1620 deletion of child ontologies (#1748) * Make removed child ontologies "not present". * Scope default children association of acts_as_tree to present ontologies. * Show only present ontologies of this file. * Fix ontology factory. * Add cucumber features. * Fix restoring children. * Fix restoring a child ontology. * Add specs for restoring children. * Really fix restoring a child ontology. * Only save the ontology if it has changed or if it is a new record.

1753 wait for sql to finish before parsing worker retry (#1761) * Remove callback for parsing a version on create. * Handle do_not_parse flag properly * Remove the sleep command. * Refactor: Put state change into a method. * Fix specs. * Only assign the distributed logic once. * Only clone asynchronously after the transaction completed. * Fix specs that clone a repository. * Remove do_not_parse flag and replace it by a do_parse flag where needed. * Obey Hound as much as possible. * Fix parsing ontologies in the seeds.

1592 committer not shown in versions (#1704) * Supply pushing user. * Code style. * Remove already executed data migration task. * Improve Commit model, add associations to User model. * Get rid of ambiguous class/module names. * Replace OntologyVersion#user by #pusher. * Display pusher information in OntologyVersions index. * Fix all the tests. * Add new tests. * Obey Hound. * Fix migration. * Add data migration for missing commits. * Add data migrations. * Shorten up method. * Remove unnecessary comment.

Improve locId (#1618) * introduce new model to ontohub * introduce new locid behavior * adding try to prevent undefined method for nil * generate the locids by object creation * introduce method to simulate an attribute * generate Locids correctly for ontologies * correct creation of child_ontology locids * remove old uniqueness validation for ontology locid * use better names vor locidportion * correct behaviour for locid creation * generate loc_id correctly for ontology * use correct class for inherritanc * remove locids on deletion of objects * rename the base model * introduce data-migration to move the locids * remove double naming in the cat ontology * obey hound * correct behaviour of external repository for locid * change factory behaviour for locid * fix missing comma * begin to fix test * change ontology factory to new locid * change factories for new LocId Model * remove unneeded test * Use proper class retrieval in factories. * Always use to_s on the class call in LocIdBaseModel. * Always use .class.to_s instead of .class when used for the database. * Fix external repository. * Be clean and unstub again. * Fix sentence factory. * Quick fix the destruction of locids. * Fix code style. * Generate locids during create process: Base class. * Generate locids during create process: Mapping. * Generate locids during create process: Sentence. * Generate locids during create process: Symbol. * Generate locids during create process: ProofAttempt. * Generate locids during create process: ProverOutput. * Generate locids during create process: Ontology #1. * Generate locids during create process: Ontology #2. * Generate locids during create process: Ontology #3. * Generate locids during create process: Factories. * Fix seeds errors. * Fix ontology spec on error while parsing The ontology needs to be reloaded because sidekiq does so as well. It always fetches a fresh record from the database. The test failed before because `NodeEvaluationHelper#clean_ontology` called destroy on all the ontology's symbols which existed in the object, but were not really persisted because of an aborted transaction. * Remove redundant space. * Move comment to the correct line. * Fix worker_spec In the production code, the locid is never set before saving the ontology. * Add gems pry-stack_explorer, awesome_print for debugging purposes. * Only start hets if there was a hets error and rollback the changes. * Destroy dependent prover output. * Fix ProofAttempt factory. * Rename assorted_object to specific and fix migration. * Fix migration code style. * Reanalyze ontologies with duplicate locids. * Fix code style. * Remove redundancies. * Remove useless association. * Obey Hound. * Directly query in the LocIdBaseModel. * Add locid routing feature. * Cache LocId query results This should speed up the routing in a great extent. For each matching `specified_get`, the LocIdRouterConstraint fetched the element once from the database. This resulted in 8 times the same SQL query for a ProofAttempt. The implemented cache reduces this to a single query. * Clear the elements cache periodically to prevent memory leaks. * Add missing dependent: :destroy. * Add Recreating repository feature. * Combine if statements. * Change Given to When. * Catch ambiguous locid error. * Fix i18n key usage. * Fix code style. * Comment on error suppression. * Add spec for Syntax Error. * Use single-quoted strings. * Fix error message check: language. * Keep parameter assignment DRY. * Rename RecreatingRepository feature to Repository. * Use local_variable_get instead of eval. * Change locid column type to text. * Implement (implicit) down-migration. * Implement (explicit) down migration. * Add migration to create missing locids. * Fix nil error. * Really fix nil error. * Fix migration. * Fix sentence migration accessing association. * Force old Mappings to have a name. * Add missing locids to symbols.

Style fixes.

Allow to delete an ontology if it is only imported from the same file.

fix tests for removal of iri on ontologies.

provide correct factories for done ontologies.

prepare ontology factories for loc/ids.

fix locid-related specs.

Run rename refactor script.