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Changelog

This project adheres to Semantic Versioning.

2.15.0 (2022-01-24)

Added

  • Add displayName to life.qbic.datamodel.samples.Status (#282)

Fixed

Dependencies

Deprecated

2.14.4 (2022-01-04)

Added

Fixed

  • CVE-2021-44832

Dependencies

  • Bump org.apache.logging.log4j:log4j-api from 2.17.0 to 2.17.1
  • Bump org.apache.logging.log4j:log4j-core from 2.17.0 to 2.17.1

Deprecated

2.14.3 (2021-12-20)

Added

Fixed

  • CVE-2021-45105

Dependencies

  • Bump org.apache.logging.log4j:log4j-api from 2.16.0 to 2.17.0
  • Bump org.apache.logging.log4j:log4j-core from 2.16.0 to 2.17.0

Deprecated

2.14.2 (2021-12-16)

Added

Fixed

  • CVE-2021-45046

Dependencies

  • org.codehaus.groovy:groovy-bom:2.5.10 -> 2.5.14
  • org.codehaus.groovy:groovy-all:2.5.10 -> 2.5.14
  • org.osgi:osgi.core:7.0.0 -> 8.0.0
  • com.github.everit-org.json-schema:org.everit.json.schema:1.12.1 -> 1.12.2
  • org.apache.logging.log4j:log4j-api:2.15.0 -> 2.16.0 (CVE-2021-45046)
  • org.apache.logging.log4j:log4j-core:2.15.0 -> 2.16.0 (CVE-2021-45046)
  • maven-surefire-plugin:2.21.0 -> 2.22.2
  • org.codehaus.gmavenplus:gmavenplus-plugin:1.12.0 -> 1.12.1
  • org.apache.maven.plugins:maven-site-plugin:3.7.1 -> 3.9.1
  • org.apache.maven.plugins:maven-project-info-reports-plugin:3.0.0 -> 3.1.1

Deprecated

2.14.1 (2021-12-13)

Added

Fixed

Dependencies

  • org.apache.logging.log4j 2.13.2 -> 2.15.0 (addresses CVE-2021-44228)

Deprecated

2.14.0 (2021-10-27)

Added

  • Added String representing product abbreviation to ProductCategory Enum (#266)
  • ProductId now provides 'From' method to be created via String representation (#264)

Fixed

Dependencies

Deprecated

  • life.qbic.datamodel.dtos.business.services.ProductType.groovy. The abbreviation is now accessible via the abbreviation property in life.qbic.datamodel.dtos.business.ProductCategory (#266)

2.13.0 (2021-10-13)

Added

  • Added new product type life.qbic.datamodel.dtos.business.services.ExternalServiceProduct (#262)
  • Added new Facility enum CEGAT in life.qbic.datamodel.dtos.business.facilities.Facility (#262)
  • Added new product type EXTERNAL_SERVICE for life.qbic.datamodel.dtos.business.ProductCategory (#262)

Fixed

Dependencies

Deprecated

2.12.1 (2021-09-13)

Added

Fixed

  • NPE when comparing life.qbic.datamodel.dtos.projectmanagement.ProjectIdentifier to null reference (#258)

Dependencies

Deprecated

2.12.0 (2021-09-10)

Added

  • Add life.qbic.datamodel.validation.* for project code validation. (#254)
  • life.qbic.datamodel.dtos.business.facilities.Facility can provide a shorthand label now (#255)

Fixed

Dependencies

Deprecated

2.11.0 (2021-08-03)

Added

  • A new enumeration for facilities life.qbic.datamodel.dtos.business.facilities.Facility (#244)
  • New properties internalUnitPrice, externalUnitPrice and serviceProvider for the life.qbic.datamodel.dtos.business.services.Product and its derivatives (#245)
  • New properties totalPrice and totalDiscountPrice for the life.qbic.datamodel.dtos.business.ProductItem and totalDiscountPrice for the life.qbic.datamodel.dtos.business.Offer
  • A life.qbic.datamodel.dtos.business.facilities.FacilityFactory to get the facility for a given string representation (#247)

Fixed

  • ProjectSpace names are now validated (#249)

Dependencies

Deprecated

  • The unitPrice property in life.qbic.datamodel.dtos.business.services.Product

2.10.0 (2021-07-19)

