Resolve "rewrite API"

Closes #1594 (closed), #846 (closed)

changed milestone to %v17.0.0~beta.0

added enhancement backward incompatible labels

assigned to @piotr.gawron

added 32 commits

• 06057466...ea3500da - 26 commits from branch master
• 2c6aadb4 - Merge branch...
• c12d2101 - use new serializers in new API
• b12d786f - provide ETag with response
• 59705212 - remove old unused code
• e1045847 - irun all web tests
• 20fb2719 - data structure for storing edit actions

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added 3 commits

• 50063e9e - don't store history in db
• c77b930b - exception handler extracted to Advice
• 76e65d7d - additional tests

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added 42 commits

• 76e65d7d...7c854fcb - 32 commits from branch master
• c811054f - create project endpoint
• 2135d9ce - update project endpoint implemented
• 45b3b684 - Merge branch '1626-all-multiple-threaded-jobs-should-use-single-queue' into 1594-rewrite-api
• 0c23c7e8 - delete project method in new API implemented
• 1341bd45 - test etag validation
• 2ccee027 - provide info about top map when serializing
• f0979372 - dao method to list with filtering and pageable
• 896839da - method that allows list project in new API
• 5416608c - decorator for adding information about project shared in minervanet
• f7aa970c - project status cannot be null

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added 18 commits

• 7e3fa84c - put project specific classes into separate package
• c4c411e8 - get project disease endpoint
• 864be167 - create disease endpoint
• 327319ab - endpoint for creating disease
• 094f44e3 - update project disease
• 6323dddf - API endpoint for delete disease
• 5d0c5229 - CRUD endpoints for organism
• f2b28639 - filtering by log entry property implemented
• bb5d68b9 - sorting implemented
• 296d00c2 - sorting by all columns implemented
• 2e6c9fa0 - get logs endpoint added in the new API
• 292042cf - api endpoint for listing overview images
• 3fd93cb1 - properties moved to dao
• aab66803 - add version column to entities
• 227d1981 - extract common filtering and sorting functionality
• 33a789a6 - unused fields removed
• dee40d0f - list of glphs provided in new api
• 66fd34a2 - API endpoint for changing topMap implemented

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added 2 commits

• 93516bd7 - missing change added
• 410062be - checkstyle issues

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added 1 commit

• d753d58c - bug when downloading genome

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added 8 commits

• d753d58c...2a51b679 - 4 commits from branch master
• cad671ad - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api
• e25f39c9 - add missing db changes
• 2d77ead2 - ignore entity version when serializing
• aebee17d - fix tests

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added 7 commits

• 58dc773a - stub implementation of new map endpoints
• 01479b43 - api endpoint allowing removing modeldata
• 612adc2f - list maps implemented
• 253a0d44 - create map endpoint implemented
• 14815a0e - unused field removed
• 43179aea - add migration script to postgres
• 54fa23b4 - missing migration script added

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added 7 commits

• 4f13d3e1 - assing creation date on map create
• 930eab90 - stub imlementation of author API endpoints
• c6781c74 - update author implemented
• 46121ee4 - get author endpoint implemented
• b0e40634 - listing authors implemented
• 3fe6aa0f - delete author implemented
• 549215b7 - create author implemented

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added 1 commit

• 8b42e70d - unused imports removed

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added 1 commit

• 778908cd - missing migration script for postgres

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added 1 commit

• 20ef919e - list of authors is an array not a flat object

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added 1 commit

• ac3c675b - api endpoints for mokdel references

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added 2 commits

• 3d576470 - unit api endpoints implemented
• 272dd4fd - checkstyle issues

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added 1 commit

• ef7394e6 - old checkstyle comments removed

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added 5 commits

• ab968f56 - CRUD endpoints for parameters implemented
• d91cbc80 - CRUD API call for functions implemented
• 299a3f2f - unit test is not necessary
• 85d35d46 - fix unit tests
• c1cca0cd - include class in the test collection

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changed the description

added 10 commits

• 2de6c4fe - stub of elements CRUD functionalities
• b65e9a4f - improve element serialization
• ddc59d87 - allow to create element
• 4ae7382b - allow to delete element
• adddca87 - serialization issue when returning element
• a11f8300 - update element implemented
• be7215ce - unit test fixed
• bec0ca69 - fix complex element serialization
• e6eedb49 - allow to create compartments
• eaec2afb - include test in the suit

