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SAK-32101 Assignments service refactor (#4712)

* SAK-32101 refactor PeerAssessment to use JPA

* SAK-32101 rename Assignment in edu service to GradebookAssignment

* SAK-32101 Persistence mostly completed

* SAK-32101 Add JSON/XML serialization to persistence

* SAK-32101 AssignmentService

* SAK-32101 AssignmentService 2

* Adapted service and persistence entities to work with existing services.

* AssignmentService Unit Tests setup with Repository

* More additions to assignment service

* Lots of new stuff but mostly Reference Reckoner.

* updated test

* remove assignmentReferenceUtil and use AssignmentReferenceReckoner

* Add test for removing assignments

* remove BaseAssignmentService after rebase

* updateAssigment test

* addSubmission implemented with test

* Rearrange persistence class inheritance

* Added removeSubmission and tests

* flush session after merge

* minor change

* updated persistence methods

* finished adding remaining methods to service

* AssignmentAction refactor part duo

* AssignmentsAction refactor part 3

* AssignmentAction refactor completed

* More AssignmentsAction refactor

* AssignmentAction builds

* Refactor around sakai in relation to AssignmentsService

* Assignment template fixes part 1

* More template fixes and content review added back

* Few more refactors after sync with master

* Rearrange project structure

* ReFormatting

* Code refactor

* AssignmentAction and template fixes

* Fixed hideduedate, modified dates, author is populated

* Reformatting

* Assignment to GradebookAssignment refactor

* Assignment to GradebookAssignment refactor 2

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    ./CombineDuplicateSubmissionsConversionHandler.java
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    ./RemoveDuplicateSubmissionsConversionHandler.java
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    ./SAXSerializablePropertiesAccess.java
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    ./SubmitterIdAssignmentsConversionHandler.java
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SAK-29791 Remove covers from assignments. (#3437)

* SAK-29791 Remove covers from /assignment

This highlights that there were some differences between the API and cover as the exceptions were different.

Updated message bundle for assignments.

Validate our dependencies in init()

Make sure we have all the services we need.

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SAK-30828 Normalize logging for 11.x (#3346)

* SAK-30828 Normalize sakai logging

- remove commons-logging (jcl)

- add logging to those projects where it was removed

- convert System.out to log messages in many projects

- add jcl-over-slf4j lib

- update many dependencies to inherit from master

- update logging for tests

- add lombok to global dependency (@Slf4j)

Conflicts:

basiclti/tsugi-util/pom-tsugi.xml

content-review/impl/dao/pom.xml

content-review/impl/turnitin/pom.xml

content-review/pom.xml

entitybroker/utils/pom.xml

gradebookng/tool/src/java/org/sakaiproject/gradebookng/business/util/Temp.java

gradebookng/tool/src/java/org/sakaiproject/gradebookng/tool/pages/BasePage.java

gradebookng/tool/src/java/org/sakaiproject/gradebookng/tool/panels/importExport/CreateGradeItemStep.java

gradebookng/tool/src/java/org/sakaiproject/gradebookng/tool/panels/importExport/GradeImportConfirmationStep.java

gradebookng/tool/src/java/org/sakaiproject/gradebookng/tool/panels/importExport/GradeImportUploadStep.java

gradebookng/tool/src/java/org/sakaiproject/gradebookng/tool/panels/importExport/GradeItemImportSelectionStep.java

* SAK-30828 switch log4j logging to slf4j

* SAK-30828 switch jcl logging to slf4j

Conflicts:

assignment/assignment-impl/impl/src/java/org/sakaiproject/assignment/impl/BaseAssignmentService.java

assignment/assignment-impl/impl/src/java/org/sakaiproject/assignment/impl/DbAssignmentService.java

basiclti/basiclti-impl/src/java/org/sakaiproject/lti/impl/LTIReportingJob.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/util/TurnitinAPIUtil.java

kernel/kernel-impl/src/main/java/org/sakaiproject/event/impl/BaseLearningResourceStoreService.java

lessonbuilder/tool/src/java/org/sakaiproject/lessonbuildertool/tool/beans/SimplePageBean.java

portal/portal-impl/impl/src/java/org/sakaiproject/portal/charon/handlers/GenerateBugReportHandler.java

samigo/samigo-app/src/java/org/sakaiproject/tool/assessment/ui/listener/evaluation/QuestionScoreListener.java

samigo/samigo-app/src/java/org/sakaiproject/tool/assessment/ui/listener/questionpool/PoolSaveListener.java

signup/impl/src/java/org/sakaiproject/signup/logic/SignupMeetingServiceImpl.java

syllabus/syllabus-impl/src/java/org/sakaiproject/component/app/syllabus/SyllabusServiceImpl.java

