Command line version produces strange file names when the source ontology is not in current directory #20
Comments
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From HDie...@lbl.gov on December 02, 2011 16:38:53 The strange file names are generated, due to the fact, that there is no ontology id present in the source file. The output file name is generated using the ontology. If not present the path is used to generate an ID, which result in this strange file name. Status: WontFix |
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From Sebastia...@charite.de on December 03, 2011 00:59:45 While appreciate this comment, please notice that this tag is new for OBO 1.4 as far as I can see it and even there it is not declared as required (only as should). In absence of this tag, I suggest to take only the last component of the path as the ontology when operating on a local filesystem, otherwise the tool behaves differently than many other build tools (e.g., gcc). |
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From HDie...@lbl.gov on December 05, 2011 17:43:00 Implemented suggested change. Now OORT checks the file name (if available) and removes the '.obo' or '.owl' suffix to create a default ontology id (committed in revision 394 ). Status: Started |
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From HDie...@lbl.gov on January 12, 2012 15:32:59 Status: Fixed |
From Sebastia...@charite.de on December 02, 2011 01:18:38
What steps will reproduce the problem?
For instance:
> bin/ontology-release-runner ../../../ontology/human-phenotype-ontology.obo
produces files such as "..%2F..%2F..%2Fontology%2Fhuman-phenotype-ontology-merged.obo" in the current directory. This is under Linux. Apparently there is some URL transformation going on.
I would expect that by default all output is placed within the current working directory with proper names.
Original issue: http://code.google.com/p/owltools/issues/detail?id=20
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