Added

  • Provide new classes that describe incoming MaxQuant data structure (#237)
  • Provide dedicated data structure life.qbic.datamodel.datasets.MaxQuantRunResult.groovy` for grouping maxQuant run data structure (#239)
  • Introduce Json schema maxquant-result-set.schema for validating a provided maxQuant dataset (#238)
  • Introduce life.qbic.datamodel.maxquant.MaxQuantOutput.groovy that provides access to the maxQuant JSON schema (#238)
  • Add MaxQuant Dataset Information to the Readme (#241)
  • Provide overviews in Readme and link javadocs (#230)

Fixed

  • Override equals() for life.qbic.datamodel.dtos.projectmanagement.Project and life.qbic.datamodel.dtos.projectmanagement.ProjectIdentifier (#236)

Dependencies

  • Replace life.qbic.datamodel.datasets.datastructure.files.nfcore.SampleIds.groovy with life.qbic.datamodel.datasets.datastructure.files.general.SampleIds.groovy (#239)

Deprecated

2.9.0 (2021-07-06)

Added

  • A new class life.qbic.datamodel.dtos.portal.PortalUser that represents a user within QBiC's data management platform. (#229)

Fixed

Dependencies

Deprecated

2.8.2 (2021-06-15)

Added

  • Add new product unit type PER_BATCH("Batch") to life.qbic.datamodel.dtos.business.services.ProductUnit (#223)

Fixed

Dependencies

Deprecated

2.8.1 (2021-06-14)

Added

  • Add new product unit type PER_FLOW_CELL("Flow Cell") to life.qbic.datamodel.dtos.business.services.ProductUnit (#221)

Fixed

Dependencies

Deprecated

2.8.0 (2021-06-07)

Added

  • Add new product unit types to life.qbic.datamodel.dtos.business.services.ProductUnit (#215)
    • PER_HOUR("Hour"),
    • PER_PROJECT("Project"),
    • PER_RUN("Run"),
    • PER_CYCLE("Cycle"),
    • PER_GEL("Gel/HpH"),
    • PER_10_MG("10 milligram"),
    • PER_MEASUREMENT("Measurement"),
    • PER_CHANNEL("Channel"),
    • PER_100_MICROGRAM_PEPTIDE_CHANNEL("100 microgram peptides channel"),
    • PER_500_ML("500 milliliter"),
    • PER_COMPARISON("Comparison")

Fixed

Dependencies

Deprecated

2.7.0 (2021-05-21)

Added

  • Make life.qbic.datamodel.dtos.business.ProductId comparable (#211)
  • Add file extensions to names in Json examples (#204)

Fixed

  • Remove @CompileStatic annotation from ProductId to enable builder pattern usage during compilation (#186)
  • Unspecified files will be ignored while creating the NfCorePipelineResult Object (#212)

Dependencies

Deprecated

2.6.1 (2021-05-12)

Added

Fixed

  • add missing leading slash to toString() method in life/qbic/datamodel/dtos/projectmanagement/ProjectIdentifier.groovy (#207)

Dependencies

Deprecated

2.6.0 (2021-05-10)

Added

  • Add json schema and wrapper for imaging data life.qbic.datamodel.datasets.imaging.ImageMetadata (#199)
  • Provide new classes that describe incoming nf-core bioinformatic pipeline data structures and contains it in a dedicated NfCorePipelineResult class (#198)

Fixed

Dependencies

Deprecated

2.5.0 (2021-04-26)

Added

  • New constructor using the new life.qbic.datamodel.dtos.business.ProductId constructor for life.qbic.datamodel.dtos.business.services.Sequencing, life.qbic.datamodel.dtos.business.services.SecondaryAnalysis, life.qbic.datamodel.dtos.business.services.ProteomicAnalysis, life.qbic.datamodel.dtos.business.services.ProjectManagement, life.qbic.datamodel.dtos.business.services.PrimaryAnalysis, life.qbic.datamodel.dtos.business.services.MetabolomicAnalysis, life.qbic.datamodel.dtos.business.services.DataStorage
  • Add Tests for life.qbic.datamodel.dtos.business.services.ProductUnitFactory#getForString(java.lang.String) (#190)
  • New EnumFactory life.qbic.datamodel.dtos.business.ProductCategoryFactory (#192)
  • New property experimentalDesign for life.qbic.datamodel.dtos.business.Offer
  • Introduce new Enum life.qbic.datamodel.dtos.business.AffiliationLabel and new EnumFactory life.qbic.datamodel.dtos.business.AffiliationLabelFactory (#194)

