Merge pull request #113 from nvnieuwk/improve-samplesheet-typecasting

Improve samplesheet typecasting
nextflow-io · Oct 16, 2023 · 9d5060b · 9d5060b
2 parents e737858 + 6aba24c
commit 9d5060b
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Showing 6 changed files with 54 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # nextflow-io/nf-validation: Changelog
 
+# Version 1.1.0
+
+## Bug fixes
+
+- Floats and doubles should now be created when using the `number` type in the schema ([#113](https://github.com/nextflow-io/nf-validation/pull/113/))
+- When `0` is used as a default value in the schema, a `0` will now be used as the value in the `.fromSamplesheet()` channel instead of `null` ([#114](https://github.com/nextflow-io/nf-validation/pull/114))
+
 # Version 1.0.0
 
 The nf-validation plugin is now in production use across many pipelines and has (we hope) now reached a point of relative stability. The bump to major version v1.0.0 signifies that it is suitable for use in production pipelines.

diff --git a/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy b/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy
@@ -164,17 +164,17 @@ class SamplesheetConverter {
                 if(metaNames) {
                     for(name : metaNames) {
                         meta[name] = (input != '' && input) ? 
-                                transform(input, field) : 
+                                castToType(input, field) : 
                             field['value']['default'] != null ? 
-                                transform(field['value']['default'] as String, field) : 
+                                castToType(field['value']['default'] as String, field) : 
                                 null
                     }
                 }
                 else {
                     def inputFile = (input != '' && input) ? 
-                            transform(input, field) : 
+                            castToType(input, field) : 
                         field['value']['default'] != null ? 
-                            transform(field['value']['default'] as String, field) : 
+                            castToType(field['value']['default'] as String, field) : 
                             []
                     output.add(inputFile)
                 }
@@ -240,14 +240,14 @@ class SamplesheetConverter {
     }
 
     // Function to transform an input field from the samplesheet to its desired type
-    private static transform(
+    private static castToType(
         String input,
         Map.Entry<String, Map> field
     ) {
         def String type = field['value']['type']
         def String key = field.key
 
-        // Check and convert string values
+        // Convert string values
         if(type == "string" || !type) {
             def String result = input as String
 
@@ -262,26 +262,47 @@ class SamplesheetConverter {
             return result
         }
 
-        // Check and convert integer values
-        else if(type == "integer" || type == "number") {
+        // Convert number values
+        else if(type == "number") {
+            try {
+                def int result = input as int
+                return result
+            }
+            catch (NumberFormatException e) {
+                log.debug("Could not convert ${input} to an integer. Trying to convert to a float.")
+            }
+
+            try {
+                def float result = input as float
+                return result
+            }
+            catch (NumberFormatException e) {
+                log.debug("Could not convert ${input} to a float. Trying to convert to a double.")
+            }
+
+            def double result = input as double
+            return result
+        }
 
-            // Stop conversion if there are errors (prevents unwanted exceptions)
-            if(this.getErrors()){ return }
+        // Convert integer values
+        else if(type == "integer") {
 
-            // Convert the string value to an integer value and return it
-            def Integer result = input as Integer
+            def int result = input as int
             return result
         }
 
-        // Check and convert boolean values
+        // Convert boolean values
         else if(type == "boolean") {
 
-            // Convert and return the boolean value
             if(input.toLowerCase() == "true") {
                 return true
             }
             return false
         }
+
+        else if(type == "null") {
+            return null
+        }
     }
 
     private static String addSample (

diff --git a/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
@@ -77,8 +77,8 @@ class SamplesheetConverterTest extends Dsl2Spec{
 
         then:
         noExceptionThrown()
-        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
-        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25, false, [], [], [], [], [], itDoesExist]")
+        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25.12, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
+        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25.08, false, [], [], [], [], [], itDoesExist]")
         stdout.contains("[[string1:dependentRequired, string2:dependentRequired, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, [], [], [], unique2, 1, itDoesExist]")
         stdout.contains("[[string1:extraField, string2:extraField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
     }
@@ -104,8 +104,8 @@ class SamplesheetConverterTest extends Dsl2Spec{
 
