This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Boulder/Store, Next: Boulder/Stream, Prev: Boulder/Omim, Up: Module List Simple persistent storage for Stone tag/value objects ***************************************************** NAME ==== Boulder::Store - Simple persistent storage for Stone tag/value objects SYNOPSIS ======== Boulder:Store; my $store=new Boulder::Store('test.db',1); my $s = new Stone (Name=>'george', Age=>23, Sex=>M, Address=>{ Street=>'29 Rockland drive', Town=>'Fort Washington', ZIP=>'77777' } ); $store->put($s); $store->put(new Stone(Name=>'fred', Age=>30, Sex=>M, Address=>{ Street=>'19 Gravel Path', Town=>'Bedrock', ZIP=>'12345'}, Phone=>{ Day=>'111-1111', Eve=>'222-2222' } )); $store->put(new Stone(Name=>'andrew', Age=>18, Sex=>M)); $store->add_index('Name'); my $stone = $store->get(0); print "name = ",$stone->Name; DESCRIPTION =========== Boulder::Store provides persistent storage for Boulder objects using a simple DB_File implementation. To use it, you need to have Berkeley db installed (also known as libdb), and the Perl DB_File module. See the DB_File package for more details on obtaining Berkeley db if you do not already have it. Boulder::Store provides an unsophisticated query mechanism which takes advantage of indexes that you specify. Despite its lack of sophistication, the query system is often very helpful. CLASS METHODS ============= $store = Boulder::Store->new("database/path",$writable) The new() method creates a new Boulder::Store object and associates it with the database file provided in the first parameter (undef is a valid pathname, in which case all methods work but the data isn't stored). The second parameter should be a *true* value if you want to open the database for writing. Otherwise it's opened read only. Because the underlying storage implementation is not multi-user, only one process can have the database for writing at a time. A *fcntl()*-based locking mechanism is used to give a process that has the database opened for writing exclusive access to the database. This also prevents the database from being opened for reading while another process is writing to it (this is a *good* thing). Multiple simultaneous processes can open the database read only. Physically the data is stored in a human-readable file with the extension ".data". OBJECT METHODS ============== $stone = $store->read_record(@taglist) The semantics of this call are exactly the same as in Boulder::Stream. Stones are returned in sequential order, starting with the first record. In addition to their built-in tags, each stone returned from this call has an additional tag called "record_no". This is the zero-based record number of the stone in the database. Use the reset() method to begin iterating from the beginning of the database. If called in an array context, *read_record()* returns a list of all stones in the database that contains one or more of the provided tags. $stone = $store->write_record($stone [,$index]) This has the same semantics as Boulder::Stream. A stone is appended to the end of the database. If successful, this call returns the record number of the new entry. By providing an optional second parameter, you can control where the stone is entered. A positive numeric index will write the stone into the database at that position. A value of -1 will use the Stone's internal record number (if present) to determine where to place it. $stone = $store->get($record_no) This is random access to the database. Provide a record number and this call will return the stone stored at that position. $record_number = $store->put($stone,$record_no) This is a random write to the database. Provide a record number and this call stores the stone at the indicated position, replacing whatever was there before. If no record number is provided, this call will look for the presence of a 'record_no' tag in the stone itself and put it back in that position. This allows you to pull a stone out of the database, modify it, and then put it back in without worrying about its record number. If no record is found in the stone, then the effect is identical to write_record(). The record number of the inserted stone is returned from this call, or -1 if an error occurred. $store->delete($stone),Boulder::Store::delete($record_no) These method calls delete a stone from the database. You can provide either the record number or a stone containing the 'record_no' tag. Warning: if the database is heavily indexed deletes can be time-consuming as it requires the index to be brought back into synch. $record_count = $store->length() This returns the length of the database, in records. $store->reset() This resets the database, nullifying any queries in effect, and causing read_record() to begin fetching stones from the first record. $store->query(%query_array) This creates a query on the database used for selecting stones in *read_record()*. The query is an associative array. Three types of keys/value pairs are allowed: (1) $index=>$value This instructs Boulder::Store to look for stones containing the specified tags in which the tag's value (determined by the Stone *index()* method) exactly matches the provided value. Example: $db->query('STS.left_primer.length'=>30); Only the non-bracketed forms of the index string are allowed (this is probably a bug...) If the tag path was declared to be an index, then this search will be fast. Otherwise Boulder::Store must iterate over every record in the database. (2) EVAL=>'expression' This instructs Boulder::Store to look for stones in which the provided expression evaluates to *true*. When the