model.
Ace is the database accessor,
and can be used to open both remote Ace databases (running aceserver or
gifaceserver), and local ones.
Ace::Object is the superclass for all objects returned from the database.
Ace and
Ace::Object are linked: if you retrieve an Ace::Object
from a particular database, it will store a reference to the database and use
it to fetch any subobjects contained within it. You may make changes to the
Ace::Object and have those changes written into the database. You may
also create
Ace::Objects from scratch and store them in the database.
Ace::Iterator is a utility class that acts as a database cursor for
long-running ACEDB queries.
Ace::Model provides object-oriented access
to ACEDB's schema.
Internally,
Ace uses the
Ace::Local class for access to local
databases and
Ace::AceDB for access to remote databases. Ordinarily you
will not need to interact directly with either of these classes.
# remote database
$db = Ace->connect(-host => 'beta.crbm.cnrs-mop.fr',
-port => 20000100);
# local (non-server) database
$db = Ace->connect(-path => '/usr/local/acedb);
Use
Ace::connect() to establish a connection to a networked or local
AceDB database. To establish a connection to an AceDB server, use the
-host and/or
-port arguments. For a local server, use the
-port argument. The database must be up and running on the indicated
host and port prior to connecting to an AceDB server. The full syntax is as
follows:
$db = Ace->connect(-host => $host,
-port => $port,
-path => $database_path,
-program => $local_connection_program
-classmapper => $object_class,
-timeout => $timeout,
-query_timeout => $query_timeout
-cache => {cache parameters},
);
The
connect() method uses a named argument calling style, and recognizes
the following arguments:
-
-host, -port
- These arguments point to the host and port of an AceDB
server. AcePerl will use its internal compiled code to establish a
connection to the server unless explicitly overridden with the
-program argument.
- -path
- This argument indicates the path of an AceDB directory on
the local system. It should point to the directory that contains the
wspec subdirectory. User name interpolations (~acedb) are OK.
- -user
- Name of user to log in as (when using socket server
only). If not provided, will attempt an anonymous login.
- -pass
- Password to log in with (when using socket server).
- -url
- An Acedb URL that combines the server type, host, port,
user and password in a single string. See the connect() method's
"single argument form" description.
- -cache
- AcePerl can use the Cache::SizeAwareFileCache module to
cache objects to disk. This can result in dramatically increased
performance in environments such as web servers in which the same Acedb
objects are frequently reused. To activate this mechanism, the
Cache::SizeAwareFileCache module must be installed, and you must pass the
-cache argument during the connect() call.
The value of -cache is a hash reference containing the arguments to be
passed to Cache::SizeAwareFileCache. For example:
-cache => {
cache_root => '/usr/tmp/acedb',
cache_depth => 4,
default_expires_in => '1 hour'
}
If not otherwise specified, the following cache parameters are assumed:
Parameter Default Value
--------- -------------
namespace Server URL (e.g. sace://localhost:2005)
cache_root /tmp/FileCache (dependent on system temp directory)
default_expires_in 1 day
auto_purge_interval 12 hours
By default, the cache is not size limited (the "max_size" property
is set to $NO_MAX_SIZE). To adjust the size you may consider calling the
Ace object's cache() method to retrieve the physical cache and then
calling the cache object's limit_size($max_size) method from time to time.
See Cache::SizeAwareFileCache for more details.
