Patch/1.10.1 (#54)

* Increase version to 1.11.0-SNAPSHOT

* Fix wrong x-ref syntax in Groovydoc

* Fix wrong Groovydoc syntax

* Ignore generated flattened-pom.xml

* Remove field access modifiers from DTOs (#52)

* Add enum final modifier to value

* Update CHANGELOG.md

* Set version to 1.10.1

Co-authored-by: Sven Fillinger <sven.fillinger@qbic.uni-tuebingen.de>

Author: KochTobi

.gitignore

@@ -16,6 +16,7 @@
 
 # Maven
 target/
+.flattened-pom.xml
 
 # Some of our applications generate logs, which should be ignored by git
 logs/
@@ -24,4 +25,4 @@ logs/
 **/.factorypath
 
 # compiled Vaadin widgetsets
-src/main/webapp/VAADIN/widgetsets
+src/main/webapp/VAADIN/widgetsets

CHANGELOG.md

@@ -1,4 +1,6 @@
 # Release Changelog for the data model library
+## 1.10.1
+* Fix field accessibility for imaging metadata DTOs #51
 
 ## 1.10.0 25-08-2020
 

pom.xml

@@ -9,7 +9,7 @@
     <version>2.3.0</version>
   </parent>
   <artifactId>data-model-lib</artifactId>
-  <version>1.10.0-SNAPSHOT</version>
+  <version>1.10.1</version>
   <packaging>jar</packaging>
   <name>Data Model Library</name>
   <url>http://github.com/qbicsoftware/data-model-lib</url>

src/main/groovy/life/qbic/datamodel/dtos/imaging/Image.groovy

@@ -21,62 +21,62 @@ final class Image {
    *
    * @see Date
    */
-  private final Date acquisitionDate
+  final Date acquisitionDate
 
   /**
    * Detailed description of image acquisition parameters.
    *
    * @see AcquisitionParameters
    */
-  private final AcquisitionParameters acquisitionParameters
+  final AcquisitionParameters acquisitionParameters
 
   /**
    * Detailed description of image analysis parameters
    *
    * @see AnalysisParameters
    */
-  private final AnalysisParameters analysisParameters
+  final AnalysisParameters analysisParameters
 
   /**
    * A detailed instrument description that was used to create the image.
    *
    * @see Instrument
    */
-  private final Instrument instrument
+  final Instrument instrument
 
   /**
    * The image identifier in OMERO.
    */
-  private final Integer imageId
+  final Integer imageId
 
   /**
    * The image modality.
    *
    * @see Modality
    */
-  private final Modality modality
+  final Modality modality
 
   /**
    * Information about the image size.
    *
    * @see ImageSize
    */
-  private final ImageSize imageSize
+  final ImageSize imageSize
 
   /**
    * Information about the time and spacial distribution of
    * a pixel.
    *
    * @see PixelSize
    */
-  private final PixelSize pixelSize
+  final PixelSize pixelSize
 
   /**
    * Describes the resolution of the image.
    * e.g. 5 nm
    *
    */
-  private final Float resolution
+  final Float resolution
 
   /**
    * This DTO class describes the image resulting from imaging experiments
@@ -101,51 +101,4 @@ final class Image {
     this.pixelSize = pixelSize
     this.resolution = resolution
   }
-/**
-   * Returns detailed image acquisition parameters.
-   * @return Image acquisition parameters.
-   */
-  AcquisitionParameters getAcquisitionParameters() {
-    return this.acquisitionParameters
-  }
-
-  /**
-   * Returns detailed image analysis parameters.
-   * @return Image analysis parameters.
-   */
-  AnalysisParameters getAnalysisParameters() {
-    return this.analysisParameters
-  }
-
-  /**
-   * Returns detailed instrument information.
-   * @return Image instrument information.
-   */
-  Instrument getInstrument(){
-    return this.instrument
-  }
-
-  /**
-   * Returns the image size of an image.
-   * @return The actual image size.
-   */
-  ImageSize getImageSize(){
-    return this.imageSize
-  }
-
-  /**
-   * Returns the pixel size.
-   * @return The actual pixel size.
-   */
-  PixelSize getPixelSize(){
-    return this.pixelSize
-  }
-
-  /**
-   * Returns image resolution information.
-   * @return The image resolution.
-   */
-  Float getResolution(){
-    return this.resolution
-  }
 }

src/main/groovy/life/qbic/datamodel/dtos/imaging/Instrument.groovy

@@ -18,38 +18,38 @@ class Instrument {
    * The manufacturer of the instrument.
    * Examples are 'Leica', 'Zeiss' and many more.
    */
-  private final String manufacturer
+  final String manufacturer
 
   /**
    * The model type of the instrument.
    */
-  private final String model
+  final String model
 
   /**
    * The serial number of the instrument.
    */
-  private final String serialNumber
+  final String serialNumber
 
   /**
    * The location of the instrument.
    *
-   * @see: #Location
+   * @see: Location
    */
-  private final Location location
+  final Location location
 
   /**
    * The type of the instrument.
    * Example: 'Confocal Microscope'.
    */
-  private final String type
+  final String type
 
   /**
    * A more detailed description of the
    * hardware setup.
    *
-   * @see: #ImagingHardware
+   * @see: ImagingHardware
    */
-  private final ImagingHardware hardware
+  final ImagingHardware hardware
 
   /**
    * DTO that describes an instrument in the imaging context
@@ -68,24 +68,5 @@ class Instrument {
     this.type = type
     this.hardware = hardware
   }
-/**
-   * Returns a deep copy of the imaging hardware.
-   *
-   * @see: #ImagingHardware
-   * @return The imaging hardware setup.
-   */
-  ImagingHardware getHardware() {
-    return this.hardware
-  }
-
-  /**
-   * Returns a deep copy of the instrument's location.
-   *
-   * @see: #Location
-   * @return The instrument location.
-   */
-  Location getLocation() {
-    return this.location
-  }
 