expression is evaluated, the variable $s will be set to the current record's stone. As a shortcut, you can use "" as shorthand for "$s->index('index.string')". (3) EVAL=>['expression1','expression2','expression3'...] This lets you provide a whole bunch of expressions, and is exactly equivalent to EVAL=>'(expression1) && (expression2) && (expression3)'. You can mix query types in the parameter provided to query(). For example, here's how to look up all stones in which the sex is male and the age is greater than 30: $db->query('sex'=>'M',EVAL=>' > 30'); When a query is in effect, *read_record()* returns only Stones that satisfy the query. In an array context, *read_record()* returns a list of all Stones that satisfy the query. When no more satisfactory Stones are found, *read_record()* returns undef until a new query is entered or reset() is called. $store->add_index(@indices) Declare one or more tag paths to be a part of a fast index. *read_record()* will take advantage of this record when processing queries. For example: $db->add_index('age','sex','person.pets'); You can add indexes any time you like, when the database is first created or later. There is a trade off: *write_record()*, put(), and other data-modifying calls will become slower as more indexes are added. The index is stored in an external file with the extension ".index". An index file is created even if you haven't indexed any tags. $store->reindex_all() Call this if the index gets screwed up (or lost). It rebuilds it from scratch. CAVEATS ======= Boulder::Store makes heavy use of the flock() call in order to avoid corruption of DB_File databases when multiple processes try to write simultaneously. flock() may not work correctly across NFS mounts, particularly on Linux machines that are not running the rpc.lockd daemon. Please confirm that your flock() works across NFS before attempting to use Boulder::Store. If the store.t test hangs during testing, this is the likely culprit. AUTHOR ====== Lincoln D. Stein , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. This module can be used and distributed on the same terms as Perl itself. SEE ALSO ======== *Note Boulder: Boulder,, *Note Boulder/Stream: Boulder/Stream,, *Note Stone: Stone,  File: pm.info, Node: Boulder/Stream, Next: Boulder/Swissprot, Prev: Boulder/Store, Up: Module List Read and write tag/value data from an input stream ************************************************** NAME ==== Boulder::Stream - Read and write tag/value data from an input stream SYNOPSIS ======== #!/bin/perl # Read a series of People records from STDIN. # Add an "Eligible" tag to all those whose # Age >= 35 and Friends list includes "Fred" use Boulder::Stream; my $stream = Boulder::Stream->newFh; while ( my $record = <$stream> ) { next unless $record->Age >= 35; my @friends = $record->Friends; next unless grep {$_ eq 'Fred'} @friends; $record->insert(Eligible => 'yes'); print $stream $record; } DESCRIPTION =========== Boulder::Stream provides stream-oriented access to *Note Boulder: Boulder, IO hierarchical tag/value data. It can be used in a magic tied filehandle mode, as shown in the synopsis, or in object-oriented mode. Using tied filehandles, *Note Stone: Stone, objects are read from input using the standard <> operator. Stone objects printed to the tied filehandle appear on the output stream in *Note Boulder: Boulder, format. By default, data is read from the magic ARGV filehandle (STDIN or a list of files provided on the command line) and written to STDOUT. This can be changed to the filehandles of your choice. Pass through behavior --------------------- When using the object-oriented form of Boulder::Stream, tags which aren't specifically requested by the get() method are passed through to output unchanged. This allows pipes of programs to be constructed easily. Most programs will want to put the tags back into the boulder stream once they're finished, potentially adding their own. Of course some programs will want to behave differently. For example, a database query program will generate but not read a *boulderio* stream, while a report generator will read but not write the stream. This convention allows the following type of pipe to be set up: query_database | find_vector | find_dups | \ | blast_sequence | pick_primer | mail_report If all the programs in the pipe follow the conventions, then it will be possible to interpose other programs, such as a repetitive element finder, in the middle of the pipe without disturbing other components. SKELETON BOULDER PROGRAM ======================== Here is a skeleton example. #!/bin/perl use Boulder::Stream; my $stream = Boulder::Stream->newFh; while ( my $record = <$stream> ) { next unless $record->Age >= 35; my @friends = $record->Friends; next unless grep {$_ eq 'Fred'} @friends; $record->insert(Eligible => 'yes'); print $stream $record; } The code starts by creating a Boulder::Stream object to handle the I/O. It reads from the stream one record at a time, returning a *Note Stone: Stone, object. We recover the *Age* and *Friends* tags, and continue looping unless the Age is greater or equal to 35, and the list of Friends contains "Fred". If these criteria match, then we insert a new tag named Eligible and print the record to the stream. The output may look like this: Name=Janice Age=36 Eligible=yes Friends=Susan Friends=Fred Friends=Ralph = Name=Ralph Age=42 Eligible=yes Friends=Janice Friends=Fred = Name=Susan Age=35 Eligible=yes Friends=Susan Friends=Fred = Note that in this case only records that meet the criteria are echoed to standard output. The object-oriented version of the program looks like this: #!