Fixed

  • Override equals() method for life.qbic.datamodel.dtos.business.OfferId and life.qbic.datamodel.dtos.business.TomatoId properly
  • Override equals() method for life.qbic.datamodel.dtos.business.ProductId properly

Dependencies

Deprecated

  • Constructor using the deprecated life.qbic.datamodel.dtos.business.ProductId constructor for life.qbic.datamodel.dtos.business.services.Sequencing, life.qbic.datamodel.dtos.business.services.SecondaryAnalysis, life.qbic.datamodel.dtos.business.services.ProteomicAnalysis, life.qbic.datamodel.dtos.business.services.ProjectManagement, life.qbic.datamodel.dtos.business.services.PrimaryAnalysis, life.qbic.datamodel.dtos.business.services.MetabolomicAnalysis, life.qbic.datamodel.dtos.business.services.DataStorage
  • Removed Deprecation for life.qbic.datamodel.people.*

2.4.0 (2021-03-18)

Added

  • Added life.qbic.datamodel.samples.Status.SAMPLE_RECEIVED, life.qbic.datamodel.samples.Status.LIBRARY_PREP_FINISHED, life.qbic.datamodel.samples.Status.DATA_AVAILABLE sample statuses (#177)
  • Added schema for sample entity codes (species/patient level) to life.qbic.datamodel.identifiers.SampleCodeFunctions (#180)
  • Added optional property associatedProject to life.qbic.datamodel.dtos.business.Offer (#179)
  • Added life.qbic.datamodel.dtos.business.ProductCategory.PROTEOMIC, life.qbic.datamodel.dtos.business.ProductCategory.METABOLOMIC product categories (#181)
  • Added life.qbic.datamodel.dtos.business.services.ProductType.PROTEOMIC, life.qbic.datamodel.dtos.business.services.ProductType.METABOLOMIC product types (#181)
  • Introduce life.qbic.datamodel.dtos.business.services.ProteomicAnalysis, life.qbic.datamodel.dtos.business.services.MetabolomicAnalysis atomic products (#181)

Fixed

  • Equals method is now properly overridden for life.qbic.datamodel.dtos.business.ProductId (#182)
  • Correctly name and use respective sample code schemata for codes with check digits and entity codes (e.g. QABCDENTITY-2) (#180)

Dependencies

Deprecated

  • Deprecated life.qbic.datamodel.identifiers.SampleCodeFunctions#QBIC_SAMPLE_ID_SCHEMA, please use life.qbic.datamodel.identifiers.SampleCodeFunctions#QBIC_SAMPLE_BARCODE_SCHEMA (#180)
  • Deprecated life.qbic.datamodel.samples.Status.DATA_AT_QBIC, please use life.qbic.datamodel.samples.Status.DATA_AVAILABLE (#180)

2.3.0 (2021-03-16)

Added

  • overheadRatio property for life.qbic.datamodel.dtos.business.Offer
  • life.qbic.datamodel.dtos.projectmanagement.ProjectIdentifier, life.qbic.datamodel.dtos.projectmanagement.ProjectCode, life.qbic.datamodel.dtos.projectmanagement.ProjectSpace and life.qbic.datamodel.dtos.projectmanagement.Project to describe QBiC projects
  • life.qbic.datamodel.dtos.business.ProjectApplication to describe a project application for registration at QBiC's data management platform
  • Added uniqueId field to life.qbic.datamodel.dtos.business.ProductId (#173)
  • Add Hour life.qbic.datamodel.dtos.business.services.ProductUnit.PER_HOUR (#175)

Fixed

Dependencies

Deprecated

  • life.qbic.datamodel.dtos.business.ProductId#identifier is replaced by life.qbic.datamodel.dtos.business.ProductId#uniqueId (#173)

2.2.0 (2021-03-02)

Added

  • Checksum property for life.qbic.datamodel.dtos.business.Offer

Fixed

Dependencies

Deprecated

2.1.0 (2021-02-24)

