Revision history for Perl extension MOBY.

1.15

• fix: There is a bug in CGI which only manifests when a server is behind more than one proxy. The bug effect is that virtual_host returns more than one host, separated by commas. This fix avoids the bug just parsing the result of virtual_host method. 1.14
• fix: dont make an un-necessary network call when instantiating a MOBY::Client::OntologyServer object. 1.13
  • fix: no longer allow colons to be used in names for terms in

    registerX methods. 1.12

• Updated CommonSubs to remove all hard coded entries for the

  namespace prefix 'moby:'. In addition, all references to nodeName were replaced with localname so that element namespace prefixes are ignored since they dont really matter. Also, the localnames/prefixes are resolved to check the namespaceURI.

1.11

• Updated the Makefile.PL to handle some missing dependencies. Changes
  • Updated the RESOURCES script to better handle trailing slashes on Objects/, Namespaces, Services/
  • Updated the regex expressions that are applied against terms when registering new nodes in the biomoby ontologies.

1.10

• Added a RESTful WSDL page to the installation. Basically, you do a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service is returned. ** Thanks to José Manuel Rodríguez Carrasco **
• Updated mobygetAttribute and mobygetAttributeNode so that the warning regarding unitialized value is no longer given when running t/CommonSubs.t or using CommonSubs.pm.

1.09

• Fixed bug where data types registered into registry could contain illegal characters.
  • added some tests to Client-Central.t to test for this condition

1.08

• Fixed META.yml in the distribution. Please refer to changes for 1.07.

1.07

• Important: run the script moby-s-update-db once you have installed this module if you have upgraded an existing installation.
  • Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and SimpleArticle that caused objects created to have 'memory'.
  • Updated the MOBY::Client::ServiceInstance module to reflect the fact that services can have >= 0 MobyUnitTests.
  • In MOBY::RDF::Utils, fixed typo in the ref ($self) =~ m// statement
  • In MOBY::RDF::Ontologies::Services, added a loop to go over the array of unit tests
  • MOBY::RDF::Parsers::ServiceParser, added a loop to parse out unit tests in those instances that more than one is defined, and added code to parse out the datatype/namespace/servicetype term from a uri/lsid.
  • Added the function 'raw_execute' to MOBY::Async::Service to allow calling of services with raw XML similarly to the method in MOBY::Client::Service.
  • Fixed typo in MOBY::Client::Service that refered to POST services as category 'post' rather than 'cgi'
  • updated service_unit_tester.pl to handle cgi/moby/moby-async services and to take into account that services can have >= 0 unit tests.
  • fixed bug in Central.pm that allowed you to register datatypes with similar articlenames to other members in the datatype.
  • added cgi-async to category of services that registry understands.

1.06

• Changes to makefile reflecting the cpan addition of wsrf.
• Added Boolean to the data sql dump file for initializing a new registry.
• Added character encoding checks to the data kept in the registry. All data used in the register methods are checked to be encoded in UTF-8
• Added $VERSION info for all the modules. Sorry if this creates some initial confusion; The longer term gains far exceed any short term disruptions.
• Cosmetic fixes in Service.pm and SimpleServer.pm.
  • Fixed a bug in WSRF.pm related to temporal file location/creation introduced by a previous commit
  • Bug fix related to asynchronous MOBY calls with empty mobyData elements. MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed.
  • Added "no warnings 'redefine';" to MOBY::Async::WSRF to suppress redefinition warnings.
  • Added Unit test predicates to FETA.pm
  • Created module that can be used to test Moby services. This module is MOBY::Client::MobyUnitTest. Methods for determining whether differences exist are complete. Currently, the method to obtain differences is unfinished.
  • Fixed the uri in the RDF returned in MobyMetadataResolver.pm when the resolver is attempting to let you know what the latest lsid is for the given entity.
  • RDF for service instances now includes unit test information if unit test information is available for the service instance.
  • fixed how references were created in MOBY::RDF::Ontologies::
  • added a unit testing script for services to the shared/cgi dir.

1.05

• Multiple bug fixes / additions to installer (thanks to Jason Stewart), as follows:

  Additions

  • detecting root and giving a warning if not root
  • creating apache file in conf.d/ if running apache2
  • added apache defaults for debian/ubuntu systems
  • added a couple longer messages to give people a heads up what is happening.
  • changed many/most of the do {...} if pprompt() to if (prompt()) {...}
  • changed the big multi-line messages from multiple say "..." to say <<EOT;
  • re-indented most of the file - the whitespace was messed up on Emacs22.

                bug fixes
                * the prompt menu for cloning the DB has a default of 'b' 
                  in the prompt string, but no default in the actual call to
                  prompt() so if the user didn't type anything they got an 
                  ugly error
                * in prompt_for_directory() switched the cases around for -e
                  and -w otherwise -e wouldn't get triggered
                * in config_file_from_template()  added an if defined $fh test
                * added a chmod 644 to the mobycentral.config because it has
                  the DB root password
                * called die() if mysql wasn't detected
        - fixed a bug in the service_tester.pl script that referenced $opt_c
          instead of $url. (thanks to Jason Stewart)
        - prompt for a username/password for the registry to access the db.
          if the user doesnt exist, we add it. This helps us stay away from
          using the root password in the mobycentral.config file.
        - Fixed bug in the service instance cache code. Services from service
          providers with other registered services was not updating itself
          correctly.
        - isAlive information is removed from cached rdf because it made 
          absolutely no sense keeping it there.
        - #'s converted to forward slashes so that the URIs are resolvable
        - fixed a bug in Services.pm that caused the incorrect domain 
          name to be placed
        - file MOBY-Server/t/MOBY.t removed because it was tesing a non-existant
          module
        - fixed the installer script, username/password, root/root was hardcoded
        - fixed a bug in MOBY::dbConfig that caused certain parameters to be
          ignored in the configuration file if a field was empty.
        - added a caching script to be used by registry providers needing to
          update their cache. 
          For more information, run: 
              moby-s-caching.pl -h

1.04

• fixed bug in MOBY::Client::Central::DUMP that resulted in an error ('Not an ARRAY reference at MOBY/Client/Central.pm line 1927') being raised. Thanks to Pieter Neerincx for finding the bug and a solution.
• fixed bug that allowed service types to be registered with empty ISA relationships.
• MOBY::Config now only reads the config file once instead of numerous times.
• Attempted fix of shared memory bugs with service_tester.pl Shared memory wasn't being recycled properly and led to the server running the script to run out of memory segments, causing the script to run, but not to produce any output.
• MOBY WSRF implementation was not WSRF compliant in some points, and the same happened with sample code. Both the libraries and the generated WSDL have been fixed.
• Added checks for those cases where RDF is wanted for a particular ontology that is empty. Instead of dying, we now return an empty document (as should be expected).
• Fixed a bug in the schema for secondary inputs. The schema was missing the column 'description'

1.00

• CVS version of MOBY released to the world via CPAN!