/bin/perl use Boulder::Stream; my $stream = Boulder::Stream->new; while ( my $record = $stream->get('Age','Friends') ) { next unless $record->Age >= 35; my @friends = $record->Friends; next unless grep {$_ eq 'Fred'} @friends; $record->insert(Eligible => 'yes'); $stream->put($record); } The get() method is used to fetch Stones containing one or more of the indicated tags. The put() method is used to send the result to standard output. The pass-through behavior might produce a set of records like this one: Name=Janice Age=36 Eligible=yes Friends=Susan Friends=Fred Friends=Ralph = Name=Phillip Age=30 = Name=Ralph Age=42 Eligible=yes Friends=Janice Friends=Fred = Name=Barbara Friends=Agatha Friends=Janice = Name=Susan Age=35 Eligible=yes Friends=Susan Friends=Fred = Notice that there are now two records ("Phillip" and "Barbara") that do not contain the Eligible tag. Boulder::Stream METHODS ======================= $stream = Boulder::Stream->new(*IN,*OUT) ---------------------------------------- $stream = Boulder::Stream->new(-in=>*IN,-out=>*OUT) --------------------------------------------------- The new() method creates a new Boulder::Stream object. You can provide input and output filehandles. If you leave one or both undefined new() will default to standard input or standard output. You are free to use files, pipes, sockets, and other types of file handles. You may provide the filehandle arguments as bare words, globs, or glob refs. You are also free to use the named argument style shown in the second heading. $fh = Boulder::Stream->newFh(-in=>*IN, -out=>*OUT) -------------------------------------------------- Returns a filehandle object tied to a Boulder::Stream object. Reads on the filehandle perform a get(). Writes invoke a put(). To retrieve the underlying Boulder::Stream object, call Perl's built-in tied() function: $stream = tied $fh; $stone = $stream->get(@taglist) ------------------------------- @stones = $stream->get(@taglist) -------------------------------- Every time get() is called, it will return a new Stone object. The Stone will be created from the input stream, using just the tags provided in the argument list. Pass no tags to receive whatever tags are present in the input stream. If none of the tags that you specify are in the current boulder record, you will receive an empty *Stone*. At the end of the input stream, you will receive undef. If called in an array context, get() returns a list of all stones from the input stream that contain one or more of the specified tags. $stone = $stream->read_record(@taglist) --------------------------------------- Identical to get(>, but the name is longer. $stream->put($stone) -------------------- Write a *Stone* to the output filehandle. $stream->write_record($stone) ----------------------------- Identical to put(), but the name is longer. Useful State Variables in a Boulder::Stream ------------------------------------------- Every Boulder::Stream has several state variables that you can adjust. Fix them in this fashion: $a = new Boulder::Stream; $a->{delim}=':'; $a->{record_start}='['; $a->{record_end}=']'; $a->{passthru}=undef; * delim This is the delimiter character between tags and values, "=" by default. * record_start This is the start of nested record character, "{" by default. * record_end This is the end of nested record character, "}" by default. * passthru This determines whether unrecognized tags should be passed through from the input stream to the output stream. This is 'true' by default. Set it to undef to override this behavior. BUGS ==== Because the delim, record_start and record_end characters in the Boulder::Stream object are used in optimized (once-compiled) pattern matching, you cannot change these values once get() has once been called. To change the defaults, you must create the Boulder::Stream, set the characters, and only then begin reading from the input stream. For the same reason, different Boulder::Stream objects cannot use different delimiters. AUTHOR ====== Lincoln D. Stein , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. This module can be used and distributed on the same terms as Perl itself. SEE ALSO ======== *Note Boulder: Boulder,, *Note Boulder/Blast: Boulder/Blast,, *Note Boulder/Genbank: Boulder/Genbank,, *Note Boulder/Medline: Boulder/Medline,, *Note Boulder/Unigene: Boulder/Unigene,, *Note Boulder/Omim: Boulder/Omim,, `Boulder::SwissProt' in this node  File: pm.info, Node: Boulder/Swissprot, Next: Boulder/Unigene, Prev: Boulder/Stream, Up: Module List Fetch SwissProt data records as parsed Boulder Stones ***************************************************** NAME ==== Boulder::SwissProt - Fetch SwissProt data records as parsed Boulder Stones SYNOPSIS ======== == missing == DESCRIPTION =========== == missing == SEE ALSO ======== *Note Boulder: Boulder,, *Note Boulder/Blast: Boulder/Blast,, *Note Boulder/Genbank: Boulder/Genbank, AUTHOR ====== Lincoln Stein . Luca I.G. Toldo Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo 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.  