creating a Bio::SeqFeature::Annotation object downloads the entire so.obo

[cjfields]

---

Author Name: Heikki Lehvaslaiho (@heikkil)
Original Redmine Issue: 2513, https://redmine.open-bio.org/issues/2513
Original Date: 2008-06-10
Original Assignee: Bioperl Guts

---

A Bio::SeqFeature::Annotated object can not be created unless there is
a network connection. It tries to downloads a song SO.obo file from sourceforce. See the stack trace below.

Does this class really need to connect to network by default?

As a first fix, I’ve disabled running of tests in t/SeqFeatAnnotated.t
unless networked tests have been enabled.

-Heikki

P.S. I committed the temporary fix to tests in a wrong directory, so all the most recent POD fixes in bioperl-live got the comment meant for this fix.

——————————- WARNING ——————————-
MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/\*checkout\*/song/ontology/so.obo?rev=HEAD, but server threw 500. retrying…
—————————————————————————-
signalled

——————- EXCEPTION: Bio::Root::Exception ——————-
MSG: failed to fetch http://song.cvs.sourceforge.net/\*checkout\*/song/ontology/so.obo?rev=HEAD, server threw 500
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/heikki/src/bioperl-live/Bio/Root/Root.pm:357
STACK: Bio::Root::IO::_initialize_io /home/heikki/src/bioperl-live/Bio/Root/IO.pm:272
STACK: Bio::OntologyIO::_initialize /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:187
STACK: Bio::OntologyIO::obo::_initialize /home/heikki/src/bioperl-live/Bio/OntologyIO/obo.pm:137
STACK: Bio::OntologyIO::new /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:162
STACK: Bio::OntologyIO::new /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:171
STACK: Bio::Ontology::OntologyStore::get_ontology /home/heikki/src/bioperl-live/Bio/Ontology/OntologyStore.pm:225
STACK: Bio::SeqFeature::Annotated::primary_tag /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:656
STACK: Bio::SeqFeature::Annotated::_initialize /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:244
STACK: Bio::SeqFeature::Annotated::new /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:210
STACK: t/SeqFeatAnnotated.t:16

[cjfields]

---

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2008-06-13T21:54:10Z

---

We could have it retrieve a local copy of the file if it is present. However my opinion has been that this needs to be reimplemented in a different way (with the end result being that we deprecate Bio::SF::Annotated):

TypeFactory
untyped (generic) SF —————> strongly-typed SF

This shouldn’t be terribly hard to do, just haven’t had anyone with the time to do it.

[cjfields]

---

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2008-11-29T15:08:44Z

---

Pushing to point release

[cjfields]

---

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-01-14T16:53:40Z

---

Bio::FeatureIO and Bio::SeqFeature::Annotation are to be refactored and split out of BioPerl (Rob Buels has already started this process). One of the key issues to be addressed is the reliance of Bio::FeatureIO on a typed seqfeature (currently Bio::SeqFeature::Annotated), this will likely be changed and B::SF::A deprecated in 1.7.0.

[cjfields]

---

Original Redmine Comment
Author Name: Chris Fields
Original Date: 2010-05-15T10:29:38Z

---

Moving to Bio::FeatureIO-specific queue

[cjfields]

This is unlikely to be fixed as we're effectively deprecating use of Bio::SeqFeature::Annotated (unless someone can modify it to allow use of a custom local version of SO).