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.

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 -class => $object_class, -timeout => $timeout, -query_timeout => $query_timeout); The connect() method uses a named argument calling style, and recognizes the following arguments: 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. 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. Name of user to log in as (when using socket server only). If not provided, will attempt an anonymous login. Password to log in with (when using socket server). 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'); The optional -class argument 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'); 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. 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: 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. 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 Open up the local database at /path/to/database using tace. Example: tace:/~acedb/elegans 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. 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.

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).

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 databse, 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 = $db->parse($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, -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(). 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: 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(); 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 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; } 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 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. 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 <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr> 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.