Sync 2.14.0 to Dev (#268)

2.14.0 (2021-10-27)
-------------------

**Added**

* Added String representing product abbreviation to ProductCategory Enum (`#266 <https://github.com/qbicsoftware/data-model-lib/pull/266>`_)
* ProductId now provides 'From' method to be created via String representation (`#264 <https://github.com/qbicsoftware/data-model-lib/pull/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 <https://github.com/qbicsoftware/data-model-lib/pull/266>`_)

Author: Steffengreiner

.github/workflows/build_docs.yml

@@ -4,7 +4,7 @@ email: sven.fillinger@qbic.uni-tuebingen.de
 project_name: data-model-lib
 project_short_description: "Data models. A collection of QBiC's central data models\
   \ and DTOs. "
-version: 2.14.0-SNAPSHOT
+version: 2.15.0-SNAPSHOT
 domain: lib
 language: groovy
 project_slug: data-model-lib

.qube.yml

@@ -4,20 +4,33 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
-2.14.0-SNAPSHOT (2021-10-13)
+2.15.0-SNAPSHOT (2021-10-27)
 ----------------------------
 
 **Added**
 
-* Added ProductTypeFactory ``life.qbic.datamodel.dtos.business.services.ProductTypeFactory``
-* ProductId now provides 'From' method to be created via String representation
+**Fixed**
+
+**Dependencies**
+
+**Deprecated**
+
+
+2.14.0 (2021-10-27)
+-------------------
+
+**Added**
+
+* Added String representing product abbreviation to ProductCategory Enum (`#266 <https://github.com/qbicsoftware/data-model-lib/pull/266>`_)
+* ProductId now provides 'From' method to be created via String representation (`#264 <https://github.com/qbicsoftware/data-model-lib/pull/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 <https://github.com/qbicsoftware/data-model-lib/pull/266>`_)
 
 2.13.0 (2021-10-13)
 -------------------

CHANGELOG.rst

@@ -55,9 +55,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '2.14.0-SNAPSHOT'
+version = '2.15.0-SNAPSHOT'
 # The full version, including alpha/beta/rc tags.
-release = '2.14.0-SNAPSHOT'
+release = '2.15.0-SNAPSHOT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/figures/MaxQuant_Data_Structure.png

@@ -7,7 +7,7 @@
 
     <groupId>life.qbic</groupId>
 	<artifactId>data-model-lib</artifactId>
-	<version>2.14.0-SNAPSHOT</version> <!-- <<QUBE_FORCE_BUMP>> -->
+	<version>2.15.0-SNAPSHOT</version> <!-- <<QUBE_FORCE_BUMP>> -->
 	<name>data-model-lib</name>
 	<url>http://github.com/qbicsoftware/data-model-lib</url>
 	<description>Data models. A collection of QBiC's central data models and DTOs. </description>

docs/conf.py

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.14.0-SNAPSHOT
+current_version = 2.15.0-SNAPSHOT
 
 [bumpversion_files_whitelisted]
 dot_qube = .qube.yml

pom.xml

@@ -9,22 +9,28 @@ package life.qbic.datamodel.dtos.business
  */
 enum ProductCategory {
 
-    SEQUENCING("Sequencing"),
-    PROJECT_MANAGEMENT("Project Management"),
-    PRIMARY_BIOINFO("Primary Bioinformatics"),
-    SECONDARY_BIOINFO("Secondary Bioinformatics"),
-    DATA_STORAGE("Data Storage"),
-    PROTEOMIC("Proteomics"),
-    METABOLOMIC("Metabolomics"),
-    EXTERNAL_SERVICE("External Service")
+    SEQUENCING("Sequencing", "SE"),
+    PROJECT_MANAGEMENT("Project Management", "PM"),
+    PRIMARY_BIOINFO("Primary Bioinformatics", "PB"),
+    SECONDARY_BIOINFO("Secondary Bioinformatics", "SB"),
+    DATA_STORAGE("Data Storage", "DS"),
+    PROTEOMIC("Proteomics", "PR"),
+    METABOLOMIC("Metabolomics", "ME"),
+    EXTERNAL_SERVICE("External Service", "EXT")
 
     /**
      * Value describing the enum type with a string
      */
-    private final String value
+    private String value
 
