Prepare Version 2.20.0 (#325)

Steffengreiner · wow-such-code · web-flow · commit efe896ad80b0 · 2022-08-26T11:15:45.000+02:00
* increase snapshot to 2.20.0 * Adjust Nf-core pipeline result to account for sarekv3 file structure * Remove replacement of hyphens with underscores in project spaces (#326) Co-authored-by: wow-such-code <andreas.friedrich@uni-tuebingen.de>
diff --git a/doc/figures/ER_diagram_pipeline_results.png b/doc/figures/ER_diagram_pipeline_results.png
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
 
   <groupId>life.qbic</groupId>
   <artifactId>data-model-lib</artifactId>
-  <version>2.19.1</version>
+  <version>2.20.0-SNAPSHOT</version>
   <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>
diff --git a/src/main/groovy/life/qbic/datamodel/datasets/NfCorePipelineResult.groovy b/src/main/groovy/life/qbic/datamodel/datasets/NfCorePipelineResult.groovy
@@ -3,7 +3,7 @@ package life.qbic.datamodel.datasets
 
 import life.qbic.datamodel.datasets.datastructure.files.DataFile
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.ExecutionReport
-import life.qbic.datamodel.datasets.datastructure.files.nfcore.PipelineReport
+
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.RunId
 import life.qbic.datamodel.datasets.datastructure.files.general.SampleIds
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.SoftwareVersions
@@ -33,7 +33,6 @@ final class NfCorePipelineResult {
     private final static Set nfCoreFileTypes = [
             FQDN_FILES + ".ExecutionReport",
             GENERAL_FILES + ".SampleIds",
-            FQDN_FILES + ".PipelineReport",
             FQDN_FILES + ".SoftwareVersions",
             FQDN_FILES + ".RunId"
     ]
@@ -85,9 +84,8 @@ final class NfCorePipelineResult {
         Objects.requireNonNull(bioinformaticPipelineOutput.get("processFolders"), "The root folder must contain at least one process folder.")
         //Check if all required files are in the pipeline_info directory
         Map pipelineInfoMap = bioinformaticPipelineOutput["pipelineInformation"] as Map
-        Objects.requireNonNull(pipelineInfoMap.get("softwareVersions"), "The pipeline_info folder must contain a softwareVersions.csv file.")
-        Objects.requireNonNull(pipelineInfoMap.get("executionReport"), "The pipeline_info folder must contain a executionReport.txt file.")
-        Objects.requireNonNull(pipelineInfoMap.get("pipelineReport"), "The pipeline_info folder must contain a pipeline_info.txt file.")
+        Objects.requireNonNull(pipelineInfoMap.get("softwareVersions"), "The pipeline_info folder must contain a softwareVersions.yml file.")
+        Objects.requireNonNull(pipelineInfoMap.get("executionReport"), "The pipeline_info folder must contain a executionReport.html file.")
         //Check if all required files are in root directory
         Objects.requireNonNull(bioinformaticPipelineOutput.get("runId"), "The root folder must contain a run_id.txt file.")
         Objects.requireNonNull(bioinformaticPipelineOutput.get("sampleIds"), "The root folder must contain an sample_ids.txt file.")
@@ -105,11 +103,9 @@ final class NfCorePipelineResult {
         //These files are not stored as children but as properties of the pipeline_info folder
         DataFile softwareVersions = parseFile(pipelineInfoMap.get("softwareVersions") as Map)
         DataFile executionReport = parseFile(pipelineInfoMap.get("executionReport") as Map)
-        DataFile pipelineReport = parseFile(pipelineInfoMap.get("pipelineReport") as Map)
 
         //Set information of pipelineInformation properties
         pipelineInformation.softwareVersions = softwareVersions as SoftwareVersions
-        pipelineInformation.pipelineReport = pipelineReport as PipelineReport
         pipelineInformation.executionReport = executionReport as ExecutionReport
 
         //Parse all files in the root directory
diff --git a/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/ExecutionReport.groovy b/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/ExecutionReport.groovy
@@ -9,9 +9,9 @@ import life.qbic.datamodel.datasets.datastructure.files.DataFile
  */
 class ExecutionReport extends DataFile {
 
-    final private static String FILE_TYPE = "txt"
+    final private static String FILE_TYPE = "html"
 
-    final private static String NAME_SCHEMA = $/execution_report.*/$
+    final private static String NAME_SCHEMA = $/^execution_report.*/$
 
     protected ExecutionReport() {}
 
diff --git a/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/PipelineReport.groovy b/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/PipelineReport.groovy
diff --git a/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/SoftwareVersions.groovy b/src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/SoftwareVersions.groovy
@@ -9,7 +9,7 @@ import life.qbic.datamodel.datasets.datastructure.files.DataFile
  */
 class SoftwareVersions extends DataFile {
 