         then:
         noExceptionThrown()
-        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
-        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25, false, [], [], [], [], [], itDoesExist]")
+        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25.12, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
+        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25.08, false, [], [], [], [], [], itDoesExist]")
         stdout.contains("[[string1:dependentRequired, string2:dependentRequired, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, [], [], [], unique2, 1, itDoesExist]")
         stdout.contains("[[string1:extraField, string2:extraField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
     }
@@ -131,8 +131,8 @@ class SamplesheetConverterTest extends Dsl2Spec{
 
         then:
         noExceptionThrown()
-        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
-        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25, false, [], [], [], [], [], itDoesExist]")
+        stdout.contains("[[string1:fullField, string2:fullField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25.12, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/test.txt, unique1, 1, itDoesExist]" as String)
+        stdout.contains("[[string1:value, string2:value, integer1:0, integer2:0, boolean1:true, boolean2:true], string1, 25.08, false, [], [], [], [], [], itDoesExist]")
         stdout.contains("[[string1:dependentRequired, string2:dependentRequired, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, [], [], [], unique2, 1, itDoesExist]")
         stdout.contains("[[string1:extraField, string2:extraField, integer1:10, integer2:10, boolean1:true, boolean2:true], string1, 25, false, ${this.getRootString()}/src/testResources/test.txt, ${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir, unique3, 1, itDoesExist]" as String)
     }

diff --git a/plugins/nf-validation/src/testResources/correct.csv b/plugins/nf-validation/src/testResources/correct.csv
@@ -1,5 +1,5 @@
 field_1,field_2,field_3,field_4,field_5,field_6,field_7,field_8,field_9,field_10,field_11
-fullField,10,true,string1,25,false,src/testResources/test.txt,src/testResources/testDir,src/testResources/test.txt,unique1,1
-,,,string1,25,false,,,,,,
+fullField,10,true,string1,25.12,false,src/testResources/test.txt,src/testResources/testDir,src/testResources/test.txt,unique1,1
+,,,string1,25.08,false,,,,,,
 dependentRequired,10,true,string1,25,false,,,,unique2,1
 extraField,10,true,string1,25,false,src/testResources/test.txt,src/testResources/testDir,src/testResources/testDir,unique3,1
diff --git a/plugins/nf-validation/src/testResources/correct.tsv b/plugins/nf-validation/src/testResources/correct.tsv
@@ -1,5 +1,5 @@
 field_1	field_2	field_3	field_4	field_5	field_6	field_7	field_8	field_9	field_10	field_11
-fullField	10	true	string1	25	false	src/testResources/test.txt	src/testResources/testDir	src/testResources/test.txt	unique1	1
-			string1	25	false					
+fullField	10	true	string1	25.12	false	src/testResources/test.txt	src/testResources/testDir	src/testResources/test.txt	unique1	1
+			string1	25.08	false					
 dependentRequired	10	true	string1	25	false				unique2	1
 extraField	10	true	string1	25	false	src/testResources/test.txt	src/testResources/testDir	src/testResources/testDir	unique3	1
diff --git a/plugins/nf-validation/src/testResources/correct.yaml b/plugins/nf-validation/src/testResources/correct.yaml
@@ -2,15 +2,15 @@
   field_2: 10
   field_3: true
   field_4: string1
-  field_5: 25
+  field_5: 25.12
   field_6: false
   field_7: src/testResources/test.txt
   field_8: src/testResources/testDir
   field_9: src/testResources/test.txt
   field_10: unique1
   field_11: 1
 - field_4: string1
-  field_5: 25
+  field_5: 25.08
   field_6: false
 - field_1: dependentRequired
   field_2: 10