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Improve samplesheet typecasting #113

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Oct 16, 2023
Merged

Improve samplesheet typecasting #113

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6fc973d
fix number to float conversion
nvnieuwk Oct 12, 2023
40575c5
add null type
nvnieuwk Oct 12, 2023
b00acfe
add a test
nvnieuwk Oct 12, 2023
fe91c36
Merge branch 'master' into improve-samplesheet-typecasting
nvnieuwk Oct 16, 2023
8f2b1f4
Update changelog
nvnieuwk Oct 16, 2023
893a0db
fix tests
nvnieuwk Oct 16, 2023
6aba24c
fix the test finally
nvnieuwk Oct 16, 2023
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49 changes: 35 additions & 14 deletions plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -164,17 +164,17 @@ class SamplesheetConverter {
if(metaNames) {
for(name : metaNames) {
meta[name] = (input != '' && input) ?
transform(input, field) :
castToType(input, field) :
field['value']['default'] ?
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'] ?
transform(field['value']['default'] as String, field) :
castToType(field['value']['default'] as String, field) :
[]
output.add(inputFile)
}
Expand Down Expand Up @@ -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

Expand All @@ -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
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Should we catch an error here too? And maybe throw a more explanatory message saying that the input is not a value. Although this will in theory be detected by the validation before the channel conversion.

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Yeah that was my reasoning too, the values should be compatible when they are validated so they shouldn't really fail

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 (
Expand Down
12 changes: 6 additions & 6 deletions plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
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Expand Up @@ -76,8 +76,8 @@ 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, integer1:5, integer2:5, 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, integer1:5, integer2:5, 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)
}
Expand All @@ -102,8 +102,8 @@ 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, integer1:5, integer2:5, 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, integer1:5, integer2:5, 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)
}
Expand All @@ -128,8 +128,8 @@ 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, integer1:5, integer2:5, 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, integer1:5, integer2:5, 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)
}
Expand Down
4 changes: 2 additions & 2 deletions plugins/nf-validation/src/testResources/correct.csv
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Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions plugins/nf-validation/src/testResources/correct.tsv
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Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions plugins/nf-validation/src/testResources/correct.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down