-    final private static String FILE_TYPE = "csv"
+    final private static String FILE_TYPE = "yml"
 
     final private static String NAME_SCHEMA = $/software_versions.*/$
 
diff --git a/src/main/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/PipelineInformationFolder.groovy b/src/main/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/PipelineInformationFolder.groovy
@@ -2,7 +2,6 @@ package life.qbic.datamodel.datasets.datastructure.folders.nfcore
 
 import life.qbic.datamodel.datasets.datastructure.files.DataFile
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.ExecutionReport
-import life.qbic.datamodel.datasets.datastructure.files.nfcore.PipelineReport
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.SoftwareVersions
 import life.qbic.datamodel.datasets.datastructure.folders.DataFolder
 
@@ -19,8 +18,6 @@ class PipelineInformationFolder extends DataFolder {
 
     SoftwareVersions softwareVersions
 
-    PipelineReport pipelineReport
-
     ExecutionReport executionReport
 
     protected PipelineInformationFolder() {}
@@ -58,15 +55,6 @@ class PipelineInformationFolder extends DataFolder {
         return softwareVersions
     }
 
-    /**
-     * Provides access to the information stored in the runId file
-     * @return the pipeline report generated by nextflow
-     * @since 2.6.0
-     */
-    PipelineReport getPipelineReport() {
-        return pipelineReport
-    }
-
     /**
      * Provides access to the information stored in the sampleIds file
      * @return the execution report
diff --git a/src/main/groovy/life/qbic/datamodel/dtos/projectmanagement/ProjectSpace.groovy b/src/main/groovy/life/qbic/datamodel/dtos/projectmanagement/ProjectSpace.groovy
@@ -44,7 +44,6 @@ final class ProjectSpace {
     private static String formatSpaceName(String name) {
         def capitalizedName = name.trim().toUpperCase()
         def refactoredName = capitalizedName.replaceAll("\\s+", "_")
-                .replaceAll("-", "_")
         return refactoredName
     }
 
diff --git a/src/main/resources/schemas/bioinformatics-analysis-result-set.schema.json b/src/main/resources/schemas/bioinformatics-analysis-result-set.schema.json
@@ -14,12 +14,10 @@
           "properties": {
             "name": { "pattern": "pipeline_info"},
             "softwareVersions": { "$ref": "#/definitions/softwareVersions" },
-            "pipelineReport": { "$ref": "#/definitions/pipelineReport" },
             "executionReport": { "$ref": "#/definitions/executionReport" }
           },
           "required": [
             "softwareVersions",
-            "pipelineReport",
             "executionReport"
           ]
         }
@@ -34,21 +32,7 @@
         {
           "properties": {
             "name": { "pattern": "software_versions"},
-            "fileType": { "pattern": "csv" }
-          }
-        }
-      ]
-    },
-    "pipelineReport": {
-      "description": "A data file that describes the pipeline configuration.",
-      "allOf": [
-        {
-          "$ref": "data-structure-commons.json#/definitions/dataFile"
-        },
-        {
-          "properties": {
-            "name": { "pattern": "pipeline_report"},
-            "fileType": { "pattern": "txt" }
+            "fileType": { "pattern": "yml" }
           }
         }
       ]
@@ -62,7 +46,7 @@
         {
           "properties": {
             "name": { "pattern": "execution_report"},
-            "fileType": { "pattern": "txt" }
+            "fileType": { "pattern": "html" }
           }
         }
       ]
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/NfCorePipelineResultSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/NfCorePipelineResultSpec.groovy
@@ -74,9 +74,8 @@ class NfCorePipelineResultSpec extends Specification {
         runId.name == "run_id.txt"
         processFolders.get(0).name == "salmon"
         qualityControlFolder.name == "multiqc"
-        pipelineInformationFolder.getSoftwareVersions().name == "software_versions.csv"
-        pipelineInformationFolder.getPipelineReport().name == "pipeline_report.txt"
-        pipelineInformationFolder.getExecutionReport().name == "execution_report.txt"
+        pipelineInformationFolder.getSoftwareVersions().name == "software_versions.yml"
+        pipelineInformationFolder.getExecutionReport().name == "execution_report.html"
     }
 
     def "Invalid fileTree will return a NullPointerException"() {
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/ExecutionReportSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/ExecutionReportSpec.groovy
@@ -11,8 +11,8 @@ class ExecutionReportSpec extends Specification {
 
