Refactored the ontology-access APIs. Next step - refactoring the UI for the ontology-access.
Fixups. Squash into this commit.
Refactoring.
Moved the OntologyVersionRecorder listener.
Merge pull request #697 from soLEED/issue-refactor

[refactoring] Extract the HPO and OMIM ontologies into separate modules
Issue #698. Hardcoded port in solr-access-service component [AbstractSolrScriptService.java]
Merge pull request #704 from soLEED/issue-698

Issue #698. Hardcoded port in solr-access-service component
Patient JSON export/import.
This is work in progress.
Has the basic structure and interfaces setup.

- Created a separate package (org.phenotips.data.internal) for classes that hold patient data. Each class is an implementation of a new interface (PatientDataSerializer).
- Each of those classes implements a function that reads data from the wiki, exports json, and imports it.
- Export function is not implemented yet.
- So far, each class ROUGHLY corresponds to a class in xwiki (PatientClass, OntologyVersionClass).
- The idea is that the PhenoTipsPatient class would store all of its data in classes implementing PatientDataSerializer, rather than storing and dealing with data itself.
JSON import/export for patients.

Some general clean up.
Still missing some export fields.
Patient JSON export/import
Added the function that splits a field containing an hpo term into a map containing {id, label}.
Issue #684. HPO term definitions with quotes in them are trimmed up to the first internal quote.
Changed regex in SolrUpdateGenerator.
Merge pull request #707 from soLEED/issue-684

Issue #684: HPO term definitions with quotes in them are trimmed up to the first internal quote.
Issue #714. Fixing getDescription in R52090PhenoTips633DataMigration.
Merge pull request #715 from soLEED/issue-714

Issue #714: Fixing getDescription in R52090PhenoTips633DataMigration
Issue #712. Migrating field age_of_onset to global_age_of_onset (PatientClass)
Issue #713. Migrating field mode_of_inheritance to global_mode_of_inheritance (PatientClass).
Issue #706. Add a PatientRecordInitializer component role that allows setting up a new patient record.
[refactoring] Better field names, shorter code, better javadoc
Issue #684: HPO term definitions with quotes in them are trimmed up to the first internal quote
Better fix.
[cleanup] Applied codestyle
[misc] Fixed build error