File: pm.info, Node: Boulder/Unigene, Next: Boulder/XML, Prev: Boulder/Swissprot, Up: Module List Fetch Unigene data records as parsed Boulder Stones *************************************************** NAME ==== Boulder::Unigene - Fetch Unigene data records as parsed Boulder Stones SYNOPSIS ======== # parse a file of Unigene records $ug = new Boulder::Unigene(-accessor=>'File', -param => '/data/unigene/Hs.dat'); while (my $s = $ug->get) { print $s->Identifier; print $s->Gene; } # parse flatfile records yourself open (UG,"/data/unigene/Hs.dat"); local $/ = "*RECORD*"; while () { my $s = Boulder::Unigene->parse($_); # etc. } DESCRIPTION =========== Boulder::Unigene provides retrieval and parsing services for UNIGENE records Boulder::Unigene provides retrieval and parsing services for NCBI Unigene records. It returns Unigene entries in *Note Stone: Stone, format, allowing easy access to the various fields and values. Boulder::Unigene is a descendent of Boulder::Stream, and provides a stream-like interface to a series of Stone objects. Access to Unigene is provided by one *accessors*, which give access to local Unigene database. When you create a new Boulder::Unigene stream, you provide the accessors, along with accessor-specific parameters that control what entries to fetch. The accessors is: File This provides access to local Unigene entries by reading from a flat file (typically Hs.dat file downloadable from NCBI's Ftp site). The stream will return a Stone corresponding to each of the entries in the file, starting from the top of the file and working downward. The parameter is the path to the local file. It is also possible to parse a single Unigene entry from a text string stored in a scalar variable, returning a Stone object. Boulder::Unigene methods ------------------------ This section lists the public methods that the Boulder::Unigene class makes available. new() # Local fetch via File $ug=new Boulder::Unigene(-accessor => 'File', -param => '/data/unigene/Hs.dat'); The new() method creates a new Boulder::Unigene stream on the accessor provided. The only possible accessors is File. If successful, the method returns the stream object. Otherwise it returns undef. new() takes the following arguments: -accessor Name of the accessor to use -param Parameters to pass to the accessor Specify the accessor to use with the *-accessor* argument. If not specified, it defaults to File. *-param* is an accessor-specific argument. The possibilities is: For File, the *-param* argument must point to a string-valued scalar, which will be interpreted as the path to the file to read Unigene entries from. get() The get() method is inherited from Boulder::Stream, and simply returns the next parsed Unigene Stone, or undef if there is nothing more to fetch. It has the same semantics as the parent class, including the ability to restrict access to certain top-level tags. put() The put() method is inherited from the parent Boulder::Stream class, and will write the passed Stone to standard output in Boulder format. This means that it is currently not possible to write a Boulder::Unigene object back into Unigene flatfile form. OUTPUT TAGS =========== The tags returned by the parsing operation are taken from the names shown in the Flat file Hs.dat since no better description of them is provided yet by the database source producer. Top-Level Tags -------------- These are tags that appear at the top level of the parsed Unigene entry. Identifier The Unigene identifier of this entry. Identifier is a single-value tag. Example: my $identifierNo = $s->Identifier; Title The Unigene title for this entry. Example: my $titledef=$s->Title; Gene The Gene associated with this Unigene entry Example: my $thegene=$s->Gene; Cytoband The cytological band position of this entry Example: my $thecytoband=$s->Cytoband; Counts The number of EST in this record Example: my $thecounts=$s->Counts; LocusLink The id of the LocusLink entry associated with this record Example: my $thelocuslink=$s->LocusLink; Chromosome This field contains a list, of the chromosomes numbers in which this entry has been linked Example: my @theChromosome=$s->Chromosome; STS Multiple records in the form ^STS ACC=XXXXXX NAME=YYYYYY --------------------------------------------------------------------- ACC NAME TXMAP Multiple records in the form ^TXMAP XXXXXXX; MARKER=YYYYY; RHPANEL=ZZZZ ------------------------------------------------------------------------------- The TXMAP tag points to a Stone record that contains multiple subtags. Each subtag is the name of a feature which points, in turn, to a Stone that describes the feature's location and other attributes. Each feature will contain one or more of the following subtags: MARKER RHPANEL PROTSIM Multiple records in the form ^PROTSIM ORG=XXX; PROTID=DBID:YYY; PCT=ZZZ; ALN=QQQQ Where DBID is PID for indicate presence of GenPept identifier, SP to indicate SWISSPROT identifier, PIR to indicate PIR identifier, PRF to indicate ??? ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ORG PROTID PCT ALN SEQUENCE Multiple records in the form ^SEQUENCE ACC=XXX; NID=YYYY; PID = CLONE= END= LID= ----------------------------------------------------------------------------------------- ACC NID PID CLONE END LID SEE ALSO ======== *Note Boulder: Boulder,, *Note Boulder/Blast: Boulder/Blast,, *Note Boulder/Genbank: Boulder/Genbank, AUTHOR ====== Lincoln Stein . Luca I.G. Toldo Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo 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.  