- -program
- By default AcePerl will use its internal compiled code
calls to establish a connection to Ace servers, and will launch a
tace subprocess to communicate with local Ace databases. The
-program argument allows you to customize this behavior by forcing
AcePerl to use a local program to communicate with the database. This
argument should point to an executable on your system. You may use either
a complete path or a bare command name, in which case the PATH environment
variable will be consulted. For example, you could force AcePerl to use
the aceclient program to connect to the remote host by connecting
this way:
$db = Ace->connect(-host => 'beta.crbm.cnrs-mop.fr',
-port => 20000100,
-program=>'aceclient');
- -classmapper
- The optional -classmapper argument (alias
-class) points to the class you would like to return from database
queries. It is provided for your use if you subclass Ace::Object. For
example, if you have created a subclass of Ace::Object called
Ace::Object::Graphics, you can have the database return this subclass by
default by connecting this way:
$db = Ace->connect(-host => 'beta.crbm.cnrs-mop.fr',
-port => 20000100,
-class=>'Ace::Object::Graphics');
The value of -class can be a hash reference consisting of AceDB class
names as keys and Perl class names as values. If a class name does not
exist in the hash, a key named _DEFAULT_ will be looked for. If that does
not exist, then Ace will default to Ace::Object.
The value of -class can also be an object or a classname that
implements a class_for() method. This method will receive three
arguments containing the AceDB class name, object ID and database handle.
It should return a string indicating the perl class to create.
- -timeout
- If no response from the server is received within $timeout
seconds, the call will return an undefined value. Internally timeout sets
an alarm and temporarily intercepts the ALRM signal. You should be aware
of this if you use ALRM for your own purposes.
NOTE: this feature is temporarily disabled (as of version 1.40) because it
is generating unpredictable results when used with Apache/mod_perl.
- -query_timeout
- If any query takes longer than $query_timeout seconds, will
return an undefined value. This value can only be set at connect time, and
cannot be changed once set.
If arguments are omitted, they will default to the following values:
-host localhost
-port 200005;
-path no default
-program tace
-class Ace::Object
-timeout 25
-query_timeout 120
If you prefer to use a more Smalltalk-like message-passing syntax, you can open
a connection this way too:
$db = connect Ace -host=>'beta.crbm.cnrs-mop.fr',-port=>20000100;
The return value is an Ace handle to use to access the database, or undef if the
connection fails. If the connection fails, an error message can be retrieved
by calling Ace->error.
You may check the status of a connection at any time with
ping(). It will
return a true value if the database is still connected. Note that Ace will
timeout clients that have been inactive for any length of time. Long-running
clients should attempt to reestablish their connection if
ping()
returns false.
$db->ping() || die "not connected";
You may perform low-level calls using the Ace client C API by calling
db(). This fetches an Ace::AceDB object. See THE LOW LEVEL C API for
details on using this object.
$low_level = $db->db();
$db = Ace->connect('sace://stein.cshl.org:1880')
Ace->
connect() also accepts a single argument form using a URL-type
syntax. The general syntax is:
protocol://hostname:port/path
The
:port and
/path parts are protocol-dependent as described
above.
Protocols:
- sace://hostname:port
- Connect to a socket server at the indicated hostname and
port. Example:
sace://stein.cshl.org:1880
If not provided, the port defaults to 2005.
- rpcace://hostname:port
- Connect to an RPC server at the indicated hostname and RPC
service number. Example:
rpcace://stein.cshl.org:400000
If not provided, the port defaults to 200005
- tace:/path/to/database
- Open up the local database at /path/to/database
using tace. Example:
tace:/~acedb/elegans
- /path/to/database
- Same as the previous.
You can explicitly close a database by calling its
close() method:
$db->close();
This is not ordinarily necessary because the database will be automatically
close when it -- and all objects retrieved from it -- go out of scope.
The ACeDB socket server can time out. The
reopen() method will ping the
server and if it is not answering will reopen the connection. If the database
is live (or could be resurrected), this method returns true.
Once you have established a connection and have an Ace databaes handle, several
methods can be used to query the ACE database to retrieve objects. You can
then explore the objects, retrieve specific fields from them, or update them
using the
Ace::Object methods. Please see Ace::Object.
