lsw changes

Revision 39

alanr — Sun, 09 Apr 2006 00:13:24 -0000

Add Joanne's demo to start.lisp, fix a bug in generating sames for debugging the bug

trunk/bug/queries.lisp

trunk/start.lisp

Revision 38

alanr — Sun, 09 Apr 2006 00:08:40 -0000

emacs help

trunk/emacs

trunk/emacs/always-show-completion.el

trunk/emacs/completion-no-properties.el

trunk/emacs/cygwin-xemacs-init.el

Revision 37

alanr — Sat, 08 Apr 2006 23:20:39 -0000

Joanne's example

trunk/biopax/proto/pathways-with-compounds.lisp

Revision 36

alanr — Sat, 08 Apr 2006 13:33:29 -0000

a function needs to create file:// urls, so we can special case cygwin.

trunk/bug/merge.lisp

trunk/owl/abstract.lisp

Revision 35

alanr — Sat, 08 Apr 2006 04:05:44 -0000

Changes to make it run under cygwin

trunk/abcl

trunk/abcl.bat

trunk/jss/invoke.lisp

trunk/owl/lisp-syntax.lisp

trunk/owl/namespace.lisp

Revision 34

alanr — Thu, 30 Mar 2006 07:00:24 -0000

jss/invoke.lisp: fix but in set-java-field

owl/lisp-syntax.lisp,owl/namespace.lisp,owl/query.lisp : changes to
make abstract syntax and SPARQL queries look nicer by generating
qnames and appropriate PREFIX and Namespace statements. This isn't quite ready
in that it needs to make sure not to generate a qname when the URI has 
characters that are illegal in a qname. (setq *use-qnames* nil) to turn this feature
off (e.g. for debugging the bug work)

trunk/jss/invoke.lisp

trunk/owl/lisp-syntax.lisp

trunk/owl/namespace.lisp

trunk/owl/query.lisp

Revision 33

alanr — Wed, 29 Mar 2006 19:43:41 -0000

Add blank/non-distinguished variables to sparql.

Use blank node for them. Lisp syntax is [](no space) or :_ (translates to []) 
or :_foo (translates to _:foo). [:p v] syntax not supported yet.

For now, pellet needs these to be named variables with
PelletOptions.TREAT_ALL_VARS_DISTINGUISHED to nil, so I handle this in
the rendering of lisp syntax to string. When pellet uses blank nodes as
non-distinguished queries will stay the same and renderer will change. 

tests/non-distinguished-variable.lisp is an example of how this works.

Also, sparql :trace is a little cleaner, with results printed too.

trunk/owl/query.lisp

trunk/owl/tests/non-distinguished-variable.lisp

Revision 32

alanr — Mon, 27 Mar 2006 06:58:37 -0000

Show equivalent classes when describing.

trunk/owl/describe.lisp

Revision 31

alanr — Mon, 27 Mar 2006 06:54:54 -0000

:a synonym for !rdf:type, as in (?protein :a !bp2:protein)
Fix filter clause to infix "<" and ">"

trunk/owl/query.lisp

Revision 30

jeremy — Wed, 22 Mar 2006 18:23:20 -0000

Problem set 1. Create an ontology with a transitive slot, an inconsistent ontology, and an unsatisfiable class. In addition, be inconsistent in several ways

trunk/abcl

trunk/biopax/proto/pathway-participants.lisp

trunk/exercises

trunk/exercises/pset1-20060317.lisp

trunk/exercises/pset1.asn

trunk/exercises/unsatisfiable-ontology.html

trunk/exercises/unsatisfiable-ontology.owl

Revision 29

alanr — Tue, 21 Mar 2006 20:58:33 -0000

Some load dependencies fixed. 
print patch was clobbering sensible error messages in the debugger (abcl bug, methinks). Fixed now.

trunk/owl/owl.asd

trunk/patches/abcl-print.lisp

trunk/start.lisp

Revision 28

alanr — Tue, 21 Mar 2006 07:53:36 -0000

!owl:Nothing is, by definition, unsatisfiable. When checking if an ontology is
satisfiable, therefore, don't pay attention to it.

trunk/owl/lisp-syntax.lisp

Revision 27

alanr — Tue, 21 Mar 2006 07:12:45 -0000

add unsatisfiable example

trunk/owl/tests/unsatisfiable.lisp

Revision 26

alanr — Tue, 21 Mar 2006 07:09:01 -0000

* pellet.lisp

define kb-unsatisfiable-classes to return them.
Add !owl:Thing, !owl:Nothing to the list of known classes for a kb

* describe.lisp

Accept a uri as an argument to describe-entity.
If a class is unsatisfiable, then say so when describing.

* lisp-syntax.lisp

Add methods on ontology: 
(consistent ontology) return t if the ontology is consistent
(satisfiable ontology) return t if the ontology is satisfiable
(unsatisfiable-classes ontology) return a list of unsatisfiable classes.
(check ontology) returns t if an ontology is both satisfiable and consistent.

trunk/owl/describe.lisp

trunk/owl/lisp-syntax.lisp

trunk/owl/pellet.lisp

Revision 25

alanr — Tue, 21 Mar 2006 05:22:34 -0000

New test/example inconsistencies.lisp

Both property value on an individual and has value constraint in a restriction
are written value(..). Work around this by defining has-value for the latter.
Need to fix owl-to-lisp-syntax.lisp to properly parse this. 