File: pm.info, Node: Boulder/XML, Next: Bundle/ABH, Prev: Boulder/Unigene, Up: Module List XML format input/output for Boulder streams ******************************************* NAME ==== Boulder::XML - XML format input/output for Boulder streams SYNOPSIS ======== use Boulder::XML; $stream = Boulder::XML->newFh; while ($stone = <$stream>) { print $stream $stone; } DESCRIPTION =========== Boulder::XML generates BoulderIO streams from XML files and/or streams. It is also able to output Boulder Stones in XML format. Its semantics are similar to those of Boulder::Stream, except that there is never any pass-through behavior. Because XML was not designed for streaming, some care must be taken when reading an XML document into a series of Stones. Consider this XML document: Lincoln Stein Jean Siao September 29, 1999 1999 Lincoln Stein This is the abstract. It is not anything very fancy, but it will do. Fitchberg J Journal of Irreproducible Results 23 1998 Clemenson V Ecumenica 10 1968 Ruggles M Journal of Aesthetic Surgery 10 1999 Ordinarily the document will be construed as a single Paper tag containing subtags Author, Date, Copyright, Abstract, and so on. However it might be desirable to fetch out just the citation tags as a series of Stones. In this case, you can declare Citation to be the top level tag by passing the *-tag* argument to new(). Now calling get() will return each of the three Citation sections in turn. If no tag is explicitly declared to be the top level tag, then Boulder::XML will take the first tag it sees in the document. It is possible to stream XML files. You can either separate them into separate documents and use the automatic ARGV processing features of the BoulderIO library, or separate the XML documents using a delimiter string similar to the delimiters used in MIME multipart documents. By default, BoulderIO uses a delimiter of . *This is not a general XML parsing engine!* Instead, it is a way to represent BoulderIO tag/value streams in XML format. The module uses XML::Parser to parse the XML streams, and therefore any syntactic error in the stream can cause the XML parser to quit with an error. Another thing to be aware of is that there are certain XML constructions that will not translate into BoulderIO format, specifically free text that contains embedded tags. This is OK: Jean Siao but this is not: The extremely illustrious Jean Siao In BoulderIO format, tags can contain other tags or text, but cannot contain a mixture of tags and text. CONSTRUCTORS ------------ $stream = Boulder::XML->new(*IN,*OUT); $stream = Boulder::XML->new(-in=>*IN,-out=>*OUT,-tag=>$tag,-delim=>$delim,-strip=>$strip) new() creates a new Boulder::XML stream that can be read from or written to. All arguments are optional. -in Filehandle to read from. If a file name is provided, will open the file. Defaults to the magic <> filehandle. -out Filehandle to write to. If a file name is provided, will open the file for writing. Defaults to STDOUT -tag The top-level XML tag to consider as the Stone record. Defaults to the first tag seen when reading from an XML file, or to Less_Than_Special_SequenceStoneGreater_Than_Special_Sequence when writing to an output stream without previously having read. -delim Delimiter to use for delimiting multiple Stone objects in an XML stream. -strip If true, automatically strips leading and trailing whitespace from text contained within tags. $fh = Boulder::XML->newFh(*IN,*OUT); $fh = Boulder::XML->newFh(-in=>*IN,-out=>*OUT,-tag=>$tag,-delim=>$delim,-strip=>$strip) The newFh() constructor creates a tied filehandle that can read and write Boulder::XML streams. Invoking <> on the filehandle will perform a get(), returning a Stone object. Calling print() on the filehandle will perform a put(), writing a Stone object to output in XML format. METHODS ------- $stone = $stream->get() $stream->put($stone) $done = $stream->done All these methods have the same semantics as the similar methods in *Note Boulder/Stream: Boulder/Stream,, except that pass-through behavior doesn't apply. AUTHOR ====== Lincoln D. Stein , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. This module can be used and distributed on the same terms as Perl itself. SEE ALSO ======== *Note Boulder: Boulder,, *Note Boulder/Stream: Boulder/Stream,, *Note Stone: Stone,  File: pm.info, Node: Bundle/ABH, Next: Bundle/AO/Base, Prev: Boulder/XML, Up: Module List A bundle to install all Ask's favorite modules ********************************************** NAME ==== Bundle::ABH - A bundle to install all Ask's favorite modules SYNOPSIS ======== perl -MCPAN -e 'install Bundle::ABH' CONTENTS ======== Bundle::CPAN Bundle::libnet Bundle::LWP CGI ExtUtils::Embed Mail::Send Getopt::Long DB_File Bundle::DBI Devel::Peek MIME::Base64 IO::ScalarArray - For MIME::Tools MIME::Tools Tie::Handle Time::HiRes GD Storable HTML::Parser Data::ShowTable LWP::Parallel Date::Format Tie::IxHash Devel::Symdump Image::Size Convert::Translit Text::Soundex Font::AFM - Some of my favorite modules are using this Pod::Parser - For cpan-upload and more HTML::TreeBuilder Net::DNS Text::Template App::Config - For cpan-upload Bit::Vector - For MIME::Lite MIME::Lite - So nice and easy to send a MIME thingy Set::IntRange XML::Parser Date::Calc Number::Format Event DESCRIPTION =========== This bundle defines most of the modules Ask Bjoern Hansen usually install/upgrade with CPAN.pm. AUTHOR ====== Ask Bjoern Hansen  File: pm.info, Node: Bundle/AO/Base, Next: Bundle/AO/Standard, Prev: Bundle/ABH, Up: Module List libraries needed for AO servlet engine ************************************** NAME ==== Bundle::AO::Base - libraries needed for AO servlet engine DESCRIPTION =========== This bundle specifies the libraries needed for the AO servlet engine. It won't run without them. SYNOPSIS ======== perl -MCPAN -e 'install Bundle::AO::Base' CONTENTS ======== Storable Apache::Session 1.51 XML::Parser XML::XPath File::Spec  File: pm.info, Node: Bundle/AO/Standard, Next: Bundle/Apache, Prev: Bundle/AO/Base, Up: Module List libraries needed by standard AO interceptors ******************************************** NAME ==== Bundle::AO::Standard - libraries needed by standard