     def "shall create a ExecutionReport instance"() {
         given:
-        final name = "execution_report.txt"
-        final relativePath = "root/execution_report.txt"
+        final name = "execution_report.html"
+        final relativePath = "root/execution_report.html"
 
         when:
         def dataObject = ExecutionReport.create(name, relativePath)
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/PipelineReportSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/PipelineReportSpec.groovy
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/SoftwareVersionsSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/files/nfcore/SoftwareVersionsSpec.groovy
@@ -11,8 +11,8 @@ class SoftwareVersionsSpec extends Specification {
 
     def "shall create a SoftwareVersions instance"() {
         given:
-        final name = "software_versions.csv"
-        final path = "root/software_versions.csv"
+        final name = "software_versions.yml"
+        final path = "root/software_versions.yml"
 
         when:
         def dataObject = SoftwareVersions.create(name, path)
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/PipelineInformationFolderSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/PipelineInformationFolderSpec.groovy
@@ -1,7 +1,6 @@
 package life.qbic.datamodel.datasets.datastructure.folders.nfcore
 
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.ExecutionReport
-import life.qbic.datamodel.datasets.datastructure.files.nfcore.PipelineReport
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.SoftwareVersions
 import spock.lang.Specification
 
@@ -17,18 +16,15 @@ class PipelineInformationFolderSpec extends Specification {
         final def name = "pipeline_info"
         final def relativePath = "root/pipeline_info"
         final def children = []
-        final def executionReport = ExecutionReport.create("execution_report.txt", "root/execution_report.txt")
-        final def pipelineReport = PipelineReport.create("pipeline_report.txt", "root/pipeline_report.txt")
-        final def softwareVersions = SoftwareVersions.create("software_versions.csv", "root/software_versions.csv")
+        final def executionReport = ExecutionReport.create("execution_report.html", "root/execution_report.html")
+        final def softwareVersions = SoftwareVersions.create("software_versions.yml", "root/software_versions.yml")
         when:
         final def pipelineInformationFolder = PipelineInformationFolder.create(name, relativePath, children)
         pipelineInformationFolder.executionReport = executionReport
-        pipelineInformationFolder.pipelineReport = pipelineReport
         pipelineInformationFolder.softwareVersions = softwareVersions
 
         then:
         assert pipelineInformationFolder.getExecutionReport() == executionReport
-        assert pipelineInformationFolder.getPipelineReport() == pipelineReport
         assert pipelineInformationFolder.getSoftwareVersions() == softwareVersions
 
     }
@@ -38,7 +34,7 @@ class PipelineInformationFolderSpec extends Specification {
         final def name = "pipeline_unsatisfied"
         final def relativePath = "root/pipeline_unsatisfied"
         final def children = []
-        final def datafile =  ExecutionReport.create("execution_report_test.txt", "root/execution_report_test.txt")
+        final def datafile =  ExecutionReport.create("execution_report_test.html", "root/execution_report_test.html")
         children.add(datafile)
 
         when:
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/ProcessFolderSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/ProcessFolderSpec.groovy
@@ -15,7 +15,7 @@ class ProcessFolderSpec extends Specification {
         final def name = "processtest"
         final def relativePath = "root/processtest"
         final def children = []
-        final def datafile = ExecutionReport.create("execution_report.txt", "root/processtest/execution_report.txt")
+        final def datafile = ExecutionReport.create("execution_report.html", "root/processtest/execution_report.html")
         children.add(datafile)
 
         when:
diff --git a/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/QualityControlFolderSpec.groovy b/src/test/groovy/life/qbic/datamodel/datasets/datastructure/folders/nfcore/QualityControlFolderSpec.groovy
@@ -15,7 +15,7 @@ class QualityControlFolderSpec extends Specification {
         final def name = "multiqc"
         final def relativePath = "root/multiqc"
         final def children = []
-        final def datafile = ExecutionReport.create("execution_report_test.txt", "root/execution_report_test.txt")
+        final def datafile = ExecutionReport.create("execution_report_test.html", "root/execution_report_test.html")
         children.add(datafile)
 
         when:
@@ -31,7 +31,7 @@ class QualityControlFolderSpec extends Specification {
         final def name = "simpleqc"
         final def relativePath = "root/simpleqc"
         final def children = []
-        final def datafile =  ExecutionReport.create("execution_report_test.txt", "root/execution_report_test.txt")
+        final def datafile =  ExecutionReport.create("execution_report_test.html", "root/execution_report_test.html")
         children.add(datafile)
 
         when:
diff --git a/src/test/groovy/life/qbic/datamodel/dtos/projectmanagement/ProjectSpaceSpec.groovy b/src/test/groovy/life/qbic/datamodel/dtos/projectmanagement/ProjectSpaceSpec.groovy
@@ -31,15 +31,4 @@ class ProjectSpaceSpec extends Specification {
         thrown(IllegalArgumentException)
 