* SAK-30828 slf4j-log4j12 binding should be provided

* SAK-30828 Lombok @CommonsLog migrated to @Slf4j

Conflicts:

content-review/impl/dao/src/test/java/org/sakaiproject/contentreview/dao/ContentReviewDaoImplTest.java

content-review/impl/service/src/main/java/org/sakaiproject/contentreview/service/ContentReviewFederatedServiceImpl.java

content-review/impl/service/src/main/java/org/sakaiproject/contentreview/service/ContentReviewQueueServiceImpl.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/TurnitinAccountConnection.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/TurnitinContentValidator.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/TurnitinReviewServiceImpl.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/TurnitinSessionFuncs.java

content-review/impl/turnitin/src/main/java/org/sakaiproject/contentreview/turnitin/util/TurnitinAPIUtil.java

content-review/impl/vericite/src/main/java/org/sakaiproject/contentreview/vericite/ContentReviewServiceVeriCite.java

* SAK-30828 content-review slf4j conversion

* SAK-31420 Issue with import from site not working due to logger serialization (#3169)

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SAK-30828 switch jcl logging to slf4j

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SAK-30233 - Regression after SAK-30087 on old assignment submissions

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SAK-30087 & SAK-29824 - Clean up redundant attributes from submission.

Would also fix the bug with this being invalid and not maching in

assignment xml

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SAK-29406 Allow Assignment tool to grade with two decimal points

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SAK-25660 Peer Review: Instructor given grades gets wiped out if peer review is deleted or restored

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@133971 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-22436 Patch to support grade overrides for Group Submissions Original patch from Joseph Conder (Duke), mods by AZ (Unicon)

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@120595 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-22282 adding support for group submissions to the assignments tool Patch from Joseph Conder (Duke), cleanup and fixes by AZ (Unicon)

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@110665 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-21097 and SAK-21839 correct the common-lang3 package to old commons-lang package

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@105182 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-21839 update license header to re-point to opensource.org

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@105078 66ffb92e-73f9-0310-93c1-f5514f145a0a

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KNL-863 Fixing this to no longer use the utils copy of commons codec but instead to actually use commons codec directly

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@101746 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-19406

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@84106 66ffb92e-73f9-0310-93c1-f5514f145a0a

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NOJIRA code cleanup, use ArrayList instead of Vector, use apache commons StringUtils instead of Sakai StringUtil to trim String, etc.

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@77106 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-17633

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@70887 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-17628

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@70863 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-15589 update copyright years

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@59673 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-15907:assignment runconversion.sh contains out-of-date references to kernel and Tomcat: removed more redundant conversion impl files and a no-longer needed runconversion-2.4.x.sh script file

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@59054 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-15907:assignment runconversion.sh contains out-of-date references to kernel and Tomcat

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@59041 66ffb92e-73f9-0310-93c1-f5514f145a0a

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http://bugs.sakaiproject.org/jira/browse/SAK-14386 NO 228: http://qa1-nl.sakaiproject.org/codereview/trunk/api/org/sakaiproject/assignment/impl/conversion/impl/UpgradeSchema.java.html#86

85 File f = new File(config);

86 FileInputStream fin = new FileInputStream(config);

87 p.load(fin);

88 fin.close();

89

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@52599 66ffb92e-73f9-0310-93c1-f5514f145a0a

fix to SAK-14368:ASSIGNMENT_SUBMISSION conversion script does not work for mysql 4.1.22

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@52127 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-12938

Fix non-printing characters in copyright.

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@51318 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-12938

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@50147 66ffb92e-73f9-0310-93c1-f5514f145a0a

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SAK-12938

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@50068 66ffb92e-73f9-0310-93c1-f5514f145a0a

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log message for empty catch block for Alen Berg static code review

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@47255 66ffb92e-73f9-0310-93c1-f5514f145a0a

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update the content of assignment conversion to the latest version of that in post-2-4 branch

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@40117 66ffb92e-73f9-0310-93c1-f5514f145a0a

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fix to SAK-12289, remove the unnecessary checkins made in 38927

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@38928 66ffb92e-73f9-0310-93c1-f5514f145a0a

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merge fix to SAK-12289 into trunk:svn merge -r 38925:38926 https://source.sakaiproject.org/svn/assignment/branches/post-2-4/

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@38927 66ffb92e-73f9-0310-93c1-f5514f145a0a

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fix to SAK-12208:Assignment conversion needs to create indexed tables: use the ability to excuete mulitple queries to add indices after table creation and add unique index to assignment_submission as the last step of conversion

git-svn-id: https://source.sakaiproject.org/svn/assignment/trunk@38490 66ffb92e-73f9-0310-93c1-f5514f145a0a

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