AO interceptors DESCRIPTION =========== This bundle specifies the libraries needed by the standard AO interceptors. You should install this stuff if you want AO to work out of the box. If you are developing new interceptors, this bundle probably doesn't apply to you. SYNOPSIS ======== perl -MCPAN -e 'install Bundle::AO::Standard' CONTENTS ======== Apache::Request HTML::Mason DBI  File: pm.info, Node: Bundle/Apache, Next: Bundle/Apache/ASP, Prev: Bundle/AO/Standard, Up: Module List Install Apache mod_perl and related modules ******************************************* NAME ==== Bundle::Apache - Install Apache mod_perl and related modules SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Apache'' CONTENTS ======== MIME::Base64 - Used in authentication headers Digest::MD5 - Needed to do Digest authentication URI 0.10 - There are URIs everywhere Net::FTP 2.00 - If you want ftp://-support HTML::HeadParser - To get the correct $res->base LWP - The reason why you need the modules above Devel::Symdump - Symbol table browsing with Apache::Status Data::Dumper - Used by Apache::PerlSections->dump CGI - CGI.pm Tie::IxHash - For order in sections Apache - Perl interface to Apache server API Apache::DBI - Wrapper around DBI->connect to transparently maintain persistent connections Apache::DB - Run the interactive Perl debugger under mod_perl Apache::Stage - Management of document staging directories Apache::Sandwich - Layered document maker Apache::Request - Effective methods for dealing with client request data DESCRIPTION =========== This bundle contains modules used by Apache mod_perl. Asking CPAN.pm to install a bundle means to install the bundle itself along with all the modules contained in the CONTENTS section above. Modules that are up to date are not installed, of course. AUTHOR ====== Doug MacEachern  File: pm.info, Node: Bundle/Apache/ASP, Next: Bundle/BioPerl, Prev: Bundle/Apache, Up: Module List Install Apache::ASP and related modules *************************************** NAME ==== Bundle::Apache::ASP - Install Apache::ASP and related modules SYNOPSIS ======== perl -MCPAN -e 'install Bundle::Apache::ASP' CONTENTS ======== MLDBM - This is used for reading and writing multi-level hashes on disk Data::Dumper - Serializes data for MLDBM MD5 - 32 byte hash algorithm for cookie session-id CGI - Required for file upload, make test, and command line ./cgi/asp script HTML::Clean - Compress text/html with Clean config or $Response->{Clean} set to 1-9 Net::SMTP - Runtime errors can be mailed to the webmaster with MailErrorTo config HTTP::Date - Provides mapping between Perl time() and HTTP dates Devel::Symdump - Used for StatINC setting, which reloads modules dynamically Apache::DBI - Cache database connections per process Compress::Zlib - Gzip compress HTML output on the fly Tie::Cache - XLSTCacheSize, XSLT caching support Time::HiRes - Sub second timing of execution with Debug 3 enabled HTML::Parser - Required for HTML::FillInForm HTML::FillInForm - FormFill functionality which autofills HTML forms from form data Apache::ASP - A perl ASP port to Apache DESCRIPTION =========== This bundle contains modules used by Apache::ASP. AUTHOR ====== Joshua Chamas  File: pm.info, Node: Bundle/BioPerl, Next: Bundle/Bugzilla, Prev: Bundle/Apache/ASP, Up: Module List A bundle to install external CPAN modules used by BioPerl ********************************************************* NAME ==== Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl SYNOPSIS ======== Perl one liner using CPAN.pm: perl -MCPAN -e 'install Bundle::BioPerl' Use of CPAN.pm in interactive mode: $> perl -MCPAN -e shell cpan> install Bundle::BioPerl cpan> quit Just like the manual installation of perl modules, the user may need root access during this process to insure write permission is allowed within the intstallation directory. CONTENTS ======== Bundle::LWP - recommended, used for network access File::Temp - generally required after bioperl release 0.6.2 IO::Scalar - optional, used only in Bio::Tools::Blast::Run::WebBlast.pm IO::String - recommended, used by Bio::DB:WebDBSeqI HTTP::Request::Common - recommended, used for web access HTTP::Status - recommended, used for web access LWP::UserAgent - recommended, used for web access URI::Escape - recommended, used for web access XML::Parser - recommended for bioperl releases after 0.6.2 XML::Parser::PerlSAX - recommended for bioperl releases after 0.6.2 XML::Writer - recommended for bioperl releases after 0.6.2 XML::Node - recommended for bioperl releases after 0.6.2 DESCRIPTION =========== The BioPerl distribution from http://bioperl.org contains code and modules that may use or require additional 'external' perl modules for advanced functionality. Many of the external modules are not contained within the standard Perl distribution. These external modules can be obtained from the Comprehensive Perl Archive Network (CPAN) located at http://www.cpan.org. This perl module (Bundle::BioPerl) contains NO functionality or real code at all. It is essentially a special perl module meant to be used by the CPAN.pm module to simplify the task of automatically installing multiple modules in one easy step. Essentially users can tell CPAN.pm to 'install Bundle::BioPerl' and CPAN.pm will download, install and configure all of the modules listed in the BioPerl Bundle module. See the SYNOPSIS section or do `perldoc CPAN' to learn about how to use the CPAN.pm module to install bundles. NOTE: This process is complicated by the fact that some BioPerl external modules themselves have their own dependencies and prerequisites. In particular