Fix: Mixed ontology level annotations

[syphax-bouazzouni]

Context

Fix #18

Changes

• Remove sourceOntolology.getOntologies() loops (e0ad8c7)
• Extract a method addAnnoations(masterOntology) (e0ad8c7)
• Add a test to ensure that sourceOntology.annotations.count equal genertaedOntoogy.annotations.count ( 5a17c74)

Example

CNO (source)

    <owl:Ontology rdf:about="http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl">
        <dc:date rdf:datatype="&xsd;string">13/03/2012</dc:date>
        <dc:subject rdf:datatype="&xsd;string">An ontology to describe the field of Computational Neurosciences</dc:subject>
        <dc:contributor rdf:datatype="&xsd;string">Birgit Kriener</dc:contributor>
        <dc:title rdf:datatype="&xsd;string">Computational Neuroscience Ontology</dc:title>
        <dc:contributor rdf:datatype="&xsd;string">Erik De Schutter</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Fahim T. Imam</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">INCF MultiScale Modeling Task Force</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Lars Schwabe</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Padraig Gleeson</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Sean Hill</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Stephen D. Larson</dc:contributor>
        <dc:contributor rdf:datatype="&xsd;string">Subhasis Ray</dc:contributor>
        <rdfs:comment rdf:datatype="&xsd;string">This ontology is used to add the Definition class of annotation as in NIF.
The source of the definition can be defined with class from OBO-annotation</rdfs:comment>
        <rdfs:comment rdf:datatype="&xsd;string">This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.</rdfs:comment>
        <dc:creator rdf:datatype="&xsd;string">Yann Le Franc</dc:creator>
        <owl:versionInfo rdf:datatype="&xsd;string">version 0.5</owl:versionInfo>
        <owl:imports rdf:resource="http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl"/>
        <owl:imports rdf:resource="http://ontology.neuinfo.org/NIF/Backend/ro_bfo1-1_bridge.owl"/>
        <owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
        <owl:imports rdf:resource="http://purl.org/incf/ontology/Computational_Neurosciences/external_import/external.owl"/>
        <owl:imports rdf:resource="http://purl.org/obo/owl/ro"/>
        <owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
        <owl:imports rdf:resource="http://www.w3.org/2004/02/skos/core"/>
    </owl:Ontology>

Generated xrdf CNO

        <owl:Ontology rdf:about="http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl">
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Birgit Kriener</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Erik De Schutter</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fahim T. Imam</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INCF MultiScale Modeling Task Force</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lars Schwabe</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Padraig Gleeson</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sean Hill</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stephen D. Larson</dc:contributor>
        <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Subhasis Ray</dc:contributor>
        <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yann Le Franc</dc:creator>
        <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">13/03/2012</dc:date>
        <dc:subject rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An ontology to describe the field of Computational Neurosciences</dc:subject>
        <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Computational Neuroscience Ontology</dc:title>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This ontology is used to add the Definition class of annotation as in NIF.
The source of the definition can be defined with class from OBO-annotation</rdfs:comment>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.</rdfs:comment>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">version 0.5</owl:versionInfo>
    </owl:Ontology>

[syphax-bouazzouni]

Some notes:

• You can observe that in the generated ontology we lost the <owl:imports> statements, but the it was already the case before

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 63.41463% with 15 lines in your changes missing coverage. Please review.

Project coverage is 73.05%. Comparing base (419489d) to head (9156d1c).

Files with missing lines	Patch %	Lines
...g/stanford/ncbo/owlapi/wrapper/OntologyParser.java	63.41%	10 Missing and 5 partials ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##             master      #20      +/-   ##
============================================
+ Coverage     72.98%   73.05%   +0.06%     
- Complexity      165      167       +2     
============================================
  Files            15       15              
  Lines           733      746      +13     
  Branches        116      117       +1     
============================================
+ Hits            535      545      +10     
- Misses          152      153       +1     
- Partials         46       48       +2     

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