$count = $db->fetch($class,$name_pattern);
$object = $db->fetch($class,$name);
@objects = $db->fetch($class,$name_pattern,[$count,$offset]);
@objects = $db->fetch(-name=>$name_pattern,
-class=>$class
-count=>$count,
-offset=>$offset,
-fill=>$fill,
-filltag=>$tag,
-total=>\$total);
@objects = $db->fetch(-query=>$query);
Ace::fetch() retrieves objects from the database based on their class and
name. You may retrieve a single object by requesting its name, or a group of
objects by fetching a name
pattern. A pattern contains one or more
wildcard characters, where "*" stands for zero or more characters,
and "?" stands for any single character.
This method behaves differently depending on whether it is called in a scalar or
a list context, and whether it is asked to search for a name pattern or a
simple name.
When called with a class and a simple name, it returns the object referenced by
that time, or undef, if no such object exists. In an array context, it will
return an empty list.
When called with a class and a name pattern in a list context,
fetch()
returns the list of objects that match the name. When called with a pattern in
a scalar context,
fetch() returns the
number of objects that
match without actually retrieving them from the database. Thus, it is similar
to
count().
In the examples below, the first line of code will fetch the Sequence object
whose database ID is
D12345. The second line will retrieve all objects
matching the pattern
D1234*. The third line will return the count of
objects that match the same pattern.
$object = $db->fetch(Sequence => 'D12345');
@objects = $db->fetch(Sequence => 'D1234*');
$cnt = $db->fetch(Sequence =>'D1234*');
A variety of communications and database errors may occur while processing the
request. When this happens, undef or an empty list will be returned, and a
string describing the error can be retrieved by calling Ace->error.
When retrieving database objects, it is possible to retrieve a
"filled" or an "unfilled" object. A filled object contains
the entire contents of the object, including all tags and subtags. In the case
of certain Sequence objects, this may be a significant amount of data.
Unfilled objects consist just of the object name. They are filled in from the
database a little bit at a time as tags are requested. By default,
fetch() returns the unfilled object. This is usually a performance win,
but if you know in advance that you will be needing the full contents of the
retrieved object (for example, to display them in a tree browser) it can be
more efficient to fetch them in filled mode. You do this by calling
fetch() with the argument of
-fill set to a true value.
The
-filltag argument, if provided, asks the database to fill in the
subtree anchored at the indicated tag. This will improve performance for
frequently-accessed subtrees. For example:
@objects = $db->fetch(-name => 'D123*',
-class => 'Sequence',
-filltag => 'Visible');
This will fetch all Sequences named D123* and fill in their Visible trees in a
single operation.
Other arguments in the named parameter calling form are
-count, to
retrieve a certain maximum number of objects, and
-offset, to retrieve
objects beginning at the indicated offset into the list. If you want to limit
the number of objects returned, but wish to learn how many objects might have
been retrieved, pass a reference to a scalar variable in the
-total
argument. This will return the object count. This example shows how to fetch
100 Sequence objects, starting at Sequence number 500:
@some_sequences = $db->fetch('Sequence','*',100,500);
The next example uses the named argument form to fetch 100 Sequence objects
starting at Sequence number 500, and leave the total number of Sequences in
$total:
@some_sequences = $db->fetch(-class => 'Sequence',
-count => 100,
-offset => 500,
-total => \$total);
Notice that if you leave out the
-name argument the "*"
wildcard is assumed.
You may also pass an arbitrary Ace query string with the
-query argument.
This will supersede any name and class you provide. Example:
@ready_dnas= $db->fetch(-query=>
'find Annotation Ready_for_submission ; follow gene ;
follow derived_sequence ; >DNA');
If your request is likely to retrieve very many objects,
fetch() many
consume a lot of memory, even if
-fill is false. Consider using
fetch_many() instead (see below). Also see the
get() method, which is equivalent to the simple two-argument form of
fetch().