the XML::Parser module requires the prior installation of the 'xpat' package which resides outside of CPAN at http://sourceforge.net/projects/expat/. The `install Bundle::BioPerl' process may need to be repeated several times to complete the full installation of all listed modules. NOTE: This Bundle does not install BioPerl :) Just the additional modules that BioPerl code ocasionally makes use of. You will still need to get the BioPerl distribution from CPAN or http://bioperl.org and install it the usual way: perl Makefile.PL make make test make install CPAN.pm has many features - including the ability to download but not install the modules listed in the BioPerl bundle. `perldoc CPAN' is your friend :) AUTHOR ====== Chris Dagdigian <`dag@sonsorol.org'> (Author only of this bundle, not any the modules it lists)  File: pm.info, Node: Bundle/Bugzilla, Next: Bundle/Bundle-Expect, Prev: Bundle/BioPerl, Up: Module List A bundle of the modules required for Bugzilla. ********************************************** NAME ==== Bundle::Bugzilla - A bundle of the modules required for Bugzilla. SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Bugzilla'' CONTENTS ======== DBI Data::Dumper DBD::mysql Chart::Base Date::Parse DESCRIPTION =========== This bundle installs the prerequisites for Bugzilla. After installing this bundle, it is recommended that you run the magic checksetup.pl script to check that all modules are in place and setup the tables in the database. Then, you will need to edit the file called 'localconfig' with your settings for bugzilla. After this, log in to your installation and make yourself an account. Run checksetup.pl again and you will become the superuser for your bugzilla installation. Still confused? Read the INSTALL and README for more information. DBI This module is used to connect to the database that Bugzilla uses to store its information. Data::Dumper The Data::Dumper module provides data structure persistence for Perl (similar to Java's serialization). It comes with later sub-releases of Perl 5.004, but a re-installation just to be sure it's available won't hurt anything. Data::Dumper is used by the MySQL related Perl modules. DBD::mysql This module is used to connect to the mysql database that Bugzilla uses to store its information. Chart::Base Used to create the bug charts in the reporting functions in reports.cgi. Date::Parse Enables SQL-style search query statements for Bugzilla. AUTHOR ====== Zach Lipton,  File: pm.info, Node: Bundle/Bundle-Expect, Next: Bundle/CPAN, Prev: Bundle/Bugzilla, Up: Module List Everything that Expect.pm needs ******************************* NAME ==== Bundle::Expect - Everything that Expect.pm needs SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Expect'' CONTENTS ======== Expect IO::Stty IO::Tty IO::Pty DESCRIPTION =========== Everything that Expect.pm needs. What can I say more? AUTHOR ====== Roland Giersig  File: pm.info, Node: Bundle/CPAN, Next: Bundle/Cisco/Conf, Prev: Bundle/Bundle-Expect, Up: Module List A bundle to play with all the other modules on CPAN *************************************************** NAME ==== Bundle::CPAN - A bundle to play with all the other modules on CPAN SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::CPAN'' CONTENTS ======== File::Spec MD5 Compress::Zlib Archive::Tar Bundle::libnet Term::ReadKey Term::ReadLine::Perl # sorry, I'm discriminating the ::Gnu module CPAN::WAIT CPAN DESCRIPTION =========== This bundle includes CPAN.pm as the base module and CPAN::WAIT, a plugin for the first WAIT based CPAN search engine. When CPAN installs this bundle it tries immediately to enable Term::ReadLine so that you do not need to restart your CPAN session. Compress::Zlib needs as a prerequisite the zlib library. Currently (January 1998) this library is not shipped with the Compress::Zlib distribution. In this bundle Term::ReadLine::Perl is preferred over Term::ReadLine::Gnu because I expect that it gives less problems on portability. Note that all modules in this Bundle are not strict prerequisites to get a working CPAN.pm. CPAN.pm can work quite well without the other modules (except for Net::FTP which is really highly recommended). The other modules are just goodies that make using CPAN.pm more fun. AUTHOR ====== Andreas König  File: pm.info, Node: Bundle/Cisco/Conf, Next: Bundle/DBD/CSV, Prev: Bundle/CPAN, Up: Module List A bundle to install the Cisco::Conf module. ******************************************* NAME ==== Bundle::Cisco::Conf - A bundle to install the Cisco::Conf module. SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Cisco::Conf'' CONTENTS ======== Data::Dumper Net::Cmd Net::Telnet IO::AtomicFile DESCRIPTION =========== This bundle includes all that's needed to run the Cisco::Conf module.  File: pm.info, Node: Bundle/DBD/CSV, Next: Bundle/HTML/EP, Prev: Bundle/Cisco/Conf, Up: Module List A bundle to install the DBD::CSV driver *************************************** NAME ==== Bundle::DBD::CSV - A bundle to install the DBD::CSV driver SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::DBD::CSV'' CONTENTS ======== DBI 1.02 Text::CSV_XS 0.14 SQL::Statement 0.1006 DBD::CSV DESCRIPTION =========== This bundle includes all that's needed to access so-called CSV (Comma Separated Values) files via a pseudo SQL engine (SQL::Statement) and DBI.  File: pm.info, Node: Bundle/HTML/EP, Next: Bundle/HTML/Mason, Prev: Bundle/DBD/CSV, Up: Module List A bundle to install the HTML::EP package **************************************** NAME ==== Bundle::HTML::EP - A bundle to install the HTML::EP package SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::HTML::EP'' CONTENTS ======== DBI 1.02 Data::Dumper Storable CGI::Cookie Bundle::LWP Net::SMTP Mail::Internet 1.32 HTML::EP DESCRIPTION =========== This bundle includes all that's needed to run the HTML::EP package with your WWW server.  