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IBP-3305 geolocation reengineering#769

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mderamos wants to merge 169 commits intomasterIntegratedBreedingPlatform/Middleware:masterfrom IBP-3305-GeolocationReengineeringIntegratedBreedingPlatform/Middleware:IBP-3305-GeolocationReengineeringCopy head branch name to clipboard

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Commits on Jan 20, 2020

• Initial Liquibase scripts for Geolocation Re-engineering

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• Move trial environment builder methods from GeolocationDao to EnvironmentDao

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• Move/modify DAO methods used by StudyDataManager to Environment and EnvironmentProperty DAO classes

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• Move the remaining methods from GeolocationDao to EnvironmentDao

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Commits on Jan 21, 2020

• Remove geolocation property in ExperimentModel and reference to GeolocationDao

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• Removed reference to GeolocationDao

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• Remove unused searcher classes

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• Move Dao methods from GeolocationPropertyDao to EnvironmentPropertyDao

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• Delete GeolocationPropertyDao class. Remove unused imports

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• Merge branch 'master' into IBP-3389-GeolocationReengineeringSpike

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• Remove references to nd_geolocation and nd_geolocationprop in DmsProjectDao queries

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• Remove unused DataSetDao class

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Commits on Jan 22, 2020

• Remove references to nd_geolocation and nd_geolocationprop in DAO queries

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Commits on Jan 23, 2020

• Update references to geolocation id

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Commits on Jan 24, 2020

• Remove nd_geolocation reference from ExperimentDao queries

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• Remove nd_geolocation reference from ExperimentPropertyDao queries

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Commits on Jan 27, 2020

• Remove nd_geolocation reference from DAO queries

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• Remove nd_geolocation reference from Measurements query

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• Remove or comment out references to GeolocationDao in test classes to be able to build webapp (for dev testing purposes)

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• Fix query error in getting study details

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• Merge branch 'master' into IBP-3389-GeolocationReengineeringSpike

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• Remove remaining references to geolocation in ExperimentPropertyDao

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• Fix query error in getting study instances metadata

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• Fix query to get experiments of dataset

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Commits on Jan 28, 2020

• Remove unused code

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Commits on Jan 29, 2020

• Set experiment environment ID properly for different dataset and experiment types

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Commits on Jan 30, 2020

• Fix getting of trial instance number to retrieved experiments

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• Merge branch 'master' into IBP-3389-GeolocationReengineeringSpike

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• Move changesets to 14.2 Liquibase file

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• Remove unused code

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Commits on Feb 4, 2020

• Revise workbook saving logic to not save to nd_geolocation and nd_geolocationprop

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• Fix query error in getting study details

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• Fix logic for saving environment experiments

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• Delete GeolocationSaver class

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• Add logic to save environment variable values

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Commits on Feb 5, 2020

• Remove EnvironmentPropertySaver. Consolidate logic to save fieldmap information to ExperimentPropertySaver.

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• Remove ExperimentDestroyer class

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Commits on Feb 6, 2020

• Merge branch 'master' into IBP-3389-GeolocationReengineeringSpike

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Commits on Feb 13, 2020

• Merge branch 'IBP-3389-GeolocationReengineeringSpike' into IBP-3305-GeolocationReengineering

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Commits on Feb 17, 2020

• Rename services and queries using geolocation term and table

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• Modify Liquibase script to delete contents of nd_geolocation and nd_geolocationprop instead of dropping those tables

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• Fix query error in getting study details by environment id

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Remove unused code

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• Restore still relevant code removed before

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Commits on Feb 18, 2020

• Fix logic for adding study environment

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• Fix delete study instance query

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Commits on Feb 19, 2020

• Fix creation of trial environment experiments when saving a new study.

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• Fix syntax error in query.

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• Fix type conversion error.

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• Get the datasetId by experimentId instead of nd_geolocation_id

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Commits on Feb 20, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Used "environmentId" instead of "studyDbId" in parameters and method names

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• Fix issue with location value being set to null after saving an existing study.

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• Fix type conversion error.

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Commits on Feb 24, 2020

• Use String.valueOf to avoid cast error.

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• Fix query error

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• Fixed query

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• Removed nd_geolocation and nd_geolocation_prop references

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• Fix the error in opening a study if it has field map info.

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• Fix type conversion error.

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Commits on Feb 26, 2020

• Fix issue in saving/updating experiment property.

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

  

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• Extract back to separate statement to delete phenotype because its FK to experiments is not delete cascade

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• Fix criteria for getting environments for dataset, depending if given dataset is the environment dataset

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Commits on Feb 27, 2020

• Fix bug in saving phenotypes for environment when saving summary statistics

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• Fix query to return only the experiments with values that match the block id of specific dataset and instance.

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• Fix bug in saving means dataset experiments

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• Change logic for counting experiments of given dataset type and environment IDs

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

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Commits on Feb 28, 2020

• Fix showing of trial instance number for experiments for means dataset

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• Fix errors on queries for Head to Head comparison tool

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• Fix failing tests in CrossStudyDataManagerImplTest

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• Fix errors in queries for Multi-Trait Query tool

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• Merge branch 'IBP-3305-GeolocationReengineering' of https://github.com/IntegratedBreedingPlatform/Middleware into IBP-3305-GeolocationReengineering

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• Fix errors in queries for Multi-Trait Query tool

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• Merge branch 'IBP-3305-GeolocationReengineering' of https://github.com/IntegratedBreedingPlatform/Middleware into IBP-3305-GeolocationReengineering

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• Include means type experiment when updating its parent_id to environment experiment

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• Remove unnecessary setting of query parameter

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Commits on Mar 2, 2020

• Fix query for getting observations for samples to also work for sub-observation dataset

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• Experiment property entries (environment variables) should be created in all instances not just the first instance.