-
get() method
-
$object = $db->get($class,$name [,$fill]);
The get() method will return one and only one AceDB object identified
by its class and name. The optional $fill argument can be used to control
how much data is retrieved from the database. If $fill is absent or
undefined, then the method will return a lightweight "stub"
object that is filled with information as requested in a lazy fashion. If
$fill is the number "1" then the retrieved object contains all
the relevant information contained within the database. Any other true
value of $fill will be treated as a tag name: the returned object will be
prefilled with the subtree to the right of that tag.
Examples:
# return lightweight stub for Author object "Sulston JE."
$author = $db->get(Author=>'Sulston JE');
# return heavyweight object
$author = $db->get(Author=>'Sulston JE',1);
# return object containing the Address subtree
$author = $db->get(Author=>'Sulston JE','Address');
The get() method is equivalent to this form of the fetch()
method:
$object = $db->fetch($class=>$name);
$count = $db->aql($aql_query);
@objects = $db->aql($aql_query);
Ace::aql() will perform an AQL query on the database. In a scalar context
it returns the number of rows returned. In an array context it returns a list
of rows. Each row is an anonymous array containing the columns returned by the
query as an Ace::Object.
If an AQL error is encountered, will return undef or an empty list and set
Ace->error to the error message.
Note that this routine is not optimized -- there is no iterator defined. All
results are returned synchronously, leading to large memory consumption for
certain queries.
$cnt = $db->put($obj1,$obj2,$obj3);
This method will put the list of objects into the database, overwriting
like-named objects if they are already there. This can be used to copy an
object from one database to another, provided that the models are compatible.
The method returns the count of objects successfully written into the database.
In case of an error, processing will stop at the last object successfully
written and an error message will be placed in Ace->
error();
$object = $db->parse('data to parse');
This will parse the Ace tags contained within the "data to parse"
string, convert it into an object in the database, and return the resulting
Ace::Object. In case of a parse error, the undefined value will be returned
and a (hopefully informative) description of the error will be returned by
Ace->
error().
For example:
$author = $db->parse(<<END);
Author : "Glimitz JR"
Full_name "Jonathan R. Glimitz"
Mail "128 Boylston Street"
Mail "Boston, MA"
Mail "USA"
Laboratory GM
END
This method can also be used to parse several objects, but only the last object
successfully parsed will be returned.
$object = $db->parse($title,$text);
This will parse the long text (which may contain carriage returns and other
funny characters) and place it into the database with the given title. In case
of a parse error, the undefined value will be returned and a (hopefully
informative) description of the error will be returned by Ace->
error(); otherwise, a LongText object will be returned.
For example:
$author = $db->parse_longtext('A Novel Inhibitory Domain',<<END);
We have discovered a novel inhibitory domain that inhibits
many classes of proteases, including metallothioproteins.
This inhibitory domain appears in three different gene families studied
to date...
END
@objects = $db->parse_file('/path/to/file');
@objects = $db->parse_file('/path/to/file',1);
This will call
parse() to parse each of the objects found in the
indicated .ace file, returning the list of objects successfully loaded into
the database.
By default, parsing will stop at the first object that causes a parse error. If
you wish to forge on after an error, pass a true value as the second argument
to this method.
Any parse error messages are accumulated in Ace->
error().
$object = $db->new($class => $name);
This method creates a new object in the database of type $class and name $name.
If successful, it returns the newly-created object. Otherwise it returns undef
and sets $db->
error().
$name may contain
sprintf()-style patterns. If one of the patterns is %d
(or a variant), Acedb uses a class-specific unique numbering to return a
unique name. For example:
$paper = $db->new(Paper => 'wgb%06d');
The object is created in the database atomically. There is no chance to rollback
as there is in Ace::Object's object editing methods.
See also the Ace::Object->
add() and
replace() methods.
@objects = $db->list(class,pattern,[count,offset]);
@objects = $db->list(-class=>$class,
-name=>$name_pattern,
-count=>$count,
-offset=>$offset);
This is a deprecated method. Use
fetch() instead.
