Merge pull request #102 from qbicsoftware/development

Prepare version 1.12.0

pom.xml

@@ -8,7 +8,7 @@
   <description>Collection of non-Vaadin, non-Liferay utilities.</description>
   <modelVersion>4.0.0</modelVersion>
   <name>Core Utilities Library</name>
-  <version>1.11.0</version>
+  <version>1.12.0-SNAPSHOT</version>
   <url>https://github.com/qbicsoftware/core-utils-lib</url>
   <packaging>jar</packaging>
   <properties>
@@ -127,7 +127,7 @@
     <dependency>
       <artifactId>data-model-lib</artifactId>
       <groupId>life.qbic</groupId>
-      <version>2.18.0</version>
+      <version>2.19.0</version>
     </dependency>
     <dependency>
       <groupId>org.mockito</groupId>

src/main/groovy/life/qbic/utils/MaxQuantParser.groovy

@@ -118,16 +118,14 @@ class MaxQuantParser implements DatasetParser<MaxQuantRunResult> {
         rootChildren.each { currentChild ->
             if (currentChild.containsKey("children")) {
                 //folder
-                parseCombinedInformation(map)
+                parseTxtFolder(map)
             } else if (currentChild.containsKey("fileType")) {
                 //file
-                switch (currentChild.get("name")) {
-                    case "mqpar.xml":
-                        insertAsProperty(map, currentChild, RequiredRootFileKeys.RUN_PARAMETERS.getKeyName())
-                        break
-                    case "sample_ids.txt":
-                        insertAsProperty(map, currentChild, RequiredRootFileKeys.SAMPLE_ID.getKeyName())
-                        break
+                String name = currentChild.get("name")
+                if(name.equals("mqpar.xml")) {
+                    insertAsProperty(map, currentChild, RequiredRootFileKeys.RUN_PARAMETERS.getKeyName())
+                } else if(name.endsWith("sample_ids.txt")) {
+                    insertAsProperty(map, currentChild, RequiredRootFileKeys.SAMPLE_ID.getKeyName())
                 }
             }
         }
@@ -137,26 +135,17 @@ class MaxQuantParser implements DatasetParser<MaxQuantRunResult> {
      * Method which adapts the parsed content of the txt directory in place to the expected file structure.
      * @see {<a href="https://github.com/qbicsoftware/data-model-lib/blob/master/src/test/resources/examples/resultset/maxquant/valid-resultset-example.json">valid datastructure example</a>}
      *
-     * After parsing the files of the txt directory are contained in the children property of the combined directory, which itself is contained in the root directory.
+     * After parsing, the files of the txt directory are contained in the children property of the root directory.
      * The underlying datastructure however expects a mapping of the expected files as a Map entry in the root directory.
      * @param maxQuantInformation a nested map representing the parsed fileTree structure
      * @since 1.9.0
      */
-    private static void parseCombinedInformation(Map maxQuantInformation) {
+    private static void parseTxtFolder(Map maxQuantInformation) {
         List<Map> rootFolderInformation = maxQuantInformation.get("children") as List<Map>
-        def combinedFolderInformation
         def txtFolderInformation
-        def summaryFolderInformation
         rootFolderInformation.findAll { map ->
-            if (map.get("name") == "combined") {
-                combinedFolderInformation = map.get("children")
-            }
-        }
-        if (combinedFolderInformation) {
-            combinedFolderInformation.findAll { map ->
-                if (map.get("name") == "txt") {
-                    txtFolderInformation = map.get("children")  as List<Map>
-                }
+            if (map.get("name") == "txt") {
+                txtFolderInformation = map.get("children")  as List<Map>
             }
         }
         if (txtFolderInformation) {
@@ -181,19 +170,11 @@ class MaxQuantParser implements DatasetParser<MaxQuantRunResult> {
                         insertAsProperty(maxQuantInformation, child, RequiredTxtFileKeys.PROTEIN_GROUPS.getKeyName())
                         break
                     default:
-                        if(child.get("name") == "summary") summaryFolderInformation = child.get("children") as List<Map>
                         //ignoring other children
                         break
                     }
                 }
         }
-        if(summaryFolderInformation){
-            summaryFolderInformation.each{ Map child ->
-                if (child.get("name").toString().matches("summary_[0-9]{4}.*")) {
-                    insertAsProperty(maxQuantInformation, child, RequiredTxtFileKeys.SUMMARY.getKeyName())
-                }
-            }
-        }
     }
 
     /**

src/test/groovy/life/qbic/utils/MaxQuantParserSpec.groovy

@@ -32,35 +32,29 @@ class MaxQuantParserSpec extends Specification {
         assert maxQuantRunResult.runParameters.getRelativePath() == "./mqpar.xml"
         assert maxQuantRunResult.runParameters.getName()== "mqpar.xml"
 
-        assert maxQuantRunResult.sampleIds.getRelativePath() == "./sample_ids.txt"
-        assert maxQuantRunResult.sampleIds.getName()== "sample_ids.txt"
+        assert maxQuantRunResult.sampleIds.getRelativePath() == "./QABCD_sample_ids.txt"
+        assert maxQuantRunResult.sampleIds.getName()== "QABCD_sample_ids.txt"
 
-        //Files in ./combined/txt/ can be parsed
-        assert maxQuantRunResult.allPeptides.getRelativePath() == "./combined/txt/allPeptides.txt"
+        //Files in ./txt/ can be parsed
+        assert maxQuantRunResult.allPeptides.getRelativePath() == "./txt/allPeptides.txt"
         assert maxQuantRunResult.allPeptides.getName()== "allPeptides.txt"
 
-        assert maxQuantRunResult.evidence.getRelativePath() == "./combined/txt/evidence.txt"
+        assert maxQuantRunResult.evidence.getRelativePath() == "./txt/evidence.txt"
         assert maxQuantRunResult.evidence.getName()== "evidence.txt"
 
-        assert maxQuantRunResult.experimentalDesignTemplate.getRelativePath() == "./combined/txt/experimentalDesignTemplate.txt"
-        assert maxQuantRunResult.experimentalDesignTemplate.getName()== "experimentalDesignTemplate.txt"
-
-        assert maxQuantRunResult.parameters.getRelativePath() == "./combined/txt/parameters.txt"
+        assert maxQuantRunResult.parameters.getRelativePath() == "./txt/parameters.txt"
         assert maxQuantRunResult.parameters.getName()== "parameters.txt"
 
-        assert maxQuantRunResult.peptides.getRelativePath() == "./combined/txt/peptides.txt"
+        assert maxQuantRunResult.peptides.getRelativePath() == "./txt/peptides.txt"
         assert maxQuantRunResult.peptides.getName()== "peptides.txt"
 
-        assert maxQuantRunResult.proteinGroups.getRelativePath() == "./combined/txt/proteinGroups.txt"
+        assert maxQuantRunResult.proteinGroups.getRelativePath() == "./txt/proteinGroups.txt"
         assert maxQuantRunResult.proteinGroups.getName()== "proteinGroups.txt"
-
-        assert maxQuantRunResult.summary.getRelativePath() == "./combined/txt/summary/summary_1234.pdf"
-        assert maxQuantRunResult.summary.getName()== "summary_1234.pdf"
     }
 
     def "parsing an invalid file structure throws DatasetValidationException"() {
         given:
-        def pathToDirectory = Paths.get(exampleDirectoriesRoot, "fails/missing_combined_directory")
+        def pathToDirectory = Paths.get(exampleDirectoriesRoot, "fails/missing_txt_directory")
         when:
         maxQuantParser.parseFrom(pathToDirectory)
         then: