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spechub / Hets

The Heterogeneous Tool Set
http://hets.eu
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download items for ontology #1230

Closed sternk closed 8 years ago

sternk commented 10 years ago

Reported by mcodescu and assigned to maeder Migrated from http://trac.informatik.uni-bremen.de:8080/hets/ticket/1230

With the ontology from http://develop.ontohub.org/bioportal/OntoVIP.owl, I get

repos/Hets$ ./hets -g http://develop.ontohub.org/bioportal/OntoVIP.owl
fromList []
fromList [<http://vip.creatis.insa-lyon.fr/ontovip/v1.0/vip-pathological-object.owl]>
[]
### file name 'http://develop.ontohub.org/bioportal/OntoVIP.owl' does not match library name '<http://vip.creatis.insa-lyon.fr/ontovip/v1.0/vip-pathological-object.owl>'
Analyzing library <http://vip.creatis.insa-lyon.fr/ontovip/v1.0/vip-pathological-object.owl>
logic OWL
Analyzing spec <http://vip.creatis.insa-lyon.fr/ontovip/v1.0/vip-pathological-object.owl>
fromList []
fromList [<http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl]>
[]
### file name 'http://develop.ontohub.org/bioportal/OntoVIP.owl' does not match library name '<http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl>'
Analyzing library <http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl>
logic OWL
Analyzing spec <http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl>
fromList [<http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl]>
fromList [<http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl,<http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl]>>
[]
### file name 'http://develop.ontohub.org/bioportal/OntoVIP.owl' does not match library name '<http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl>'
Analyzing library <http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl>
logic OWL
Analyzing from <http://neurolog.unice.fr/ontoneurolog/v3.0/dolce-particular.owl>
Analyzing spec <http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl>
fromList [<http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl]>
fromList [<http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl,<http://neurolog.unice.fr/ontoneurolog/v3.0/study-examination-subject.owl]>>
[]
### file name 'http://develop.ontohub.org/bioportal/OntoVIP.owl' does not match library name '<http://neurolog.unice.fr/ontoneurolog/v3.0/study-examination-subject.owl>'
Analyzing library <http://neurolog.unice.fr/ontoneurolog/v3.0/study-examination-subject.owl>
logic OWL
Analyzing from <http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl>
*** Error:
non-unique name within imported library
'<http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl>'
hets: user error (Stopped due to errors)
sternk commented 10 years ago

Comment by maeder Migrated from http://trac.informatik.uni-bremen.de:8080/hets/ticket/1230#comment:2

This issue is fixed by spechub/Hets@0b8595f7a0662ff5e1f7adaf53029213cf43c4d3, but I have no fix yet for #1214 that turns up now.

sternk commented 10 years ago

Comment by maeder Migrated from http://trac.informatik.uni-bremen.de:8080/hets/ticket/1230#comment:3

This fix does not work for #1226, because there the item name http://develop.ontohub.org/sandbox/pizza.owl does not match the (unique) ontology name http://www.co-ode.org/ontologies/pizza/pizza.owl A different fix is given by spechub/Hets@ad7a1aea1e516e89649497daf9ed8e165eac352d.

mcodescu commented 8 years ago

With e.g http://ontohub.org/fois2016/ZFA_CCONT.dol, I get 

*** Error:
non-unique name within imported library
'<http://livercancer.imbi.uni-heidelberg.de/ccont>'
hets: user error (Stopped due to errors)

The same error seems to appear whenever an imported OWL ontology has imports itself.

tillmo commented 8 years ago

@cmaeder, do you have time to have a look at this? Would be much appreciated!

cmaeder commented 8 years ago

I get:

maeder@lati:~/Hets$ ./hets -g http://ontohub.org/fois2016/ZFA_CCONT.dol
Analyzing file http://ontohub.org/fois2016/ZFA_CCONT.dol as library ZFA_CCONT
Downloading <http://ontohub.org/fois2016/CCONT> ...
Analyzing library <http://ontohub.org/iswc2014/CCONT.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/CCONT.owl_module.owl>
... loaded <http://ontohub.org/fois2016/CCONT>
Downloading <http://ontohub.org/fois2016/ZFA> ...
Analyzing library <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
... loaded <http://ontohub.org/fois2016/ZFA>
logic OWL
Analyzing alignment ZFA_CCONT?ZFA2CCONT
hets: non-unique symbol match: [Entity {label = Nothing, entityKind = Class, cutIRI = QN {namePrefix = "obo", localPart = "ZFA_0009031", iriType = Abbreviated, expandedIRI = "http://purl.obolibrary.org/obo/ZFA_0009031", iriPos = nullRange}}]
[]
mcodescu commented 8 years ago

What about this: http://ontohub.org/fois2016/ZFA_UBERON.dol?