Added

  • Introduce a schema resource for bioinformatic pipeline result sets validation via life.qbic.datamodel.pipelines.PipelineOutput (#159)
  • Add field life.qbic.datamodel.dtos.business.Offer#projectObjective, will replace life.qbic.datamodel.dtos.business.Offer#projectDescription (#161)
  • Add fields life.qbic.datamodel.dtos.business.Offer#itemsWithOverhead, life.qbic.datamodel.dtos.business.Offer#itemsWithoutOverhead, life.qbic.datamodel.dtos.business.Offer#itemsWithOverheadNetPrice and life.qbic.datamodel.dtos.business.Offer#itemsWithoutOverheadNetPrice to Offer DTO (#160)

Fixed

Dependencies

Deprecated

  • life.qbic.datamodel.dtos.business.Offer#projectDescription, replaced with life.qbic.datamodel.dtos.business.Offer#projectObjective
  • life.qbic.datamodel.dtos.general.Person#personType, can be replaced by subclassing life.qbic.datamodel.dtos.general.Person

2.0.0 (2021-02-15)

Added

  • Introduce profiles to pom to differentiate between OSGI and non-OSGI packaging (#122)
  • Added a netPrice, taxes and overheads property to the offer DTO
  • Add bnd.bnd file to enable OSGI bundling
  • Add new possible sample statuses (#149)
  • Add price fields to life.qbic.datamodel.dtos.business.Offer (#127)
  • Add currency field to life.qbic.datamodel.dtos.business.services.Product (#131)
  • Add @EqualsAndHashCode to life.qbic.datamodel.dtos.business.services.* (#129)
  • Add a meaningful toString() method to life.qbic.datamodel.dtos.business.TomatoId (#140)
  • Add life.qbic.datamodel.dtos.business.AcademicTitle.PHD (#144)
  • Add life.qbic.datamodel.dtos.business.ProductId attribute to Product DTOs in life.qbic.datamodel.dtos.business.services (#146)

Fixed

  • life.qbic.datamodel.datasets.OxfordNanoporeMeasurement#extractLibraryKit(String) now throws MissingPropertyException instead of groovyjarjarcommonscli.MissingArgumentException
  • Change life.qbic.datamodel.dtos.business.services.ProductUnit.PER_GIGABYTE String representation to Gigabyte (#125)
  • Change life.qbic.datamodel.dtos.business.TomatoId and extending classes now provide the version as String (#134)
  • Add missing dependencies for report generation. Fix issue #145 with PR #147

Dependencies

  • Add bnd-maven-plugin 5.1.2 to support OSGI packaging
  • Add maven-jar-plugin 3.2.0 to support OSGI packaging
  • Add org.osgi:osgi.core:jar:7.0.0
  • Remove parent-pom:3.1.3
  • Remove io.swagger.core.v3:swagger-annotations:jar:2.0.8
  • Upgrade com.fasterxml.jackson.core:jackson-annotations:jar:2.9.9 -> 2.12.0
  • Upgrade info.picocli:picocli:jar:3.7.0 -> 4.0.1
  • Upgrade junit:junit:jar:4.12 -> junit:junit:jar:4.13
  • Upgrade org.codehaus.groovy:groovy-all:pom:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-ant:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-cli-commons:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-cli-picocli:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-console:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-datetime:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-docgenerator:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-groovydoc:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-groovysh:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-jmx:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-json:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-jsr223:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-macro:jar:2.5.4 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-nio:jar:2.5.4 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-servlet:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-sql:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-swing:jar:2.5.7 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-templates:jar:2.5.4 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-test:jar:2.5.4 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy-xml:jar:2.5.4 -> 2.5.10
  • Upgrade org.codehaus.groovy:groovy:jar:2.5.4 -> 2.5.10

Deprecated

  • life.qbic.datamodel.dtos.business.TomatoId#getIdentifier is replaced by life.qbic.datamodel.dtos.business.TomatoId#toString
  • life.qbic.datamodel.dtos.general.Person#personType is deprecated. Please subclass this class instead of using this property.