Add with-ontology form for short-lived ontologies that you don't want to set
a global variable to.

trunk/owl/lisp-syntax.lisp

trunk/owl/tests/inconsistencies.lisp

Revision 24

alanr — Mon, 20 Mar 2006 23:31:39 -0000

New example, from discussion with Andrea. 
fix "value" in abstract syntax

trunk/owl/lisp-syntax.lisp

trunk/owl/tests/complete-versus-partial.lisp

Revision 23

alanr — Mon, 20 Mar 2006 22:10:28 -0000

fix bug in kb method reported by Jeremy.

trunk/owl/lisp-syntax.lisp

Revision 22

alanr — Mon, 20 Mar 2006 05:50:11 -0000

In owl/

* lisp-syntax.lisp: 

The ontology name doesn't have to be the same as the base, so 
add an :about keyword and slot. 

Add function (literal value-as-string type) for specifying the type of
a literal. e.g. (literal "foo" !xsd:string)

Keep track of keywords, versus functions, and a couple of lookup tables to
support owl-to-lisp-syntax.lisp

* owl-to-lisp-syntax.lisp

New. (pprint-owl-lisp-syntax  "http://www.biopax.org/release/biopax-level2.owl" 'biopax-level-2)
will print out a form which can be evaluated to and create an instance of owl-ontology bound to 
the variable biopax-level-2

* namespace.lisp

Add reactome: proto: xsd: namespaces.

uri.lisp

Support calling reader macro with first character #\< too.

* describe.lisp

Various cleanups/bug fixes.

(describe !bp2:control) now dispatches to (describe-entity "bp2:control")

* owl.asd

Add owl-to-lisp-syntax.lisp

* query.lisp

Fix :union. Can now write, e.g. 

(sparql 
     '(:select (?mol1) () 
	(:union 
	 ((?mol1 !bug:hasCharge -1))
         ((:union
            ((?mol1 !bug:hasCharge 1))
	    ((?mol1 !bug:hasCharge 0)))))))

* pellet.lisp

Add has-entity? function

* patches/abcl-trace.lisp, patches/patches.asd

New. Fix abcl not adequately protecting *trace-level* from interrupts.

* jss/invoke.lisp

Fix bug in resolving full class name (said it was ambiguous when it wasn't)

trunk/jss/invoke.lisp

trunk/owl/describe.lisp

trunk/owl/lisp-syntax.lisp

trunk/owl/namespace.lisp

trunk/owl/owl-to-lisp-syntax.lisp

trunk/owl/owl.asd

trunk/owl/pellet.lisp

trunk/owl/query.lisp

trunk/owl/uri.lisp

trunk/patches/abcl-trace.lisp

trunk/patches/patches.asd

Revision 21

mt — Sat, 18 Mar 2006 05:36:08 -0000

Mike Travers' fix to sparql with negative integer. 
Alan: uri's returned from sparql are now uri structs.
Testing check in with Mike's user and password

trunk/owl/query.lisp

Revision 20

alanr — Mon, 13 Mar 2006 06:58:21 -0000

owl/lisp-syntax.lisp

"Annotation" is a different term than "annotation". The former is 
for an ontology property and the latter is for an annotation property.
Annotation becomes ontology-property in lisp syntax. Modify define-owl-term 
to handle specifying the lisp syntax explicitly.

Add a few more terms I missed.

****************************************************************
owl/uri.lisp

More work on this. Fix so that unabbreviate-namespace happens at run
time, not read time. Define eval-uri-reader-macro for those situations
where you are reading uris within a quoted form.

****************************************************************
owl/query.lisp

Add :trace keyword, which if passed a string, prints the string, and the 
sparql query. For demos.

****************************************************************
extlib/commons-codec-1.3.jar
extlib/commons-httpclient-3.0.jar
extlib/xmlrpc-2.0.1.jar
server/lsw-server.asd
server/xmlrpc.lisp

Beginnings of an xmlrpc server so we can have perl and other non-lisp
clients. Works, except for exceptions. Not loaded yet.

****************************************************************
start.lisp

Add server to asdf central registry.

****************************************************************
extlib/pellet.jar

new version with infinite chain fixed.

****************************************************************
owl/describe.lisp

Bug fixes. 
 - reversed sense of direct/all for sub/superproperties
 - handle empty range
 - fix inverse property query

****************************************************************
README.txt

add apache license

****************************************************************
trunk/biopax/proto/pathway-participants.lisp

Examples against extension of biopax that makes the following changes:
Define property PARTICIPANTS*
Make PARTICIPANTS, PATHWAY-COMPONENTS, STEP-INTERACTIONS, subproperty of PARTICIPANTS*
Make PARTICIPANTS* transitive.

Enables one to query for pathways that have a protein in some interaction that is part of 
the pathway, and for pathways that a protein participates in .

trunk/README.txt

trunk/biopax/proto/pathway-participants.lisp

trunk/biopax/proto/unfilled-slot-warning.lisp

trunk/extlib/commons-codec-1.3.jar

trunk/extlib/commons-httpclient-3.0.jar

trunk/extlib/pellet.jar

trunk/extlib/xmlrpc-2.0.1.jar

trunk/owl/describe.lisp

trunk/owl/lisp-syntax.lisp

trunk/owl/query.lisp

trunk/owl/uri.lisp

trunk/server

trunk/server/lsw-server.asd

trunk/server/xmlrpc.lisp

trunk/start.lisp