Skip to content
This repository has been archived by the owner on Aug 20, 2024. It is now read-only.

Monochrome logs is option in functions rather than global parameter #101

Merged
merged 13 commits into from
Oct 10, 2023
Merged

Monochrome logs is option in functions rather than global parameter #101

Show file tree
Hide file tree
Changes from 11 commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
59d5fe8
Make monochrome_logs argument of function
adamrtalbot Sep 26, 2023
cab2a40
monochrome_logs is optional named argument in functions
adamrtalbot Oct 2, 2023
e76b137
fixup
adamrtalbot Oct 2, 2023
0c110a8
Changed schema_filename to schemaFilename for consistency
adamrtalbot Oct 2, 2023
4da106f
Add default string as positional argument to validateParameters
adamrtalbot Oct 2, 2023
b4d474e
more fixy
adamrtalbot Oct 2, 2023
ab22dc5
More fixy
adamrtalbot Oct 2, 2023
b0759ad
FIXY FIXY
adamrtalbot Oct 2, 2023
a632b78
Monochrome logs documentation
adamrtalbot Oct 2, 2023
70ccc06
Support params.monochromeLogs as well as params.monochrome_logs
adamrtalbot Oct 5, 2023
2821277
Update docs to use monochromeLogs as well as monochrome_logs
adamrtalbot Oct 5, 2023
71bef86
Merge branch 'master' of https://github.com/nextflow-io/nf-validation…
mirpedrol Oct 10, 2023
c11cf7b
update changelog
mirpedrol Oct 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion docs/parameters/help_text.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ params.validationShowHiddenParams = true

By default, the help output is coloured using ANSI escape codes.

If you prefer, you can disable these by using `--monochrome_logs` or `params.monochrome_logs = true`.
If you prefer, you can disable these by using the argument monochrome_logs, e.g. `paramsHelp(monochrome_logs: true)`. Alternatively this can be set at a global level via parameter `--monochrome_logs` or adding `params.monochrome_logs = true` to a configuration file. Not `--monochromeLogs` or `params.monochromeLogs` is also supported.

=== "Default (coloured)"

Expand Down
2 changes: 1 addition & 1 deletion docs/parameters/summary_log.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ Output:

By default, the summary output is coloured using ANSI escape codes.

If you prefer, you can disable these by using `--monochrome_logs` or `params.monochrome_logs = true`.
If you prefer, you can disable these by using the argument monochrome_logs, e.g. `paramsHelp(monochrome_logs: true)`. Alternatively this can be set at a global level via parameter `--monochrome_logs` or adding `params.monochrome_logs = true` to a configuration file. Not `--monochromeLogs` or `params.monochromeLogs` is also supported.

=== "Default (coloured)"

Expand Down
79 changes: 50 additions & 29 deletions plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -130,11 +130,11 @@ class SchemaValidator extends PluginExtensionPoint {
//
// Resolve Schema path relative to main workflow directory
//
static String getSchemaPath(String baseDir, String schema_filename='nextflow_schema.json') {
if (Path.of(schema_filename).exists()) {
return schema_filename
static String getSchemaPath(String baseDir, String schemaFilename='nextflow_schema.json') {
if (Path.of(schemaFilename).exists()) {
return schemaFilename
} else {
return "${baseDir}/${schema_filename}"
return "${baseDir}/${schemaFilename}"
}
}

Expand Down Expand Up @@ -220,9 +220,6 @@ class SchemaValidator extends PluginExtensionPoint {
if( !params.containsKey("validationLenientMode") ) {
params.validationLenientMode = false
}
if( !params.containsKey("monochrome_logs") ) {
params.monochrome_logs = false
}
if( !params.containsKey("help") ) {
params.help = false
}
Expand All @@ -247,7 +244,6 @@ class SchemaValidator extends PluginExtensionPoint {
def List expectedParams = [
"validationFailUnrecognisedParams",
"validationLenientMode",
"monochrome_logs",
"help",
"validationShowHiddenParams",
"validationSchemaIgnoreParams",
Expand All @@ -263,10 +259,17 @@ class SchemaValidator extends PluginExtensionPoint {
* whether the given parameters adhere to the specifications
*/
@Function
void validateParameters(String schema_filename='nextflow_schema.json') {
void validateParameters(
Map options = null,
String schemaFilename
) {

def Map params = initialiseExpectedParams(session.params)
def String baseDir = session.baseDir
def Boolean useMonochromeLogs = options?.containsKey('monochrome_logs') ? options.monochrome_logs as Boolean :
params.monochrome_logs ? params.monochrome_logs as Boolean :
params.monochromeLogs ? params.monochromeLogs as Boolean :
false
log.debug "Starting parameters validation"

// Clean the parameters
Expand All @@ -277,7 +280,7 @@ class SchemaValidator extends PluginExtensionPoint {
//=====================================================================//
// Check for nextflow core params and unexpected params
def slurper = new JsonSlurper()
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schema_filename)) )
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schemaFilename)) )
def Map schemaParams = (Map) parsed.get('definitions')
def specifiedParamKeys = params.keySet()

