Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/README @ 11:6ca67b155e32

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
parents 3f31c0eb7539
children 7e6604a5ee55
comparison
equal deleted inserted replaced
10:3f31c0eb7539 11:6ca67b155e32
1
2
3
4 ===========
5 OPPL-GALAXY
6 ===========
7 1
8 2
9 3
10 INSTALLATION 4 INSTALLATION
11 ============ 5 ============
12 6
13 1.- Stop Galaxy. 7 1.- Stop Galaxy.
14 8
15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 9 2.- Copy the following files and dirs to
16 and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/ 10 /galaxy-dist/tool-data/shared/jars/:
11
12 oppl_galaxy_tool.jar
13 oppl_galax_lib/
14 FaCT++-linux-v1.5.2/
15 FaCT++-OSX-v1.5.2/
16 inference.jar
17 inference_lib/
17 18
18 3.- Create directory /galaxy-dist/tools/OPPL/ 19 3.- Create directory /galaxy-dist/tools/OPPL/
19 20
20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/ 21 4.- Copy oppl.xml and inference.xml to /galaxy-dist/tools/OPPL/
21 22
22 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 23 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
23 24
24 <section name="Ontology Pre Processor Language" id="oppl"> 25 <section name="Ontology Pre Processor Language" id="oppl">
25 <tool file="OPPL/oppl.xml"/> 26 <tool file="OPPL/oppl.xml"/>
27 <tool file="OPPL/inference.xml"/>
26 </section> 28 </section>
27 29
28 6.- Start Galaxy. 30 6.- Start Galaxy.
29 31
30 32
31 33
32 USAGE
33 =====
34
35 An ontology and an OPPL file are needed (test.owl and test.oppl can be
36 used as samples). Load both:
37
38 Get Data
39 >> Upload File from your computer
40
41 Then execute the OPPL file against the OWL file:
42
43 Ontology Pre Processor Language
44 >> Execute an OPPL file against an OWL file
45
46 An ontology produced by another galaxy tool can also be used.
47
48 Test.oppl and test.owl can be used as examples. More OPPL-Galaxy
49 examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and
50 general OPPL script that may be useful to use with OPPL-Galaxy can be
51 obtained at http://oppl2.sourceforge.net/taggedexamples/.
52
53 A public instance of Galaxy with pre-installed OPPL-Galaxy can be used
54 at http://sele.inf.um.es:8080/.
55
56
57
58 FORESEEN FEATURES 34 FORESEEN FEATURES
59 ================= 35 =================
60 36
61 Choose which inferred axioms to add to the output ontology (Right now 37 OPPL:
62 only subsumption between named classes is available).
63 38
64 Rendering definition (URI fragment, label, etc). 39 - Support for processing ontologies that import other ontologies loaded
40 in galaxy.
65 41
66 XML catalog support for imported URIs. 42 - Rendering definition (URI fragment, label, etc).
67 43
68 OWLLink and Racer support. 44 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
45 cell).
46
47 - OWLLink and Racer support.
48
49
50 Inference:
51
52 - DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals,
53 ...
54
69 55
70 56
71 57
72 KNOWN BUGS AND ISSUES 58 KNOWN BUGS AND ISSUES
73 ===================== 59 =====================
74 60
75 Currently Galaxy interprets any information thrown to stderr as a tool 61 Currently Galaxy interprets any information thrown to stderr as a tool
76 error, which is bad since OPPL (And many other tools) throw info to 62 error, which is bad since OPPL (And many other tools) throw info to
77 sdterr even if working properly. In OPPL Galaxy, stderr is redirected to 63 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
78 /dev/null to avoid the problem, but that means that OPPL Galaxy does not 64 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
79 fail gracefully (It simply stops). A wrapper will be implemented. 65 not fail gracefully (It simply stops). A wrapper will be implemented.
80 66
81 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr 67 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
82
83
84
85 TESTS
86 =====
87
88 To run the functional test, first complete installation and then:
89
90 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/
91
92 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample
93
94 <section name="Ontology Pre Processor Language" id="oppl">
95 <tool file="OPPL/oppl.xml"/>
96 </section>
97
98 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl
99 68
100 69
101 70
102 CONTACT 71 CONTACT
103 ======= 72 =======
116 COPYRIGHT AND LICENSE 85 COPYRIGHT AND LICENSE
117 ===================== 86 =====================
118 87
119 Copyright (c) 2011 Mikel Egaña Aranguren. 88 Copyright (c) 2011 Mikel Egaña Aranguren.
120 89
121 OPPL-Galaxy is free software: you can redistribute it and/or modify 90 (OPPL|Inference)-Galaxy is free software: you can redistribute it and/or
122 it under the terms of the GNU General Public License as published by 91 modify it under the terms of the GNU General Public License as published
123 the Free Software Foundation, either version 3 of the License, or 92 by the Free Software Foundation, either version 3 of the License, or (at
124 (at your option) any later version. 93 your option) any later version.
125 94
126 This program is distributed in the hope that it will be useful, 95 This program is distributed in the hope that it will be useful,
127 but WITHOUT ANY WARRANTY; without even the implied warranty of 96 but WITHOUT ANY WARRANTY; without even the implied warranty of
128 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 97 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
129 GNU General Public License for more details. 98 GNU General Public License for more details.