 }

src/main/groovy/life/qbic/datamodel/dtos/imaging/Location.groovy

@@ -15,14 +15,14 @@ class Location {
   /**
    * An identifier for a room an instrument is located at.
    */
-  private final String roomId
+  final String roomId
 
   /**
    * An address that describes the location of an instrument.
    *
    * @see: #life.qbic.datamodel.people.Address
    */
-  private final Address address
+  final Address address
 
   /**
    * DTO that describes the location of an instrument.

src/main/groovy/life/qbic/datamodel/dtos/imaging/parameters/AcquisitionParameters.groovy

@@ -26,7 +26,7 @@ class AcquisitionParameters {
    *
    * Binning is always a positive Integer value.
    */
-  private final Integer binning
+  final Integer binning
 
   /**
    * Creates a description of acquisition parameters during image analysis.

src/main/groovy/life/qbic/datamodel/dtos/imaging/parameters/AnalysisParameters.groovy

@@ -9,5 +9,5 @@ package life.qbic.datamodel.dtos.imaging.parameters
  * @since 1.10.0
  */
 abstract class AnalysisParameters {
-    //todo do we want to keep this class?
+    //TODO implement. This is a preparation for upcoming changes.
 }

src/main/groovy/life/qbic/datamodel/dtos/imaging/parameters/electronmicroscopy/ElectronMicroscopyParameters.groovy

@@ -22,7 +22,7 @@ class ElectronMicroscopyParameters extends AcquisitionParameters{
      *
      * e.g 120 kV
      */
-    private final Integer acceleratingVoltage
+    final Integer acceleratingVoltage
 
     /**
      * Shift of focus of the objective lens.
@@ -33,14 +33,14 @@ class ElectronMicroscopyParameters extends AcquisitionParameters{
      * This could be for example -4 nm.
      * Usually this value is negative.
      */
-    private final Float targetDefocus
+    final Float targetDefocus
 
     /**
      * The accumulated amount of electrons that are applied to an area of the sample
      *
      * Measured in electrons per unit area e.g 100 electrons/Angstrom^2
      */
-    private final Float cumulativeElectronDose
+    final Float cumulativeElectronDose
 
     /**
      * Creates a description of the properties of electron microscopy

src/main/groovy/life/qbic/datamodel/dtos/imaging/parameters/lightmicroscopy/LightMicroscopyParameters.groovy

@@ -5,7 +5,6 @@ import life.qbic.datamodel.dtos.imaging.properties.Area
 import life.qbic.datamodel.dtos.imaging.properties.EmissionRange
 import life.qbic.datamodel.dtos.imaging.properties.Position
 import life.qbic.datamodel.dtos.imaging.properties.ScanMode
-import life.qbic.datamodel.dtos.imaging.properties.Unit
 
 /**
  * Description of light microscope parameters during image analysis.
@@ -40,15 +39,15 @@ class LightMicroscopyParameters extends AcquisitionParameters{
      *
      * @see EmissionRange
      */
-    private final List<EmissionRange> emissionPerChannel
+    final List<EmissionRange> emissionPerChannel
 
     /**
      * Total Internal Reflection Fluorescence (TIRF)
      * Amount of power of the laser beam at the TIRF lens.
      *
      * It is measured in milliwats (mW)
      */
-    private final Float laserPowerTIRFLens
+    final Float laserPowerTIRFLens
 
     /**
      * Amount of power of the laser beam split at the beam splitter.
@@ -57,21 +56,21 @@ class LightMicroscopyParameters extends AcquisitionParameters{
      * It is measured in milliwatts (mW)
      *
      */
-    private final Float laserPowerBeamSplitter
+    final Float laserPowerBeamSplitter
 
     /**
      * Time required to generate an image with the camera
      *
      * Described in ms (e.g 100 ms)
      */
-    private final Float cameraAcquisitionTime
+    final Float cameraAcquisitionTime
 
     /**
      * Position of the light beam on the scanning area
      *
      * Described by coordinates in pixels e.g position (x,y,z)
      */
-    private final Position position
+    final Position position
 
     /**
      * Time-Correlated Single Photon Counting (TCSPC)
@@ -80,7 +79,7 @@ class LightMicroscopyParameters extends AcquisitionParameters{
      *
      * Describes the timing resolution of TCSPC in ps e.g. 32 ps
      */
-    private final Integer tcspcTimingResolution
+    final Integer tcspcTimingResolution
 
     /**
      * Position for the TCSPC.
@@ -89,30 +88,30 @@ class LightMicroscopyParameters extends AcquisitionParameters{
      *
      * e.g position (x,y,z)
      */
-    private final Position tcspcPosition
+    final Position tcspcPosition
 
     /**
      * Describes the scan mode of the used for the TCSPC microscopy.
      *
      * @see ScanMode
      */
-    private final ScanMode tscpcScanMode
+    final ScanMode tscpcScanMode
 
     /**
      * Describes the time for the acquisition of an image area in pixels.
      * The rate is defined as time/px and has the unit ms.
      *
      * e.g. 5ms
      */
-    private final Integer scanAcquisitionRate
+    final Integer scanAcquisitionRate
 
     /**
      * The size of the scanned area
      * e.g. the area (40,40) in µm of on the image plane xy
      *
      * @see Area
      */
-    private final Area scanSize
+    final Area scanSize
 
     /**
      * Creates a description of light microscope parameters during image analysis.