Expand Down Expand Up @@ -329,7 +332,7 @@ class SchemaValidator extends PluginExtensionPoint {

//=====================================================================//
// Validate parameters against the schema
def String schema_string = Files.readString( Path.of(getSchemaPath(baseDir, schema_filename)) )
def String schema_string = Files.readString( Path.of(getSchemaPath(baseDir, schemaFilename)) )
final rawSchema = new JSONObject(new JSONTokener(schema_string))
final SchemaLoader schemaLoader = SchemaLoader.builder()
.schemaJson(rawSchema)
Expand All @@ -346,8 +349,7 @@ class SchemaValidator extends PluginExtensionPoint {
}

// Colors
def Boolean monochrome_logs = params.monochrome_logs
def colors = logColours(monochrome_logs)
def colors = logColours(useMonochromeLogs)

// Validate
try {
Expand Down Expand Up @@ -406,7 +408,7 @@ class SchemaValidator extends PluginExtensionPoint {
fileContent = file_path.splitCsv(header:true, strip:true, sep:delimiter)
fileContentCasted = castToType(fileContent, types)
}
if (validateFile(monochrome_logs, key, fileContentCasted, schema_name, baseDir)) {
if (validateFile(useMonochromeLogs, key, fileContentCasted, schema_name, baseDir)) {
log.debug "Validation passed: '$key': '$file_path' with '$schema_name'"
}
}
Expand All @@ -420,13 +422,13 @@ class SchemaValidator extends PluginExtensionPoint {
//
// Function to obtain the variable types of properties from a JSON Schema
//
Map variableTypes(String schema_filename, String baseDir) {
Map variableTypes(String schemaFilename, String baseDir) {
def Map variableTypes = [:]
def String type = ''

// Read the schema
def slurper = new JsonSlurper()
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schema_filename)) )
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schemaFilename)) )

// Obtain the type of each variable in the schema
def Map properties = (Map) parsed['items']['properties']
Expand Down Expand Up @@ -498,10 +500,12 @@ class SchemaValidator extends PluginExtensionPoint {
// Function to validate a file by its schema
//
/* groovylint-disable-next-line UnusedPrivateMethodParameter */
boolean validateFile(Boolean monochrome_logs, String paramName, Object fileContent, String schema_filename, String baseDir) {
boolean validateFile(
Boolean monochrome_logs, String paramName, Object fileContent, String schemaFilename, String baseDir
) {

// Load the schema
def String schema_string = Files.readString( Path.of(getSchemaPath(baseDir, schema_filename)) )
def String schema_string = Files.readString( Path.of(getSchemaPath(baseDir, schemaFilename)) )
final rawSchema = new JSONObject(new JSONTokener(schema_string))
final SchemaLoader schemaLoader = SchemaLoader.builder()
.schemaJson(rawSchema)
Expand All @@ -523,7 +527,7 @@ class SchemaValidator extends PluginExtensionPoint {
//=====================================================================//
// Check for params with expected values
def slurper = new JsonSlurper()
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schema_filename)) )
def Map parsed = (Map) slurper.parse( Path.of(getSchemaPath(baseDir, schemaFilename)) )
def Map schemaParams = (Map) ["items": parsed.get('items')]

// Collect expected parameters from the schema
Expand Down Expand Up @@ -648,16 +652,25 @@ class SchemaValidator extends PluginExtensionPoint {
// Beautify parameters for --help
//
@Function
String paramsHelp(String command, String schema_filename='nextflow_schema.json') {
String paramsHelp(
Map options = null,
String command
) {
def Map params = initialiseExpectedParams(session.params)
def String baseDir = session.baseDir
def Boolean monochrome_logs = params.monochrome_logs
def colors = logColours(monochrome_logs)

def String schemaFilename = options?.containsKey('parameters_schema') ? options.parameters_schema as String : 'nextflow_schema.json'
def Boolean useMonochromeLogs = options?.containsKey('monochrome_logs') ? options.monochrome_logs as Boolean :
params.monochrome_logs ? params.monochrome_logs as Boolean :
params.monochromeLogs ? params.monochromeLogs as Boolean :
false

def colors = logColours(useMonochromeLogs)
Integer num_hidden = 0
String output = ''
output += 'Typical pipeline command:\n\n'
output += " ${colors.cyan}${command}${colors.reset}\n\n"
Map params_map = paramsLoad( Path.of(getSchemaPath(baseDir, schema_filename)) )
Map params_map = paramsLoad( Path.of(getSchemaPath(baseDir, schemaFilename)) )
Integer max_chars = paramsMaxChars(params_map) + 1
Integer desc_indent = max_chars + 14
Integer dec_linewidth = 160 - desc_indent
Expand Down Expand Up @@ -741,7 +754,7 @@ class SchemaValidator extends PluginExtensionPoint {
// Groovy Map summarising parameters/workflow options used by the pipeline
//
@Function
public LinkedHashMap paramsSummaryMap(WorkflowMetadata workflow, String schema_filename='nextflow_schema.json') {
public LinkedHashMap paramsSummaryMap(WorkflowMetadata workflow, String schemaFilename='nextflow_schema.json') {

def String baseDir = session.baseDir
def Map params = session.params
Expand All @@ -768,7 +781,7 @@ class SchemaValidator extends PluginExtensionPoint {

