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Changed schema_filename to schemaFilename for consistency
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@adamrtalbot
adamrtalbot committed Oct 2, 2023
1 parent e76b137 commit 0c110a8
Showing 1 changed file with 25 additions and 24 deletions.
49 changes: 25 additions & 24 deletions plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy
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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 @@ -260,13 +260,13 @@ class SchemaValidator extends PluginExtensionPoint {
*/
@Function
void validateParameters(
Map options = null,
Map options = null
) {

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 : false
def Map params = initialiseExpectedParams(session.params)
def String baseDir = session.baseDir
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 : false
log.debug "Starting parameters validation"

// Clean the parameters
Expand All @@ -277,7 +277,7 @@ 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 +329,7 @@ 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 Down Expand Up @@ -419,13 +419,13 @@ 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 @@ -498,11 +498,11 @@ class SchemaValidator extends PluginExtensionPoint {
//
/* groovylint-disable-next-line UnusedPrivateMethodParameter */
boolean validateFile(
Boolean monochrome_logs, String paramName, Object fileContent, String schema_filename, String baseDir
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 @@ -524,7 +524,7 @@ 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 @@ -653,17 +653,18 @@ class SchemaValidator extends PluginExtensionPoint {
Map options = null,
String command
) {
// String schema_filename='nextflow_schema.json', Boolean monochrome_logs=false
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 : false
def Map params = initialiseExpectedParams(session.params)
def String baseDir = session.baseDir

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 : 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 @@ -747,7 +748,7 @@ 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 @@ -774,7 +775,7 @@ 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 @@ -827,15 +828,15 @@ class SchemaValidator extends PluginExtensionPoint {
Map options = null
) {

// String schema_filename='nextflow_schema.json', Boolean monochrome_logs=false
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 : false
def String baseDir = session.baseDir
def Map params = session.params

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 : 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

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