$count = $db->count($class,$pattern);
$count = $db->count(-query=>$query);
This function queries the database for a list of objects matching the specified
class and pattern, and returns the object count. For large sets of objects
this is much more time and memory effective than fetching the entire list.
The class and name pattern are the same as the
list() method above.
You may also provide a
-query argument to instead specify an arbitrary
ACE query such as "find Author COUNT Paper > 80". See
find() below.
@objects = $db->find($query_string);
@objects = $db->find(-query => $query_string,
-offset=> $offset,
-count => $count
-fill => $fill);
This allows you to pass arbitrary Ace query strings to the server and retrieve
all objects that are returned as a result. For example, this code fragment
retrieves all papers written by Jean and Danielle Thierry-Mieg.
@papers = $db->find('author IS "Thierry-Mieg *" ; >Paper');
You can find the full query syntax reference guide plus multiple examples at
http://probe.nalusda.gov:8000/acedocs/index.html#query.
In the named parameter calling form,
-count,
-offset, and
-fill have the same meanings as in
fetch().
$obj = $db->fetch_many($class,$pattern);
$obj = $db->fetch_many(-class=>$class,
-name =>$pattern,
-fill =>$filled,
-chunksize=>$chunksize);
$obj = $db->fetch_many(-query=>$query);
If you expect to retrieve many objects, you can fetch an iterator across the
data set. This is friendly both in terms of network bandwidth and memory
consumption. It is simple to use:
$i = $db->fetch_many(Sequence,'*'); # all sequences!!!!
while ($obj = $i->next) {
print $obj->asTable;
}
The iterator will return undef when it has finished iterating, and cannot be
used again. You can have multiple iterators open at once and they will operate
independently of each other.
Like
fetch(),
fetch_many() takes an
optional
-fill (or
-filled) argument which retrieves the entire
object rather than just its name. This is efficient on a network with high
latency if you expect to be touching many parts of the object (rather than
just retrieving the value of a few tags).
fetch_many() retrieves objects from the database in groups
of a certain maximum size, 40 by default. This can be tuned using the optional
-chunksize argument. Chunksize is only a hint to the database. It may
return fewer objects per transaction, particularly if the objects are large.
You may provide raw Ace query string with the
-query argument. If present
the
-name and
-class arguments will be ignored.
This is an alias for
fetch_many(). It is now deprecated.
@objects = $db->keyset($keyset_name);
This method returns all objects in a named keyset. Wildcard characters are
accepted, in which case all keysets that match the pattern will be retrieved
and merged into a single list of unique objects.
@objects = $db->grep($grep_string);
$count = $db->grep($grep_string);
@objects = $db->grep(-pattern => $grep_string,
-offset=> $offset,
-count => $count,
-fill => $fill,
-filltag => $filltag,
-total => \$total,
-long => 1,
);
This performs a "grep" on the database, returning all object names or
text that contain the indicated grep pattern. In a scalar context this call
will return the number of matching objects. In an array context, the list of
matching objects are retrieved. There is also a named-parameter form of the
call, which allows you to specify the number of objects to retrieve, the
offset from the beginning of the list to retrieve from, whether the retrieved
objects should be filled initially. You can use
-total to discover the
total number of objects that match, while only retrieving a portion of the
list.
By default, grep uses a fast search that only examines class names and lexiques.
By providing a true value to the
-long parameter, you can search inside
LongText and other places that are not usually touched on, at the expense of
much more CPU time.
Due to "not listable" objects that may match during grep, the list of
objects one can retrieve may not always match the count.
$model = $db->model('Author');
This will return an
Ace::Model object corresponding to the indicated
class.
$obj = $db->new($class,$name);
$obj = $db->new(-class=>$class,
-name=>$name);
Create a new object in the database with the indicated class and name and return
a pointer to it. Will return undef if the object already exists in the
database. The object isn't actually written into the database until you call
Ace::Object::commit().
$r = $db->raw_query('Model');
Send a command to the database and return its unprocessed output. This method is
necessary to gain access to features that are not yet implemented in this
module, such as model browsing and complex queries.
@classes = $db->classes();
@all_classes = $db->classes(1);
This method returns a list of all the object classes known to the server. In a
list context it returns an array of class names. In a scalar context, it the
number of classes defined in the database.
Ordinarily
classes() will return only those classes
that are exposed to the user interface for browsing, the so-called
"visible" classes. Pass a true argument to the call to retrieve
non-visible classes as well.
%classes = $db->class_count()
This returns a hash in which the keys are the class names and the values are the
total number of objects in that class. All classes are returned, including
invisible ones. Use this method if you need to count all classes
simultaneously. If you only want to count one or two classes, it may be more
efficient to call
count($class_name) instead.
This method transiently uses a lot of memory. It should not be used with Ace 4.5
servers, as they contain a memory leak in the counting routine.
%status = $db->status;
$status = $db->status;
Returns various bits of status information from the server. In an array context,
returns a hash of hashes. In a scalar context, returns a reference to a hash
of hashes. Keys and subkeys are as follows
code
program name of acedb binary
version version of acedb binary
build build date of acedb binary in format Jan 25 2003 16:21:24
database
title name of the database
version version of the database
dbformat database format version number
directory directory in which the database is stored
session session number
user user under which server is running
write whether the server has write access
address global address - not known if this is useful
resources
classes number of classes defined
keys number of keys defined
memory amount of memory used by acedb objects (bytes)
For example, to get the program version:
my $version = $db->status->{code}{version};
my $title = $db->title
Returns the version of the current database, equivalent to
$db->status->{database}{title};
my $version = $db->version;
Returns the version of the current database, equivalent to
$db->status->{database}{version};
$style = $db->date_style();
$style = $db->date_style('ace');
$style = $db->date_style('java');
For historical reasons, AceDB can display dates using either of two different
formats. The first format, which I call "ace" style, puts the year
first, as in "1997-10-01". The second format, which I call
"java" style, puts the day first, as in "01 Oct 1997
00:00:00" (this is also the style recommended for Internet dates). The
default is to use the latter notation.
date_style() can be used to set or retrieve the current
style. Called with no arguments, it returns the current style, which will be
one of "ace" or "java." Called with an argument, it will
set the style to one or the other.
$timestamps_on = $db->timestamps();
$db->timestamps(1);
Whenever a data object is updated, AceDB records the time and date of the
update, and the user ID it was running under. Ordinarily, the retrieval of
timestamp information is suppressed to conserve memory and bandwidth. To turn
on timestamps, call the
timestamps() method with a true
value. You can retrieve the current value of the setting by calling the method
with no arguments.
Note that activating timestamps disables some of the speed optimizations in
AcePerl. Thus they should only be activated if you really need the
information.
Sets or queries the
auto_save variable. If true, the "save"
command will be issued automatically before the connection to the database is
severed. The default is true.
Examples:
$db->auto_save(1);
$flag = $db->auto_save;
Ace->error;
This returns the last error message. Like UNIX errno, this variable is not reset
between calls, so its contents are only valid after a method call has returned
a result value indicating a failure.
For your convenience, you can call
error() in any of several ways:
print Ace->error();
print $db->error(); # $db is an Ace database handle
print $obj->error(); # $object is an Ace::Object
There's also a global named $Ace::Error that you are free to use.
$datetime = Ace->datetime($time);
$today = Ace->datetime();
$date = Ace->date($time);
$today = Ace->date([$time]);
These convenience functions convert the UNIX timestamp given by $time (seconds
since the epoch) into a datetime string in the format that ACEDB requires.
date() will truncate the time portion.
If not provided, $time defaults to
localtime().
$debug_level = Ace->debug([$new_level])
This class method gets or sets the debug level. Higher integers increase
verbosity. 0 or undef turns off debug messages.