// Get pipeline parameters defined in JSON Schema
def Map params_summary = [:]
def Map params_map = paramsLoad( Path.of(getSchemaPath(baseDir, schema_filename)) )
def Map params_map = paramsLoad( Path.of(getSchemaPath(baseDir, schemaFilename)) )
for (group in params_map.keySet()) {
def sub_params = new LinkedHashMap()
def Map group_params = params_map.get(group) as Map // This gets the parameters of that particular group
Expand Down Expand Up @@ -816,15 +829,23 @@ class SchemaValidator extends PluginExtensionPoint {
// Beautify parameters for summary and return as string
//
@Function
public String paramsSummaryLog(WorkflowMetadata workflow, String schema_filename='nextflow_schema.json') {
public String paramsSummaryLog(
Map options = null,
WorkflowMetadata workflow
) {

def String baseDir = session.baseDir
def Map params = session.params

def Boolean monochrome_logs = params.monochrome_logs
def colors = logColours(monochrome_logs)
def String schemaFilename = options?.containsKey('parameters_schema') ? options.parameters_schema as String : 'nextflow_schema.json'
def Boolean useMonochromeLogs = options?.containsKey('monochrome_logs') ? options.monochrome_logs as Boolean :
params.monochrome_logs ? params.monochrome_logs as Boolean :
params.monochromeLogs ? params.monochromeLogs as Boolean :
false

def colors = logColours(useMonochromeLogs)
String output = ''
def LinkedHashMap params_map = paramsSummaryMap(workflow, schema_filename)
def LinkedHashMap params_map = paramsSummaryMap(workflow, schemaFilename)
def max_chars = paramsMaxChars(params_map)
for (group in params_map.keySet()) {
def Map group_params = params_map.get(group) as Map // This gets the parameters of that particular group
Expand Down
26 changes: 13 additions & 13 deletions plugins/nf-validation/src/test/nextflow/validation/PluginExtensionMethodsTest.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.monochrome_logs = true
include { validateParameters } from 'plugin/nf-validation'

validateParameters('src/testResources/nextflow_schema.json')
validateParameters('src/testResources/nextflow_schema.json', monochrome_logs: params.monochrome_logs)
"""

when:
Expand Down Expand Up @@ -226,7 +226,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.validationFailUnrecognisedParams = true
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand All @@ -251,7 +251,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.outdir = 10
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand Down Expand Up @@ -303,7 +303,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.max_time = '10.day'
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand Down Expand Up @@ -378,7 +378,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.max_cpus = 1.2
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand All @@ -404,7 +404,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.max_memory = '10'
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand Down Expand Up @@ -432,7 +432,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{

def command = "nextflow run <pipeline> --input samplesheet.csv --outdir <OUTDIR> -profile docker"

def help_msg = paramsHelp(command, '$schema')
def help_msg = paramsHelp(command, parameters_schema: '$schema')
log.info help_msg
"""

Expand Down Expand Up @@ -466,7 +466,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.validationShowHiddenParams = true
def command = "nextflow run <pipeline> --input samplesheet.csv --outdir <OUTDIR> -profile docker"

def help_msg = paramsHelp(command, '$schema')
def help_msg = paramsHelp(command, parameters_schema: '$schema')
log.info help_msg
"""

Expand All @@ -493,7 +493,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{

def command = "nextflow run <pipeline> --input samplesheet.csv --outdir <OUTDIR> -profile docker"

def help_msg = paramsHelp(command, '$schema')
def help_msg = paramsHelp(command, parameters_schema: '$schema')
log.info help_msg
"""

Expand Down Expand Up @@ -526,7 +526,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{

def command = "nextflow run <pipeline> --input samplesheet.csv --outdir <OUTDIR> -profile docker"

def help_msg = paramsHelp(command, '$schema')
def help_msg = paramsHelp(command, parameters_schema: '$schema')
log.info help_msg
"""

Expand Down Expand Up @@ -554,7 +554,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.outdir = "outDir"
include { paramsSummaryLog } from 'plugin/nf-validation'

def summary_params = paramsSummaryLog(workflow, '$schema')
def summary_params = paramsSummaryLog(workflow, parameters_schema: '$schema')
log.info summary_params
"""

Expand Down Expand Up @@ -616,7 +616,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.input = 'src/testResources/samplesheet_wrong_pattern.csv'
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand All @@ -640,7 +640,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
params.input = 'src/testResources/samplesheet_no_required.csv'
include { validateParameters } from 'plugin/nf-validation'

validateParameters('$schema')
validateParameters('$schema', monochrome_logs: params.monochrome_logs)
"""

when:
Expand Down