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• Fix query syntax.

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• Fixed logic checking for existing trial experiments

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• Inner Join sideId(LocationId)

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• Revert "Inner Join sideId(LocationId)"

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• Fixed query in retrieving the study details

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Commits on Mar 3, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Fix failing unit tests in StudyDataManagerImplTest.

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• Removed duplicate code

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Commits on Mar 4, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

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Commits on Mar 9, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

  

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Commits on Mar 10, 2020

• Renamed 'environment' to 'instance'

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• Renamed 'environment' to 'instance'

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• Renamed 'environment' to 'instance'

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• Renamed 'environment' to 'instance'

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• Revert "Renamed 'environment' to 'instance'"

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• Revert "Renamed 'environment' to 'instance'"

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• Revert "Renamed 'environment' to 'instance'"

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• Revert "Renamed 'environment' to 'instance'"

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Commits on Mar 13, 2020

• Fixed some failing unit tests

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• Renamed EnvironmentDao to InstanceDao

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• Removed unused method

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• Used TermId constant for 1020 value

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• Used DatasetTypeEnum for hardcoded dataset_type_id values

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• Optimize query to get phenotypes of environments of germplasm pairs

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• Fix query error

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Commits on Mar 16, 2020

• Clean up

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• Merge branch 'IBP-3305-GeolocationReengineering' of https://github.com/IntegratedBreedingPlatform/Middleware into IBP-3305-GeolocationReengineering

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Remove unused code

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• Remove redundant join condition

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• Optimize query to get environments where traits are observed

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• Merge branch 'IBP-3305-GeolocationReengineering' of https://github.com/IntegratedBreedingPlatform/Middleware into IBP-3305-GeolocationReengineering

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• Optimize queries for getting numeric, character and categorical trait information for given environment Ids for just selected trait ids.

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• Fix compile errors in test classes

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• Optimize query for getting observations of selected traits on selected environments

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• Fix select clause to get correct environment ID

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Commits on Mar 17, 2020

• Adjust query recently merged for BrAPI get and count Studies

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• Fix logic to count stocks of an environment, dataset and trait

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Commits on Mar 18, 2020

• Fix query error

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

  

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

  

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• Fixed failing tests

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• Fixed failing tests

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• Fixed failing unit test

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• Fixed unit tests

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Commits on Mar 19, 2020

• Fixed failing unit tests

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Commits on Mar 20, 2020

• Fixed failing unit test

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• Removed logging

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• Fixed failing unit tests and removed unused methods

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• Removed unused methods and attributes

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• Fixed failing unit test

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Commits on Mar 22, 2020

• Fixed failing unit tests

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• Fixed failing unit tests

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• Fixed failing unit tests

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Commits on Mar 23, 2020

• Fixed query

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Commits on Mar 24, 2020

• Move Geolocation Re-engineering changesets to 14.3 Liquibase file

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• Create index for nd_experiment.parent_id

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• Removed 14_2_0 file from crop_master.xml

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• Make proper join to environment for all dataset types (trial environment, plot or sub-observation)

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• Merge branch 'IBP-3305-GeolocationReengineering' of https://github.com/IntegratedBreedingPlatform/Middleware into IBP-3305-GeolocationReengineering

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• Correct the join to environment experiment when getting experiments of a dataset

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• Remove unnecessary joins in the query to improve performance.

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• Implement services to check if dataset ID is valid and if a dataset ID belongs to study. These can be used for validation instead of the heavy getDatasets method.

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Commits on Mar 25, 2020

• Fix query to return only the number of instances with observation units.

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• Fix issue in sub-observation batch action update.

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• Corrected query to properly get the phenotype of a specified dataset and instance.

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• Added DatasetBasicDTO

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Commits on Mar 26, 2020

• Added getDatasetBasicDTOs method

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

  

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Commits on Mar 27, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Optimized subquery for getting if environment can be deleted or has measurements.

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• Optimized query for loading observation units by not joining to environment experiment. Since the query works for plot and sub-obs level, it is the join to environment experiment that causes slow p…

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• Fix compile error

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• Fix TRIAL_INSTANCE select clause

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• Fix TRIAL_INSTANCE data type

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Commits on Apr 6, 2020

• Merge branch 'master' into IBP-3305-GeolocationReengineering

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• Add back the join to environment experiment row to fix the filtering by trial instance number issue

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• Remove creation of index on nd_experiment.parent_id

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Commits on Apr 8, 2020

• Optimize query for getting dataset instances by only getting environment metadata related to experimental design only if the dataset is the environment dataset

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Commits on Apr 14, 2020

• Merge branch 'master' of https://github.com/IntegratedBreedingPlatform/Middleware

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• Optimize the detached criteria for getting environments in dataset

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Commits on Apr 15, 2020

• Fix query error introduced by recent merge of master code

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Commits on Apr 16, 2020

• Optimize queries for getting/counting observation units by considering if dataset type is sub-observation dataset

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• Set flag whether dataset is subobservation dataset to prevent NPE in ObservationUnitSearchDao usage

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• Fix query error when retrieving environment dataset instances

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Commits on Apr 21, 2020

• Optimize query for checking if dataset instance has at least 2 germplasm entries with observed value that could be used for BV analysis

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• Optimized queries design to work for both plot and sub-obs datasets to pass if flag dataset is sub-observation dataset

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• Merge branch 'master' into IBP-3305-GeolocationReengineering

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