Resolve "Small molecules annotators to be rearranged"

Closes #617 (closed)

added 33 commits

• 00c4a96a...d4e295ac - 10 commits from branch master
• 29b7294c - unit test uses mockito mocks
• c5780de4 - annotation parameter type changed to enum and parameters are integrated into collection class
• b9ba7dba - annotateElement action takes input identifiers that are used in annotation process
• f1bd1a2f - formatting
• e3495c66 - chebi use generic set synonyms method
• ac34e430 - ensembl use generics addHgnc methods
• 66d3a829 - unused annotator removed
• 7ca7ec75 - synonym can have up to 512 characters
• e2e95c91 - redundant code removed
• ed99dba9 - debug removed
• e0b3fdda - redundant unit tests mreged
• 388d6558 - unused methods removed
• 49c76af9 - unused method removed
• 0fe1feff - unit test for removed method deleted
• 99b3c8f9 - annotators must defined set of output parameters
• 1863dea6 - setSymbol is executed only when output is declared to include it
• ee6cd069 - only defined outputs are modified
• d7b9e15b - annotators use proxy object to add data into BioEntity
• 78a55aba - methods bypassing proxy removed
• 634e2c2f - createMiriamData method removed and replaced with the setAnnotator in the Proxy object
• 6dd3bd08 - precomputed prefix removed
• 23133c3c - there is a function that should return valid example annotation that could be used by the annotator
• e4f83cf3 - list of implemented annotators is provided by spring

Compare with previous version

added 123 commits

• e4f83cf3...4e25f790 - 90 commits from branch master
• 26f00da4 - unit test uses mockito mocks
• c93b4150 - annotation parameter type changed to enum and parameters are integrated into collection class
• b03caabd - annotateElement action takes input identifiers that are used in annotation process
• d181db78 - formatting
• 3e21aaf0 - chebi use generic set synonyms method
• 10ed88bf - ensembl use generics addHgnc methods
• af88458e - unused annotator removed
• c8b41917 - synonym can have up to 512 characters
• 24820df1 - redundant code removed
• 83bc1f11 - debug removed
• ecd87af8 - redundant unit tests mreged
• d8636777 - unused methods removed
• eb360729 - unused method removed
• 21e5cdd3 - unit test for removed method deleted
• b8566f9e - annotators must defined set of output parameters
• 8d22f064 - setSymbol is executed only when output is declared to include it
• ea104c63 - only defined outputs are modified
• c940cd00 - annotators use proxy object to add data into BioEntity
• 11bf671e - methods bypassing proxy removed
• 5f958430 - createMiriamData method removed and replaced with the setAnnotator in the Proxy object
• 22b06052 - precomputed prefix removed
• ce85cfcd - there is a function that should return valid example annotation that could be used by the annotator
• 5e941587 - list of implemented annotators is provided by spring
• 6a915eff - NPE fixed
• cefe0850 - unit tests making sure that requested output is provided by annotator added
• 4de904f1 - test parameters are assigned via test framework
• b92e6633 - unit test verifying if only defined output parameters can be added by annotator
• 49228c2c - old unused code removed
• 8d8a60a1 - unused imports removed
• 07dc75f4 - Annotator is identified by AnnotatorData class not a class string element in the model
• 07f63f1c - UserAnnotatorsParam moved
• 90f175b9 - AnnotatorParemeter is hibernate bean
• c706f87b - AnnotatorConfigParameter and UserAnnotatorsParam are merged

Compare with previous version

added 55 commits

• 8e496fb1 - serialization fix
• c76bd434 - AnnotatorParameter is included in AnnotatorData instead of UserAnnotationSchema
• aa45dab2 - nnotatorInputParameter/AnnotatorOutputParameter moved to model
• a731c0b5 - AnnotationParameters and AnnotatorData merged
• 95932a47 - performAnnotations takes UserAnnotationSchema as an argument
• abd2d7be - annotateModel takes annotationSchema as parameter
• ebda41a8 - annotating elements and reactions is done in the same loop
• 98f1e7ad - ModelAnnotator.annotateModel assumes that annotationSchema must be not null
• a001fcbf - constructor of AnnotatorData without parameters restricted to protected
• 0cfa874d - missing method renames
• 067d69b3 - UserAnnotationSchema.getAnnotatorsParams removed
• b1b49e71 - UserAnnotationSchema.addAnnotatorParam
• 2a99f277 - ModelAnnotator.getAvailableDefaultAnnotators(Class<?> clazz) changed to package private
• 5f0f29e2 - imports organized
• a63caa6c - default parameters are added to AnnotatorData when created from ElementAnnotator
• c360bc2f - disable jsbml warn logs
• ad6abe1a - api provides annotator parameters
• baa38ad6 - elementAnnotaor provides by default empty config parameters in AnnotatorData
• ee2a29cf - NPE fixed
• 4bdf678e - API import/export of annotator parameters added
• 14a2b056 - order of annotator parameters added
• 9f751bc3 - unsued method removed
• bf448ab7 - migration of the old database into new schema
• 6ebb1e16 - old table should be removed
• d6290594 - update script fixed to provide urls without doubled slashes
• 32a8581b - Sets returned via API retain order
• 7eeee314 - new mock API responses
• 521f9561 - error reporting improved
• 81fa3d10 - configuration contains new information about annotators
• 3e05b9c6 - new API responses
• 8f74234f - rest api parsing improved
• 610d62b7 - fronted adapted for the new rest api responses regarding annotators
• 7935dac6 - remove superclass annotators
• bda71e26 - provide additional info about config parameters
• ce640e7b - annotator parameters are visible and separated into three groups
• 33ff5b80 - property name includes both name and miriam type
• 275e88eb - ServerConnector is obtained from class (not global variable)
• 1ea58e93 - createAnnotatorsParams function moved to class
• 4ac803dd - add/remove annotator parameter method implemented
• 52a50bb9 - make sure that annotators data is properly saved into database
• 512acc48 - createParameterInput extracted
• 0bdb7d02 - checkbox is selected when parameter is included in the annotator
• e812c452 - on select shows annotator parameters
• 7d56a61f - value to annotator is passed as a copy of the object
• e49127ac - removing parameter fixed
• 50b44623 - definition of parameters is taken from list of available parameters
• 9d19d557 - when new annotator is selected create a copy
• 9813e5fe - tree doesn't contain reaction subclasses
• d1eb5dde - tree of elements changed into a list
• 0d05d2c6 - applying something to a subtree is no longer supported when copying annotation
• bdc0f010 - list of bioentity fields is provided via configuration
• 1a93dd88 - field common name is used
• 2db1a8c0 - when tree children are not visible send data for all children from node
• 697ff853 - configuration is retrieved within a single call
• a0b7f7a0 - description was set without respecting output field restrictions

Compare with previous version

unmarked as a Work In Progress

enabled an automatic merge when the pipeline for a0b7f7a0 succeeds

canceled the automatic merge

added 28 commits

• a0b7f7a0...2f5b7a48 - 26 commits from branch master
• 9b30d1e2 - Merge branch 'master' into 617-small-molecules-annotators-to-be-rearranged
• 7a546dca - changelog updated

Compare with previous version

enabled an automatic merge when the pipeline for 7a546dca succeeds

added 1 commit

• a3e3f6ed - unit tests fix

Compare with previous version

added 34 commits

• a3e3f6ed...3919d996 - 33 commits from branch master
• 846abbc5 - Merge remote-tracking branch 'origin/master' into 617-small-molecules-annotators-to-be-rearranged

Compare with previous version

enabled an automatic merge when the pipeline for 846abbc5 succeeds

mentioned in commit 6bd42dac

merged