     }
-
-    def "Dashes are replaced by underscores"() {
-        given:
-        String projectSpaceName = "my-new-space"
-
-        when:
-        ProjectSpace space = new ProjectSpace(projectSpaceName)
-
-        then:
-        space.name.equals("MY_NEW_SPACE")
-    }
 }
diff --git a/src/test/resources/examples/resultset/missing-process-folders-resultset-example.json b/src/test/resources/examples/resultset/missing-process-folders-resultset-example.json
@@ -4,19 +4,14 @@
     "path": "./",
     "children": [],
     "softwareVersions": {
-      "name": "software_versions.csv",
-      "fileType": "csv",
-      "path": "pipeline_info/software_versions.csv"
-    },
-    "pipelineReport": {
-      "name": "pipeline_report.txt",
-      "fileType": "txt",
-      "path": "pipeline_info/pipeline_report.txt"
+      "name": "software_versions.yml",
+      "fileType": "yml",
+      "path": "pipeline_info/software_versions.yml"
     },
     "executionReport": {
-      "name": "execution_report.txt",
-      "fileType": "txt",
-      "path": "pipeline_info/execution_report.txt"
+      "name": "execution_report.html",
+      "fileType": "html",
+      "path": "pipeline_info/execution_report.html"
     }
   },
   "qualityControl": {
diff --git a/src/test/resources/examples/resultset/missing-quality-control-resultset-example.json b/src/test/resources/examples/resultset/missing-quality-control-resultset-example.json
diff --git a/src/test/resources/examples/resultset/valid-resultset-example.json b/src/test/resources/examples/resultset/valid-resultset-example.json

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,6 @@ final class ProjectSpace {`
`44`	`44`	`private static String formatSpaceName(String name) {`
`45`	`45`	`def capitalizedName = name.trim().toUpperCase()`
`46`	`46`	`def refactoredName = capitalizedName.replaceAll("\\s+", "_")`
`47`		`- .replaceAll("-", "_")`
`48`	`47`	`return refactoredName`
`49`	`48`	`}`
`50`	`49`
Original file line number	Diff line number	Diff line change
`@@ -14,12 +14,10 @@`
`14`	`14`	`"properties": {`
`15`	`15`	`"name": { "pattern": "pipeline_info"},`
`16`	`16`	`"softwareVersions": { "$ref": "#/definitions/softwareVersions" },`
`17`		`- "pipelineReport": { "$ref": "#/definitions/pipelineReport" },`
`18`	`17`	`"executionReport": { "$ref": "#/definitions/executionReport" }`
`19`	`18`	`},`
`20`	`19`	`"required": [`
`21`	`20`	`"softwareVersions",`
`22`		`- "pipelineReport",`
`23`	`21`	`"executionReport"`
`24`	`22`	`]`
`25`	`23`	`}`
`@@ -34,21 +32,7 @@`
`34`	`32`	`{`
`35`	`33`	`"properties": {`
`36`	`34`	`"name": { "pattern": "software_versions"},`
`37`		`- "fileType": { "pattern": "csv" }`
`38`		`- }`
`39`		`- }`
`40`		`- ]`
`41`		`- },`
`42`		`- "pipelineReport": {`
`43`		`- "description": "A data file that describes the pipeline configuration.",`
`44`		`- "allOf": [`
`45`		`- {`
`46`		`- "$ref": "data-structure-commons.json#/definitions/dataFile"`
`47`		`- },`
`48`		`- {`
`49`		`- "properties": {`
`50`		`- "name": { "pattern": "pipeline_report"},`
`51`		`- "fileType": { "pattern": "txt" }`
	`35`	`+ "fileType": { "pattern": "yml" }`
`52`	`36`	`}`
`53`	`37`	`}`
`54`	`38`	`]`
`@@ -62,7 +46,7 @@`
`62`	`46`	`{`
`63`	`47`	`"properties": {`
`64`	`48`	`"name": { "pattern": "execution_report"},`
`65`		`- "fileType": { "pattern": "txt" }`
	`49`	`+ "fileType": { "pattern": "html" }`
`66`	`50`	`}`
`67`	`51`	`}`
`68`	`52`	`]`