$db = Ace->name2db($name [,$database])
This class method associates a database URL with an Ace database object. This is
used internally by the Ace::Object class in order to discover what database
they "belong" to.
Get or set the Cache::SizeAwareFileCache object, if one has been created.
$obj = $db->memory_cache_fetch($class,$name)
Given an object class and name return a copy of the object from the in-memory
cache. The object will only be cached if a copy of the object already exists
in memory space. This is ordinarily called internally.
Store an object into the memory cache. This is ordinarily called internally.
Delete an object from the memory cache. This is ordinarily called internally.
Completely clears the memory cache.
$obj = $db->file_cache_fetch($class,$name)
Given an object class and name return a copy of the object from the file cache.
This is ordinarily called internally.
Store an object into the file cache. This is ordinarily called internally.
Delete an object from the file cache. This is ordinarily called internally.
Internally Ace.pm makes C-language calls to libace to send query strings to the
server and to retrieve the results. The class that exports the low-level calls
is named Ace::AceDB.
The following methods are available in Ace::AceDB:
- new($host,$port,$query_timeout)
- Connect to the host $host at port $port. Queries will time
out after $query_timeout seconds. If timeout is not specified, it defaults
to 120 (two minutes).
If successful, this call returns an Ace::AceDB connection object. Otherwise,
it returns undef. Example:
$acedb = Ace::AceDB->new('localhost',200005,5)
|| die "Couldn't connect";
The Ace::AceDB object can also be accessed from the high-level Ace interface
by calling the ACE::db() method:
$db = Ace->new(-host=>'localhost',-port=>200005);
$acedb = $db->db();
- query($request)
- Send the query string $request to the server and return a
true value if successful. You must then call read() repeatedly in
order to fetch the query result.
- read()
- Read the result from the last query sent to the server and
return it as a string. ACE may return the result in pieces, breaking
between whole objects. You may need to read repeatedly in order to fetch
the entire result. Canonical example:
$acedb->query("find Sequence D*");
die "Got an error ",$acedb->error() if $acedb->status == STATUS_ERROR;
while ($acedb->status == STATUS_PENDING) {
$result .= $acedb->read;
}
- status()
- Return the status code from the last operation. Status
codes are exported by default when you use Ace.pm. The status codes
you may see are:
STATUS_WAITING The server is waiting for a query.
STATUS_PENDING A query has been sent and Ace is waiting for
you to read() the result.
STATUS_ERROR A communications or syntax error has occurred
- error()
- Returns a more detailed error code supplied by the Ace
server. Check this value when STATUS_ERROR has been returned. These
constants are also exported by default. Possible values:
ACE_INVALID
ACE_OUTOFCONTEXT
ACE_SYNTAXERROR
ACE_UNRECOGNIZED
Please see the ace client library documentation for a full description of
these error codes and their significance.
- encore()
- This method may return true after you have performed one or
more read() operations, and indicates that there is more data to
read. You will not ordinarily have to call this method.
1. The ACE model should be consulted prior to updating the database.
2. There is no automatic recovery from connection errors.
3. Debugging has only one level of verbosity, despite the best of intentions.
4. Performance is poor when fetching big objects, because of many object
references that must be created. This could be improved.
5. When called in an array context at("tag[0]") should return the
current tag's entire column. It returns the current subtree instead.
6. There is no way to add comments to objects.
7. When timestamps are active, many optimizations are disabled.
8. Item number eight is still missing.
Ace::Object, Ace::Local, Ace::Model, Ace::Sequence,Ace::Sequence::Multi.
Lincoln Stein <
[email protected]> with extensive help from Jean Thierry-Mieg
<
[email protected]>
Copyright (c) 1997-1998 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
Hey!
The above document had some coding errors, which are explained
below:
- Around line 1194:
- '=item' outside of any '=over'
- Around line 1224:
- You forgot a '=back' before '=head2'