Removed

  • life.qbic.datamodel.workflows.*

1.12.0 (2020-11-23)

Added

  • Add hashValue and equals to package life.qbic.datamodel.dtos classes
  • Add EnumFactory
  • Add EnumFactory implementation for AffiliationCategory, AcademicTitle
  • Support for QUBE template sync
  • Introduce life/qbic/datamodel/dtos/general/Person.groovy DTO based on an abstract builder pattern
  • Introduce life/qbic/datamodel/dtos/general/CommonPerson.groovy DTO as extension of Person DTO
  • Introduce life/qbic/datamodel/dtos/business/Customer.groovy DTO as extension of Person DTO
  • Introduce life/qbic/datamodel/dtos/business/ProjectManager.groovy DTO as extension of Person DTO
  • Introduce life/qbic/datamodel/dtos/general/Address.groovy DTO
  • Update life/qbic/datamodel/accounting/CostEstimate.groovy so it matches the properties of the Offer DTO
  • life/qbic/datamodel/accounting/ProductItem.groovy no longer provides the computeTotalCost method
  • Introduce life/qbic/datamodel/dtos/business/Offer.groovy DTO
  • Update and introduce Builder Pattern to DTO classes for offer management
  • Refactor life/qbic/datamodel/accounting/CostEstimate.groovy into Builder pattern
  • Add diagram and description of DTO structure related to Offer management to README
  • Add enum factory for product units
  • Remove "Unknown" member from Affiliation Category Enum

Fixed

  • Add default values to previous Address Implementation to avoid NullExceptions
  • Increase gha-git-credentials version (#108)
  • Customer hashCode() not working as expected (#107)
  • Refactor old accounting classes into DTOs (#101)

Dependencies

Deprecated

  • Deprecate life/qbic/datamodel/people/Person.groovy
  • Deprecate life/qbic/datamodel/people/Address.groovy
  • Deprecate "PersonType" property of life/qbic/datamodel/dtos/general/Person.groovy
  • Deprecate life/qbic/datamodel/accounting/Offer.groovy

1.11.0 (2020-09-23)

  • Add DTOs for the offer management business process
  • Reference parent pom 3.0.0

Added

Fixed

Dependencies

Deprecated

1.10.1 (2020-08-28)

  • Fix field accessibility for imaging metadata DTOs (#51)

Added

Fixed

Dependencies

Deprecated

1.10.0 (2020-08-25)

  • Provide DTO classes for imaging metadata

Added

Fixed

Dependencies

Deprecated

1.9.4 (2021-02-12)

  • Fix implementation of containsAtLeastOneBarcodedFolder, such that the method checks all child elements to contain at least one barcoded folder in order to flag the measurement as pooled measurement.

Added

Fixed

Dependencies

Deprecated

1.9.3 (2020-07-17)

Added

Fixed

Dependencies

Deprecated

1.9.2 (2020-07-10)

  • Adds missing getter method for the measurement adapter

Added

Fixed

Dependencies

Deprecated

1.9.1 (2020-07-10)

  • Fix for getRawDataPerSample(), which failed in the presence of unclassified folders.

Added

Fixed

Dependencies

Deprecated

1.9.0 (2020-07-08)

  • New class OxfordNanoporeInstrumentOutput that provides access to the instrument output JSON schema
  • Support for unclassified reads
    • Two new folder classes UnclassifiedFast5Folder and UnclassifiedFastQFolder
    • New API method getUnclassifiedData() for the OxfordNanoporeMeasurement class
  • Bugfix for object comparison infinity crisis
  • Bugfix for wrong data assignment on pooled sample data

Added

Fixed

Dependencies

Deprecated

1.8.3 (2020-05-26)

  • OxfordNanoporeMeasurement:getLogFiles now provides a list with all the log files

Added

Fixed

Dependencies

Deprecated

1.8.2 (0000-00-00)

  • Fix recursion error, when client code wants to access OxfordNanoporeMeasurement:getRelativePath

Added

Fixed

Dependencies

Deprecated

1.8.1 (0000-00-00)

  • Provide JAR with all dependencies included for single deployment (i.e. ETL dropboxes, etc.)

Added

Fixed

Dependencies

Deprecated

1.8.0 (0000-00-00)

  • Provide new classes that describe incoming Oxford Nanopore instrument data structures
  • Provide new classes that describe a Oxford Nanopore Experiment(OxfordNanoporeExperiment.class) and its containing Oxford Nanopre Measurements (OxfordNanoporeMeasurement.class)
  • Provide a new method in the SampleCodeFunction.class public static List<String> findAllQbicSampleCodes(String text) that can be used to find all QBiC sample identifiers in a String object

Added

Fixed

Dependencies

Deprecated