https://sourceforge.net/p/srsurlapi/wiki/SrsUrlApi/Recent changes to SrsUrlApienSat, 03 May 2014 11:32:41 -0000https://sourceforge.net/p/srsurlapi/wiki/SrsUrlApi/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -1,4 +1,3 @@ - Introduction ============ @@ -31,7 +30,7 @@ Download ======== -For releases see [downloads](https://sourceforge.net/project/showfiles.php?group_id=256372), or for the current state of development see the [Subversion repository](https://sourceforge.net/scm/?type=svn&amp;group_id=256372). +For releases see [downloads](https://sourceforge.net/projects/srsurlapi/files/), or for the current state of development see the [Subversion repository](https://sourceforge.net/p/srsurlapi/code/). Installation ============ </pre> </div>Hamish McWilliamSat, 03 May 2014 11:32:41 -0000https://sourceforge.net26b57cb08f298a1df0879de10c0a4ddca3ef6b71https://sourceforge.net/p/srsurlapi/wiki/SrsUrlApi/<pre>--- v1 +++ v2 @@ -1,8 +1,148 @@ -Welcome to your wiki! -This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. +Introduction +============ -The wiki uses [Markdown](/p/srsurlapi/wiki/markdown_syntax/) syntax. +A [Perl](http://www.perl.com/) implementation of an API for accessing data in SRS via web page retrievals via LWP. +Features supported: + + * Multiple SRS versions: known to work with 5.x, 6.x, 7.x, 8.0 and 8.1 + * Partial support for SRS 8.2. + * Handling of SRS error messages + * Configurable pauses between requests, as required for use with public servers such as [SRS@EBI](http://srs.ebi.ac.uk/) + * Support for retrieval of results in chunks + +Examples +======== + + * **getCount.pl**: get the number of entries matching a query. + * **getDatabanks.pl**: list the databanks available from an SRS server. + * **getEntriesList.pl**: get the complete entries for an SRS query. + * **getEntriesStr.pl**: retrieving entries from SRS using a query. + * **urlgetz.pl**: an implementation of a subset of the ''getz'' command-line interface to SRS. + * **srsservers**: implementation of the public SRS servers list. + +Requirements +============ + + * [Perl](http://www.perl.com/) 5.x + * [LWP](http://search.cpan.org/dist/libwww-perl/lib/LWP.pm) + +Download +======== + +For releases see [downloads](https://sourceforge.net/project/showfiles.php?group_id=256372), or for the current state of development see the [Subversion repository](https://sourceforge.net/scm/?type=svn&group_id=256372). + +Installation +============ + +The module can be installed in the standard Perl way: + + perl Makefile.PL + make + make test + make install + +Alternatively the module can be used directly by adding the `lib/` directory to the Perl `@INC` path. + +NB: the SRS version tests depend on the availability of public SRS servers and some properties of the data available through those servers. Thus these tests may fail due to inability to access a server, or due to data changes. Please take care when interpreting failures in these tests. Since public SRS servers have to be used for these tests the test suites for SRS 6.0 and 8.0 are currently set to be skipped, since we know of no public servers running these versions. If you have access to one of these versions you can enable the appropriate tests by editing the corresponding `.t` file in the `t/` directory, setting the server URL, commenting out the server URL check and uncommenting the test count indicator. + +API Documentation +================= + +The `Srs::BasicApi::SrsUrlApi` module contains POD mark-up usable with the `perldoc` documentation reader. To access this documentation either install the module into your Perl installation, or change the current directory to the `lib/` directory containing the module, and run the following command: + + perldoc Srs::BasicApi::SrsUrlApi + +Example +======= + +getEntries.pl +------------- + +A simple script to get a set of entries from the command-line: + + # Load the module + use Srs::BasicApi::SrsUrlApi; + # Usage message + my $usageMsg = "Usage: getEntries.pl <queryStr> [srsUrl]\n"; + # Set the defaults + my (%config) = ( + 'srsUrl' => 'http://srs.ebi.ac.uk/srs/', # EBI + 'queryStr' => '', + 'htmlMode' => 0, # ASCII, no HTML markup + 'viewName' => '', # will default to complete entries + 'chunkSize' => 100, # maximum size of a chunk + ); + # Process command-line + if(length(@ARGV) > 0) { + # First argument is the query + $config{'queryStr'} = $ARGV[0]; + if($ARGV[1] ne '') { + # Second is the URL + $config{'srsUrl'} = $ARGV[1]; + } + } + # Check for query + if($config{'queryStr'} eq '') { + die "Error: no query specified\n",$usageMsg; + } + # Create a connection object + my $srsUrlApi = Srs::BasicApi::SrsUrlApi->new(); + $srsUrlApi->setSrsUrl($config{'srsUrl'}); + # How many entries + my $numEntries = $srsUrlApi->getCount($config{'queryStr'}); + # Get in chunks + for(my $i=1; $i<=$numEntries; $i+=$config{'chunkSize'}) { + # Get the chunk as a string + print $srsUrlApi->getEntriesStr($config{'queryStr'}, + $config{'htmlMode'}, + $config{'viewName'}, + $i, + $config{'chunkSize'} + ); + } + +To Do +===== + + * Databank information: + * Field information + * Subentry information + * Link information + * Views/loaders + * Release + * Virtual libraries (members) + * Sessions + * Access to named permanent and temporary sessions + * Persistent access through a session (currently no session access used) + * Project support for permanent sessions: listing and selection + * Access to query history + * Views + * Custom view creation (needs session support) + * Specification of column and record separators (default: cs = `\t`, rs = `\n`) + * Listing of views applicable to a result/databank + * SRS 7+ XML from loader functionality + * Listing of loaders available for result set + * Retrieval of XML using "Generic Format" + * Retrieval of XML using "Specific Format" + * Workarounds for problems with SRS 8.2 wgetz support + * Tests: + * Test SRS error messages + * Tests for SRS 6.0, 7.0 and 8.0 servers + * Query tests for all SRS versions + * Sample getz-like client (`urlgetz.pl`) + * Default configuration support (`~/.urlgetz.rc`) + * `-f` support (requires custom view support) + * `-vf` support (requires custom view support) + * `-sf` and `-af` support to control sequence and alignment formats (requires custom view support) + * `-rs` and `-cs` support for table view separators + * `-lv` and `-lmin` support to view index tokens + * `-lb` and `-ll` support for chunking results + * `-info` support for databank details + * `-id` support to specify a user ID + * `-sort` and `-sortDir` support to specify sorting for a result set + +[[project_screenshots]] [[project_admins]] [[download_button]] </pre>Hamish McWilliamSun, 16 Sep 2012 06:30:03 -0000https://sourceforge.netc003951326c81442c05ab299b319a3fceb348bb1https://sourceforge.net/p/srsurlapi/wiki/Home/Welcome to your wiki! This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/srsurlapi/wiki/markdown_syntax/) syntax. [[project_admins]] [[download_button]] Hamish McWilliamSat, 15 Sep 2012 18:06:25 -0000https://sourceforge.netd912fc5f0a0d401ac2b234896a8728b7b6e77cd9