-    ProductCategory(String value) {
+    /**
+     * Abbreviation for the enum type name
+     */
+    private String abbreviation
+
+    ProductCategory(String value, String abbreviation) {
         this.value = value
+        this.abbreviation = abbreviation
     }
 
     /**
@@ -35,4 +41,14 @@ enum ProductCategory {
     String getValue() {
         return value
     }
+
+    /**
+     * Returns the abbreviation associated to the given enum
+     * This is <em>NOT</em> the same as {@link #toString}
+     * @return a user-friendly string value
+     */
+    String getAbbreviation() {
+        return abbreviation
+    }
+
 }

qube.cfg

@@ -27,4 +27,20 @@ class ProductCategoryFactory extends EnumFactory<ProductCategory>{
         }
         return desiredKey
     }
+
+    /**
+     * This method returns the enum with the provided String abbreviation.
+     *
+     * @throws IllegalArgumentException in case the String could not be mapped
+     * @param abbreviation the String corresponding to the abbreviation stored in the enum
+     * @return the enum key for the provided abbreviation
+     */
+    ProductCategory getForAbbreviation(String abbreviation) {
+        ProductCategory desiredKey
+        desiredKey = ProductCategory.values().find {it.abbreviation.equals(abbreviation.trim())}
+        if (!desiredKey) {
+            throw new IllegalArgumentException("Unknown abbreviation'$abbreviation' for ${ProductCategory.getSimpleName()}")
+        }
+        return desiredKey
+    }
 }

src/main/groovy/life/qbic/datamodel/dtos/business/ProductCategory.groovy

@@ -1,8 +1,6 @@
 package life.qbic.datamodel.dtos.business
 
 import groovy.transform.EqualsAndHashCode
-import life.qbic.datamodel.dtos.business.services.ProductType
-import life.qbic.datamodel.dtos.business.services.ProductTypeFactory
 
 /**
  * A DTO describing Product Identifiers
@@ -29,6 +27,9 @@ class ProductId implements Comparable<ProductId>{
     /**
      * A builder for ProductId instances.
      */
+
+    private static final ProductCategoryFactory productCategoryFactory = new ProductCategoryFactory()
+
     static class Builder {
         private String productType
         private long uniqueId
@@ -119,34 +120,33 @@ class ProductId implements Comparable<ProductId>{
      * Returns a ProductId from a given String representation
      *
      * Expects a ProductIdString with the Format P_N
-     * P being the one of the abbreviation values stored in {@link ProductType} enum
+     * P being the one of the abbreviation values stored in {@link ProductCategory} enum
      * N being an Integer Number
      *
      * @param String representation of a productId
-     * @return ProductId containing type and uniqueNumber of String representation
+     * @return ProductId containing productCategory abbreviation and uniqueNumber of String representation
      */
     static ProductId from(String productId) {
         if (!productId.contains("_")) {
-            throw new IllegalArgumentException("Not a valid product identifier.")
+            throw new IllegalArgumentException("${productId} is not a valid product identifier.")
         }
         def splitId = productId.split("_")
-        String productTypeString
-        String runningNumberString
+        String productCategoryString = splitId[0].trim()
+        String runningNumberString = splitId[1].trim()
         Long runningNumber
+        ProductCategory productCategory
         try {
-            ProductTypeFactory productTypeFactory = new ProductTypeFactory()
-            productTypeString = splitId[0].trim()
-            runningNumberString = splitId[1].trim()
             runningNumber = Long.parseUnsignedLong(runningNumberString)
-            ProductType productType = productTypeFactory.getForString(productTypeString)
+            productCategory = productCategoryFactory.getForAbbreviation(productCategoryString)
         }
         catch (NumberFormatException numberFormatException) {
-            throw new NumberFormatException("Provided productId does not have a valid uniqueID")
+            throw new NumberFormatException("Provided productId does not have a valid uniqueID. Provided unique id: ${runningNumberString}")
         }
         catch (IllegalArgumentException illegalArgumentException) {
-            throw new IllegalArgumentException("ProductId does not have a valid ProductType")
+            throw new IllegalArgumentException("ProductId does not have a valid ProductCategory abbreviation. Provided abbreviation: ${productCategoryString}")
+
         }
-        return new Builder(productTypeString, runningNumber).build()
+        return new Builder(productCategory.getAbbreviation() , runningNumber).build()
     }
 
     /**