Could you please give me the version of hets you are using?

mcodescu commented 8 years ago

PS: this is a large file, so I had to increase stack.

cmaeder commented 8 years ago

I'm using the master branch

maeder@lati:~/Hets$ ./hets --version
version of hets: v0.99, 1452515368

maeder@lati:~/Hets$ ./hets -g http://ontohub.org/fois2016/ZFA_UBERON.dol
Analyzing file http://ontohub.org/fois2016/ZFA_UBERON.dol as library ZFA_UBERON
Downloading <http://ontohub.org/fois2016/UBERON> ...
Analyzing library <http://ontohub.org/iswc2014/UBERON.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/UBERON.owl_module.owl>
... loaded <http://ontohub.org/fois2016/UBERON>
Downloading <http://ontohub.org/fois2016/ZFA> ...
Analyzing library <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
... loaded <http://ontohub.org/fois2016/ZFA>
Analyzing alignment ZFA_UBERON?ZFA2UBERON
*** Error: symbolsOf1: Logic OWL expected, but CASL found
hets: user error (Stopped due to errors)
mcodescu commented 8 years ago

I'm working on https://github.com/spechub/Hets/tree/1564_improve_analysis_of_alignments, which should not have modified the library imports in HETS.

About the ZFA_UBERON file, the current logic should be set to OWL before the error occurs. Ontohub has a bug that prevents me from pushing the change there. 

$ ./hets -g +RTS -K1G -RTS ~/repos/fois2016/ZFA_UBERON.dol
Analyzing file /home/mcodescu/repos/fois2016/ZFA_UBERON.dol as library ZFA_UBERON
Downloading <http://ontohub.org/iswc2014/UBERON> ...
Analyzing library <http://purl.obolibrary.org/obo/uberon/nbo_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/nbo_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/cl_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/cl_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/references/references.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/references/references.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/ncbitaxon_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/ncbitaxon_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/ro_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/ro_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/pato_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/pato_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/go_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/go_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/pr_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/pr_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/envo_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/envo_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/chebi_import.owl>
logic OWL
Analyzing spec <http://purl.obolibrary.org/obo/uberon/chebi_import.owl>
Analyzing library <http://purl.obolibrary.org/obo/uberon/ext.owl>
logic OWL
Analyzing from <http://purl.obolibrary.org/obo/uberon/pr_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/nbo_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/chebi_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/go_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/cl_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/references/references.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/ro_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/pato_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/envo_import.owl>
Analyzing from <http://purl.obolibrary.org/obo/uberon/ncbitaxon_import.owl>
Analyzing spec <http://purl.obolibrary.org/obo/uberon/ext.owl>
... loaded <http://ontohub.org/iswc2014/UBERON>
*** Error:
non-unique name within imported library
'<http://purl.obolibrary.org/obo/uberon/ext.owl>'
hets: user error (Stopped due to errors)
mcodescu@nuance:~/repos/HETS$ ./hets --version
version of hets: v0.99, 1452515368
mcodescu commented 8 years ago

The last error I received when working on the master branch.

mcodescu commented 8 years ago

Now the logic was set to OWL.

cmaeder commented 8 years ago

Works for me (but I'm still waiting for the dg to pop up)

maeder@lati:~/Hets$ ./hets -g http://ontohub.org/fois2016/ZFA_UBERON.dol
Analyzing file http://ontohub.org/fois2016/ZFA_UBERON.dol as library ZFA_UBERON
Downloading <http://ontohub.org/fois2016/UBERON> ...
Analyzing library <http://ontohub.org/iswc2014/UBERON.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/UBERON.owl_module.owl>
... loaded <http://ontohub.org/fois2016/UBERON>
Downloading <http://ontohub.org/fois2016/ZFA> ...
Analyzing library <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
logic OWL
Analyzing spec <http://ontohub.org/iswc2014/ZFA.owl_module.owl>
... loaded <http://ontohub.org/fois2016/ZFA>
logic OWL
Analyzing alignment ZFA_UBERON?ZFA2UBERON
Analyzing spec ZFA_UBERON?ZFA2UBERON_c
mcodescu commented 8 years ago

The dg won't pop up, it's a bug I'm trying to fix, but this is for me to solve.

I have sent you two files that cause this non-unique name within imported library error when the ontologies are imported from a different Ontohub repository.

cmaeder commented 8 years ago

With your file ZFA_UBERON.dol` I can reproduce your above output.

./hets -g http://purl.obolibrary.org/obo/uberon/ext.owl -i owl

consumes all my RAM (> 6 GB) without ever showing a DG. Maybe all imports contribute a DG to the library uberon/ext.owl an make it thus non-unique. Has uberon/ext.owl a cycle?

mcodescu commented 8 years ago

http://ontohub.org/sandbox/import.dol is a much smaller file that reproduces the behavior. Will try to follow your hint from the email. Many thanks for your help!

cmaeder commented 8 years ago

Could you try to merge in my branch https://github.com/spechub/Hets/tree/1230-unique_name?