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added 2 commits

• d157a0ef - PI endpoints for element synonyms
• f4031a60 - checkstyle issues

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added 17 commits

• f4031a60...948129af - 4 commits from branch master
• 15769659 - former symbols API endpoints
• 24ddb9fb - CRUD endpoints for element references
• 3600e424 - API endpoint for listing element children
• 7b8307a2 - rename functions
• 2440fe53 - element-complex endpoints implemented
• 60cafc2e - unused field removed
• a1af2daf - element-compartment API endpoints implemented
• 83ec8bf6 - API endpoints for editing element glyph
• d7678e08 - Merge branch 'sbml-unit-type-as-unit' into 1594-rewrite-api
• e3c50f87 - endpoint for accessing modifying species unit
• b13f6ad4 - ArticleDao uses generi Property filtering
• 4dfa028e - getCount by filter extracted to separate method
• 8fa20e2b - we don't need to fetch missing because they are fetched in the background

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added 3 commits

• c1163566 - make sure that we join by pubmed ids
• b737116b - don't use generic lists
• 58010198 - checkstyle issues

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added 11 commits

• 5f554145 - use class specific generics
• f4b11dc9 - ReactionProperty is alligned with other MinervaProperty search functionlaities
• 00954f04 - old unused code removed
• b3749bce - filter by participantId added
• f50d2cd5 - redundant method removed
• 5f46f3f6 - unit tests for author dao
• d54d1cbf - getById replaced by filtering
• 6c081dae - tests for glyph dao
• dc1783eb - unify functionDao with other search interfaces
• eebf175e - unused override method
• 99ac9c25 - unused method removed

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added 19 commits

• 136553e5 - extract CrudInterface for servic
• c1ce4954 - GlyphService extends CRUD
• 9baaaa20 - ModelService implements CRUD interface
• f01b44bc - overviewImage implements CRUD interface
• 3eacebad - projectService implements CRUD interface
• 52fa4440 - publicationService implement CRUD interface
• e398eeac - reactionService implements CRUD interface
• 3640612b - sbmlFunctionService implements CRUD interface
• 0a6476da - CRUD interface contains getCount
• 46fc429f - crud interface should contain add method
• 5a018de2 - text search does not return reaction by id
• 92c12d4d - don't delete unit when deleting element
• 06373644 - use new interface
• ecd9102d - don't allow to remove unit when it's in use
• 97b23551 - don't allow to remove top map
• 3b961882 - bug in new function service
• 568873f9 - fetch article for tests
• 5eca78a0 - unit name is optional
• ad895b70 - make sure that modelId match integer id or "*"

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added 6 commits

• 4cd39826 - unit function moved to UnitService from ModelService
• 8d78b64e - generic filtering for SbmlParameter implemented
• 19ebc47e - list parameters moved from ModelService into ParametersService
• caccb2b9 - unused method removed
• 2e39732e - unused method removed
• ed74e24b - remove getModelByProjcectId

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added 9 commits

• e81d1780 - stub endpoints for creating new reactions
• c6cfe1b8 - remove reaction implemented
• 96f9a38d - reaction creation implemented
• 0b6d1f99 - update reaction
• 53f6e95f - abstractDTO introduced
• a70d4629 - reorganize tests
• ec1e2fbe - fix unit test
• 334d142a - tests checking synonyms endpoint
• fac3aedb - API endpoint for reaction line

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added 1 commit

• 8318a9ad - checkstyle issues

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added 1 commit

• 8f6a2135 - old invalid tests removed

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added 17 commits

• 1cd560be - apin endopoints for reaction references
• b654f09d - CRUD functionalities for reactants
• 548ec633 - CRUD functionality for reactant line
• 32d92dcd - CRUD functionalities for reactant element
• 3a95cdf0 - filtering works also with reaction parameters
• 1e5488dd - typo
• f2314537 - parameters search should be done in dao and filter by map list only when list is not empty
• 1782ab22 - validate modelId in comment rest api
• d1d400a2 - search with invalid project id returned too much data
• f70184ea - suggested query list had problem wwith invalid projectId
• b33a1544 - simplify query for element statistics
• 9bdbc67f - return empty page for unknown project
• 14ebac06 - always validate modelId
• cdcb5b2c - simplify getting publication statistics
• 630857f0 - unit tests fixed after api changed
• 793d3d32 - validate ids
• 37a50e0c - check if statistics are empty for invalid project