File: pm.info, Node: Bundle/HTML/Mason, Next: Bundle/Interchange, Prev: Bundle/HTML/EP, Up: Module List A bundle to install the HTML::Mason package ******************************************* NAME ==== Bundle::HTML::Mason - A bundle to install the HTML::Mason package SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::HTML::Mason'' CONTENTS ======== Data::Dumper MLDBM HTML::Mason DESCRIPTION =========== This bundle includes all that's needed to run the HTML::Mason package.  File: pm.info, Node: Bundle/Interchange, Next: Bundle/IspMailGate, Prev: Bundle/HTML/Mason, Up: Module List A bundle of the modules nice to have for Interchange. ***************************************************** NAME ==== Bundle::Interchange - A bundle of the modules nice to have for Interchange. SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Interchange'' CONTENTS ======== MD5 MIME::Base64 Bundle::LWP Term::ReadKey Term::ReadLine::Perl Business::UPS SQL::Statement Storable DBI Safe::Hole DESCRIPTION =========== This bundle installs the prerequisites for Interchange as well as some modules that are not strictly necessary. (Interchange was formerly known as Minivend.) After installing this bundle, it is recommended that you quit the current session and then run Interchange's `makecat' program. That will give you the benefit of line completion and history. The core functions of Interchange *will* run with a stock Perl, but to use some features of Interchange (like the administrative interface) you will need these modules. MD5 This module is used to generate unique cache keys. If you don't have it, then keys will be computed with a checksum that has a very low but not infinitesimal chance of causing a cache conflict. Bundle::LWP Certain parts of these modules (URI::URL and MIME::Base64) are required for Interchange's internal HTTP server. Also, Business::UPS, for calculating shipping, requires this. Storable If you have this module session save speed increases by anywhere from 25-60%. Highly recommended for busy systems. Business::UPS Enables lookup of shipping costs directly from www.ups.com. SQL::Statement Enables SQL-style search query statements for Interchange. Safe::Hole This helps Interchange deal with the object-creation restrictions of *Safe.pm*, used to encourage security. DBI Most people want to use SQL with Interchange, and this is a requirement. You will also need the appropriate DBD module, i.e. DBD::mysql to support *MySQL*. Term::ReadKey Helps Term::ReadLine::Perl generate completions and editing. Term::ReadLine::Perl Gives you filename completion and command history in the makecat program. Not used otherwise. AUTHOR ====== Mike Heins,  File: pm.info, Node: Bundle/IspMailGate, Next: Bundle/LWP, Prev: Bundle/Interchange, Up: Module List A bundle to install the IspMailGate email filter. ************************************************* NAME ==== Bundle::IspMailGate - A bundle to install the IspMailGate email filter. SYNOPSIS ======== `perl -MCPAN -e 'install IspMailGate'' CONTENTS ======== MD5 MIME::Base64 Net::SMTP Mail::Internet MIME::Tools IO::Tee DESCRIPTION =========== This bundle includes all that's needed to run the HTML::EP package with your WWW server.  File: pm.info, Node: Bundle/LWP, Next: Bundle/MP3, Prev: Bundle/IspMailGate, Up: Module List A bundle to install all libwww-perl related modules *************************************************** NAME ==== Bundle::LWP - A bundle to install all libwww-perl related modules SYNOPSIS ======== perl -MCPAN -e 'install Bundle::LWP' CONTENTS ======== URI 1.10 - There are URIs everywhere Net::FTP 2.00 - If you want ftp://-support MIME::Base64 - Used in authentication headers Digest::MD5 - Needed to do Digest authentication HTML::Tagset - Needed by HTML::Parser HTML::Parser - Need by HTML::HeadParser HTML::HeadParser - To get the correct $res->base LWP - The reason why you need the modules above DESCRIPTION =========== This bundle defines all reqreq modules for libwww-perl. AUTHOR ====== Gisle Aas  File: pm.info, Node: Bundle/MP3, Next: Bundle/Mail/IspMailGate, Prev: Bundle/LWP, Up: Module List A bundle to install all MP3-related modules ******************************************* NAME ==== Bundle::MP3 - A bundle to install all MP3-related modules SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::MP3'' CONTENTS ======== MP3::Info - For MP3::Info by Chris Sandor Digest::MD5 - Used by MP3::Napster MP3::Napster - For MP3::Napster by Lincoln Stein Bundle::Xmms - For Xmms by Doug MacEachern DESCRIPTION =========== This bundle installs a bunch of modules related to sharing and playing MP3 files, including MP3::Info by Chris Sandor, MP3::Napster, by Lincoln Stein, and the Xmms bundle by Doug MacEachern. AUTHOR ====== Lincoln Stein <`lstein@cshl.org'>  File: pm.info, Node: Bundle/Mail/IspMailGate, Next: Bundle/Minivend, Prev: Bundle/MP3, Up: Module List A bundle to install the IspMailGate *********************************** NAME ==== Bundle::Mail::IspMailGate - A bundle to install the IspMailGate SYNOPSIS ======== `perl -MCPAN -e 'install Bundle::Mail::IspMailGate'' CONTENTS ======== IO::Scalar IO::Tee Net::SMTP Mail::Internet Digest::MD5 MIME::Base64 MIME::Tools DESCRIPTION =========== This bundle includes all that's needed to install the IspMailGate. Usage: perl -MCPAN -e shell install Bundle::Mail::IspMailGate