connect() -- multiple argument form

    # 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();

connect() -- single argument form

  $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.

close() Method

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.

reopen() Method

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.

fetch() method

    $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);
    

aql() method

    $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.

put() method

   $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();

parse() method

  $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.

parse_longtext() method

  $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

parse_file() method

  @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().

new() method

  $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.

list() method

    @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() method

    $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.

find() method

    @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().

fetch_many() method

    $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.

find_many() method

This is an alias for fetch_many(). It is now deprecated.

keyset() method

    @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.

grep() method

    @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() method

  $model = $db->model('Author');

This will return an Ace::Model object corresponding to the indicated class.

new() method

   $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().

raw_query() method

    $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() method

   @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.

class_count() method

   %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() method

    %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};

title() method

    my $title = $db->title

Returns the version of the current database, equivalent to $db->status->{database}{title};

version() method

    my $version = $db->version;

Returns the version of the current database, equivalent to $db->status->{database}{version};

date_style() method

  $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() method

  $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.

auto_save()

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;

error() method

    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() and date()

  $datetime = Ace->datetime($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()

  $debug_level = Ace->debug([$new_level])

This class method gets or sets the debug level. Higher integers increase verbosity. 0 or undef turns off debug messages.

name2db()

 $db = Ace->name2db($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.

cache()

Get or set the Cache::SizeAwareFileCache object, if one has been created.

memory_cache_fetch()

  $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.

memory_cache_store($obj)

Store an object into the memory cache. This is ordinarily called internally.

memory_cache_delete($obj)

Delete an object from the memory cache. This is ordinarily called internally.

memory_cache_clear()

Completely clears the memory cache.

file_cache_fetch()

  $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.

file_cache_store($obj)

Store an object into the file cache. This is ordinarily called internally.

file_cache_delete($obj)

Delete an object from the file cache. This is ordinarily called internally.