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added 1 commit

• a9339ad3 - checkstyle issus

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added 1 commit

• 16c3e316 - silence some debug info

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added 77 commits

• 16c3e316...e4b8309e - 76 commits from branch master
• 964d8182 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api

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added 7 commits

• 964d8182...d097c7e3 - 3 commits from branch master
• f7896426 - product crud functionality implemented
• 8164fbbe - stub for creating modifiers over API
• d7f1a468 - Merge branch 'reactant-product-must-have-element-in-constructor' into 1594-rewrite-api
• cdff128f - create reactant/product/modifier properly

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added 78 commits

• cdff128f...acf5d07d - 77 commits from branch master
• b1572954 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api

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added 7 commits

• b1572954...cf97419e - 4 commits from branch master
• e1017354 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api
• 8e26b69d - handle situation when unit name is null
• c0a76aef - adjust unit test to new test data

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added 1 commit

• 9df6abc0 - checkstyle issues

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added 27 commits

• 9df6abc0...2869a8c5 - 14 commits from branch master
• f32f6063 - don't suppress warning that is not needed
• 55eaf28f - don't create extra mock class
• e6d46768 - provide sbo term mapping for operators
• 81e6f8d9 - remove suppression of warning that does not exist
• a13f589b - first attempt for operators API endpoint
• cdaa64c3 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api
• bd1144f2 - fix problem with removing operator
• 06f1665f - api endpoints for modyfing operator line
• 3c6729c2 - api endopoints for oprator inputs
• 077f9ccf - API endpoints for operator outputs
• 55e0cc7b - error response should be a json
• 72cf16da - filter by element id did not work
• 063b383c - provide sboTerm for every Element

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added 4 commits

• e6aecef1 - redundant loggers removed
• 25954cc3 - fix on disable CORS
• 4f73d35a - fix error handler
• 8ae9f8ae - color deserialization implemented

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added 1 commit

• a61d15a8 - height was not updated properly

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added 40 commits

• a61d15a8...9f399693 - 37 commits from branch master
• 1186a896 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api
• 9503cd21 - fix search by reaction_id
• 9f689763 - fix unit tests and logic for removal

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added 2 commits

• 337ffcd6 - fix unit test
• f37b1193 - ElementDao uses search by criteria

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added 1 commit

• 3062f364 - sorting by article columns implemented

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added 3 commits

• 2ac3f650 - filter by compartment_id implemented
• 75be6bed - filtering by complex id implemented
• b0dec521 - dont filter by ids if we don't have ids

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added 50 commits

• b0dec521...e11fae10 - 49 commits from branch master
• eed3dca2 - Merge remote-tracking branch 'origin/master' into 1594-rewrite-api

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added 992 commits

• eed3dca2...f46b3be7 - 917 commits from branch master
• f46b3be7...9c50c32a - 65 earlier commits
• 9eb51f70 - list of comments if empty if map id does not match project id
• ca5fa567 - throw unsupported media type if provided type is invalid
• af87add3 - constructor without parameters
• e5d375f4 - return proper status code when object does not exist
• 11bb17ba - when there is a problem with mapping path paramteres return 400
• a360368f - fix user tests
• b34eb88c - fetch info about articles when uploading project
• 43f75eb0 - set class list only when it's not empty
• f440ad39 - setup test properly
• af780fc4 - converter returns one problem

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added 1 commit

• 39539a70 - checkstyle issues

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added 28 commits

• 39539a70...eaf05459 - 7 commits from branch master
• eaf05459...98b93af2 - 11 earlier commits
• 7ddceb9a - Merge remote-tracking branch 'origin/devel_17.1.x' into 1594-rewrite-api
• 2d2142cd - /new_api => /minerva/new_api
• 85613806 - stub mapping between modification residue and SBO term
• 5002b1c7 - tests for mapping
• d813f252 - mapping contains proper class names
• f9215d17 - missing constructores added
• a1a85e69 - test are more verbose
• f1fe3101 - modificartion residue has entity version
• ec7add4e - provide info about SBO term
• 78ba570e - basic endpoint for providing serialized object for modificatin residue

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added 35 commits

• 78ba570e...d0430618 - 34 commits from branch master
• 17e64863 - Merge branch '2029-orcid-user-should-inherit-access-privs-from-anonymous' into 1594-rewrite-api

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